nimbleSCR

Rd files

checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup?
    59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3
       |      ^
checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup?
    59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3
       |                                                          ^
checkRd: (-1) dcatState1Alive1Dead.Rd:60: Lost braces; missing escapes or markup?
    60 | Individuals in dead states (z_{i,t} = 3 ) remain in that state with probability 1, the absorbing state.
       |                               ^
checkRd: (-1) dcatState1Alive1Dead.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState1Alive1Dead.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup?
    68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup?
    68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |      ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |                                                                                                     ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup?
    71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1.
       |                               ^
checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup?
    71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1.
       |                                                               ^
checkRd: (-1) dcatState1Alive2Dead.Rd:36: Lost braces; missing escapes or markup?
    36 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState1Alive2Dead.Rd:38: Lost braces; missing escapes or markup?
    38 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup?
    92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup?
    92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |                                                                                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup?
    94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). 
       |                                                                                                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup?
    94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). 
       |                                                                                                                                                                                          ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |                                                                                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup?
    97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1.
       |                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup?
    97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1.
       |                                                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:48: Lost braces; missing escapes or markup?
    48 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:50: Lost braces; missing escapes or markup?
    50 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dpoisppLocalDetection_normal.Rd:148-152: Lost braces
   148 | for(i in 1:nrow(x)){
       |                    ^
checkRd: (-1) sampler_categorical_general.Rd:19: Lost braces
    19 | The \code{categorical_general} sampler operates within \code{nimble}'s MCMC engine to perform Gibbs sampling for a single node, which must in essence follow a categorical distribution.  However, the prior distribution need not be \code{nimble}'s \code{dcat} distribution, but rather can be any (potentially user-defined) distribution which has the same support as a standard categorical (\code{dcat}) distribution.  Specifically: the distribution must define a discrete random variable, which can only attain values from the set {1, 2, 3, ..., \code{numCategories}}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^

Rd files

checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup?
    59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3
       |      ^
checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup?
    59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3
       |                                                          ^
checkRd: (-1) dcatState1Alive1Dead.Rd:60: Lost braces; missing escapes or markup?
    60 | Individuals in dead states (z_{i,t} = 3 ) remain in that state with probability 1, the absorbing state.
       |                               ^
checkRd: (-1) dcatState1Alive1Dead.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState1Alive1Dead.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup?
    68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup?
    68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |      ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |                                                                                                     ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup?
    71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1.
       |                               ^
checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup?
    71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1.
       |                                                               ^
checkRd: (-1) dcatState1Alive2Dead.Rd:36: Lost braces; missing escapes or markup?
    36 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState1Alive2Dead.Rd:38: Lost braces; missing escapes or markup?
    38 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup?
    92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup?
    92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |                                                                                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup?
    94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). 
       |                                                                                                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup?
    94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). 
       |                                                                                                                                                                                          ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |                                                                                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup?
    97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1.
       |                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup?
    97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1.
       |                                                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:48: Lost braces; missing escapes or markup?
    48 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:50: Lost braces; missing escapes or markup?
    50 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dpoisppLocalDetection_normal.Rd:148-152: Lost braces
   148 | for(i in 1:nrow(x)){
       |                    ^
checkRd: (-1) sampler_categorical_general.Rd:19: Lost braces
    19 | The \code{categorical_general} sampler operates within \code{nimble}'s MCMC engine to perform Gibbs sampling for a single node, which must in essence follow a categorical distribution.  However, the prior distribution need not be \code{nimble}'s \code{dcat} distribution, but rather can be any (potentially user-defined) distribution which has the same support as a standard categorical (\code{dcat}) distribution.  Specifically: the distribution must define a discrete random variable, which can only attain values from the set {1, 2, 3, ..., \code{numCategories}}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^

Rd files

checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup?
    59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3
       |      ^
checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup?
    59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3
       |                                                          ^
checkRd: (-1) dcatState1Alive1Dead.Rd:60: Lost braces; missing escapes or markup?
    60 | Individuals in dead states (z_{i,t} = 3 ) remain in that state with probability 1, the absorbing state.
       |                               ^
checkRd: (-1) dcatState1Alive1Dead.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState1Alive1Dead.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup?
    68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup?
    68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |      ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |                                                                                                     ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup?
    71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1.
       |                               ^
checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup?
    71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1.
       |                                                               ^
checkRd: (-1) dcatState1Alive2Dead.Rd:36: Lost braces; missing escapes or markup?
    36 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState1Alive2Dead.Rd:38: Lost braces; missing escapes or markup?
    38 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup?
    92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup?
    92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |                                                                                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup?
    94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). 
       |                                                                                                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup?
    94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). 
       |                                                                                                                                                                                          ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |                                                                                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup?
    97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1.
       |                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup?
    97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1.
       |                                                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:48: Lost braces; missing escapes or markup?
    48 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:50: Lost braces; missing escapes or markup?
    50 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dpoisppLocalDetection_normal.Rd:148-152: Lost braces
   148 | for(i in 1:nrow(x)){
       |                    ^
checkRd: (-1) sampler_categorical_general.Rd:19: Lost braces
    19 | The \code{categorical_general} sampler operates within \code{nimble}'s MCMC engine to perform Gibbs sampling for a single node, which must in essence follow a categorical distribution.  However, the prior distribution need not be \code{nimble}'s \code{dcat} distribution, but rather can be any (potentially user-defined) distribution which has the same support as a standard categorical (\code{dcat}) distribution.  Specifically: the distribution must define a discrete random variable, which can only attain values from the set {1, 2, 3, ..., \code{numCategories}}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^

dependencies in R code

Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.

Rd files

checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup?
    59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3
       |      ^
checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup?
    59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3
       |                                                          ^
checkRd: (-1) dcatState1Alive1Dead.Rd:60: Lost braces; missing escapes or markup?
    60 | Individuals in dead states (z_{i,t} = 3 ) remain in that state with probability 1, the absorbing state.
       |                               ^
checkRd: (-1) dcatState1Alive1Dead.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState1Alive1Dead.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup?
    68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup?
    68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |      ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |                                                                                                     ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup?
    71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1.
       |                               ^
checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup?
    71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1.
       |                                                               ^
checkRd: (-1) dcatState1Alive2Dead.Rd:36: Lost braces; missing escapes or markup?
    36 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState1Alive2Dead.Rd:38: Lost braces; missing escapes or markup?
    38 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup?
    92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup?
    92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |                                                                                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup?
    94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). 
       |                                                                                                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup?
    94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). 
       |                                                                                                                                                                                          ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |                                                                                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup?
    97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1.
       |                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup?
    97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1.
       |                                                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:48: Lost braces; missing escapes or markup?
    48 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:50: Lost braces; missing escapes or markup?
    50 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dpoisppLocalDetection_normal.Rd:148-152: Lost braces
   148 | for(i in 1:nrow(x)){
       |                    ^
checkRd: (-1) sampler_categorical_general.Rd:19: Lost braces
    19 | The \code{categorical_general} sampler operates within \code{nimble}'s MCMC engine to perform Gibbs sampling for a single node, which must in essence follow a categorical distribution.  However, the prior distribution need not be \code{nimble}'s \code{dcat} distribution, but rather can be any (potentially user-defined) distribution which has the same support as a standard categorical (\code{dcat}) distribution.  Specifically: the distribution must define a discrete random variable, which can only attain values from the set {1, 2, 3, ..., \code{numCategories}}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^

dependencies in R code

Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.

Rd files

checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup?
    59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3
       |      ^
checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup?
    59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3
       |                                                          ^
checkRd: (-1) dcatState1Alive1Dead.Rd:60: Lost braces; missing escapes or markup?
    60 | Individuals in dead states (z_{i,t} = 3 ) remain in that state with probability 1, the absorbing state.
       |                               ^
checkRd: (-1) dcatState1Alive1Dead.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState1Alive1Dead.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup?
    68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup?
    68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |      ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |                                                                                                     ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup?
    71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1.
       |                               ^
checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup?
    71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1.
       |                                                               ^
checkRd: (-1) dcatState1Alive2Dead.Rd:36: Lost braces; missing escapes or markup?
    36 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState1Alive2Dead.Rd:38: Lost braces; missing escapes or markup?
    38 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup?
    92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup?
    92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |                                                                                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup?
    94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). 
       |                                                                                                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup?
    94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). 
       |                                                                                                                                                                                          ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |                                                                                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup?
    97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1.
       |                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup?
    97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1.
       |                                                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:48: Lost braces; missing escapes or markup?
    48 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:50: Lost braces; missing escapes or markup?
    50 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dpoisppLocalDetection_normal.Rd:148-152: Lost braces
   148 | for(i in 1:nrow(x)){
       |                    ^
checkRd: (-1) sampler_categorical_general.Rd:19: Lost braces
    19 | The \code{categorical_general} sampler operates within \code{nimble}'s MCMC engine to perform Gibbs sampling for a single node, which must in essence follow a categorical distribution.  However, the prior distribution need not be \code{nimble}'s \code{dcat} distribution, but rather can be any (potentially user-defined) distribution which has the same support as a standard categorical (\code{dcat}) distribution.  Specifically: the distribution must define a discrete random variable, which can only attain values from the set {1, 2, 3, ..., \code{numCategories}}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^

Rd files

checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup?
    59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3
       |      ^
checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup?
    59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3
       |                                                          ^
checkRd: (-1) dcatState1Alive1Dead.Rd:60: Lost braces; missing escapes or markup?
    60 | Individuals in dead states (z_{i,t} = 3 ) remain in that state with probability 1, the absorbing state.
       |                               ^
checkRd: (-1) dcatState1Alive1Dead.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState1Alive1Dead.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup?
    68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup?
    68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |      ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |                                                                                                     ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup?
    71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1.
       |                               ^
checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup?
    71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1.
       |                                                               ^
checkRd: (-1) dcatState1Alive2Dead.Rd:36: Lost braces; missing escapes or markup?
    36 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState1Alive2Dead.Rd:38: Lost braces; missing escapes or markup?
    38 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup?
    92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup?
    92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |                                                                                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup?
    94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). 
       |                                                                                                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup?
    94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). 
       |                                                                                                                                                                                          ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |                                                                                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup?
    97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1.
       |                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup?
    97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1.
       |                                                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:48: Lost braces; missing escapes or markup?
    48 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:50: Lost braces; missing escapes or markup?
    50 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dpoisppLocalDetection_normal.Rd:148-152: Lost braces
   148 | for(i in 1:nrow(x)){
       |                    ^
checkRd: (-1) sampler_categorical_general.Rd:19: Lost braces
    19 | The \code{categorical_general} sampler operates within \code{nimble}'s MCMC engine to perform Gibbs sampling for a single node, which must in essence follow a categorical distribution.  However, the prior distribution need not be \code{nimble}'s \code{dcat} distribution, but rather can be any (potentially user-defined) distribution which has the same support as a standard categorical (\code{dcat}) distribution.  Specifically: the distribution must define a discrete random variable, which can only attain values from the set {1, 2, 3, ..., \code{numCategories}}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^

Rd files

checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup?
    59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3
       |      ^
checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup?
    59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3
       |                                                          ^
checkRd: (-1) dcatState1Alive1Dead.Rd:60: Lost braces; missing escapes or markup?
    60 | Individuals in dead states (z_{i,t} = 3 ) remain in that state with probability 1, the absorbing state.
       |                               ^
checkRd: (-1) dcatState1Alive1Dead.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState1Alive1Dead.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup?
    68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup?
    68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |      ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |                                                                                                     ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup?
    71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1.
       |                               ^
checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup?
    71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1.
       |                                                               ^
checkRd: (-1) dcatState1Alive2Dead.Rd:36: Lost braces; missing escapes or markup?
    36 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState1Alive2Dead.Rd:38: Lost braces; missing escapes or markup?
    38 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup?
    92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup?
    92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |                                                                                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup?
    94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). 
       |                                                                                                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup?
    94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). 
       |                                                                                                                                                                                          ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |                                                                                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup?
    97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1.
       |                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup?
    97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1.
       |                                                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:48: Lost braces; missing escapes or markup?
    48 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:50: Lost braces; missing escapes or markup?
    50 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dpoisppLocalDetection_normal.Rd:148-152: Lost braces
   148 | for(i in 1:nrow(x)){
       |                    ^
checkRd: (-1) sampler_categorical_general.Rd:19: Lost braces
    19 | The \code{categorical_general} sampler operates within \code{nimble}'s MCMC engine to perform Gibbs sampling for a single node, which must in essence follow a categorical distribution.  However, the prior distribution need not be \code{nimble}'s \code{dcat} distribution, but rather can be any (potentially user-defined) distribution which has the same support as a standard categorical (\code{dcat}) distribution.  Specifically: the distribution must define a discrete random variable, which can only attain values from the set {1, 2, 3, ..., \code{numCategories}}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^

installed package size

  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       4.0Mb
    extdata   1.8Mb

Rd files

checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup?
    59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3
       |      ^
checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup?
    59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3
       |                                                          ^
checkRd: (-1) dcatState1Alive1Dead.Rd:60: Lost braces; missing escapes or markup?
    60 | Individuals in dead states (z_{i,t} = 3 ) remain in that state with probability 1, the absorbing state.
       |                               ^
checkRd: (-1) dcatState1Alive1Dead.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState1Alive1Dead.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup?
    68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup?
    68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |      ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |                                                                                                     ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup?
    71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1.
       |                               ^
checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup?
    71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1.
       |                                                               ^
checkRd: (-1) dcatState1Alive2Dead.Rd:36: Lost braces; missing escapes or markup?
    36 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState1Alive2Dead.Rd:38: Lost braces; missing escapes or markup?
    38 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup?
    92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup?
    92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |                                                                                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup?
    94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). 
       |                                                                                                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup?
    94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). 
       |                                                                                                                                                                                          ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |                                                                                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup?
    97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1.
       |                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup?
    97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1.
       |                                                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:48: Lost braces; missing escapes or markup?
    48 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:50: Lost braces; missing escapes or markup?
    50 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dpoisppLocalDetection_normal.Rd:148-152: Lost braces
   148 | for(i in 1:nrow(x)){
       |                    ^
checkRd: (-1) sampler_categorical_general.Rd:19: Lost braces
    19 | The \code{categorical_general} sampler operates within \code{nimble}'s MCMC engine to perform Gibbs sampling for a single node, which must in essence follow a categorical distribution.  However, the prior distribution need not be \code{nimble}'s \code{dcat} distribution, but rather can be any (potentially user-defined) distribution which has the same support as a standard categorical (\code{dcat}) distribution.  Specifically: the distribution must define a discrete random variable, which can only attain values from the set {1, 2, 3, ..., \code{numCategories}}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^

installed package size

  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       4.0Mb
    extdata   1.8Mb

Rd files

checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup?
    59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3
       |      ^
checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup?
    59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3
       |                                                          ^
checkRd: (-1) dcatState1Alive1Dead.Rd:60: Lost braces; missing escapes or markup?
    60 | Individuals in dead states (z_{i,t} = 3 ) remain in that state with probability 1, the absorbing state.
       |                               ^
checkRd: (-1) dcatState1Alive1Dead.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState1Alive1Dead.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup?
    68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup?
    68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |      ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |                                                                                                     ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup?
    71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1.
       |                               ^
checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup?
    71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1.
       |                                                               ^
checkRd: (-1) dcatState1Alive2Dead.Rd:36: Lost braces; missing escapes or markup?
    36 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState1Alive2Dead.Rd:38: Lost braces; missing escapes or markup?
    38 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup?
    92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup?
    92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |                                                                                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup?
    94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). 
       |                                                                                                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup?
    94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). 
       |                                                                                                                                                                                          ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |                                                                                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup?
    97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1.
       |                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup?
    97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1.
       |                                                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:48: Lost braces; missing escapes or markup?
    48 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:50: Lost braces; missing escapes or markup?
    50 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dpoisppLocalDetection_normal.Rd:148-152: Lost braces
   148 | for(i in 1:nrow(x)){
       |                    ^
checkRd: (-1) sampler_categorical_general.Rd:19: Lost braces
    19 | The \code{categorical_general} sampler operates within \code{nimble}'s MCMC engine to perform Gibbs sampling for a single node, which must in essence follow a categorical distribution.  However, the prior distribution need not be \code{nimble}'s \code{dcat} distribution, but rather can be any (potentially user-defined) distribution which has the same support as a standard categorical (\code{dcat}) distribution.  Specifically: the distribution must define a discrete random variable, which can only attain values from the set {1, 2, 3, ..., \code{numCategories}}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^

installed package size

  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       4.0Mb
    extdata   1.8Mb

Rd files

checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup?
    59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3
       |      ^
checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup?
    59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3
       |                                                          ^
checkRd: (-1) dcatState1Alive1Dead.Rd:60: Lost braces; missing escapes or markup?
    60 | Individuals in dead states (z_{i,t} = 3 ) remain in that state with probability 1, the absorbing state.
       |                               ^
checkRd: (-1) dcatState1Alive1Dead.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState1Alive1Dead.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup?
    68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup?
    68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |      ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |                                                                                                     ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup?
    71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1.
       |                               ^
checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup?
    71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1.
       |                                                               ^
checkRd: (-1) dcatState1Alive2Dead.Rd:36: Lost braces; missing escapes or markup?
    36 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState1Alive2Dead.Rd:38: Lost braces; missing escapes or markup?
    38 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup?
    92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup?
    92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |                                                                                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup?
    94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). 
       |                                                                                                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup?
    94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). 
       |                                                                                                                                                                                          ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |                                                                                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup?
    97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1.
       |                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup?
    97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1.
       |                                                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:48: Lost braces; missing escapes or markup?
    48 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:50: Lost braces; missing escapes or markup?
    50 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dpoisppLocalDetection_normal.Rd:148-152: Lost braces
   148 | for(i in 1:nrow(x)){
       |                    ^
checkRd: (-1) sampler_categorical_general.Rd:19: Lost braces
    19 | The \code{categorical_general} sampler operates within \code{nimble}'s MCMC engine to perform Gibbs sampling for a single node, which must in essence follow a categorical distribution.  However, the prior distribution need not be \code{nimble}'s \code{dcat} distribution, but rather can be any (potentially user-defined) distribution which has the same support as a standard categorical (\code{dcat}) distribution.  Specifically: the distribution must define a discrete random variable, which can only attain values from the set {1, 2, 3, ..., \code{numCategories}}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^

Rd files

checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup?
    59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3
       |      ^
checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup?
    59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3
       |                                                          ^
checkRd: (-1) dcatState1Alive1Dead.Rd:60: Lost braces; missing escapes or markup?
    60 | Individuals in dead states (z_{i,t} = 3 ) remain in that state with probability 1, the absorbing state.
       |                               ^
checkRd: (-1) dcatState1Alive1Dead.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState1Alive1Dead.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup?
    68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup?
    68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |      ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |                                                                                                     ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup?
    71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1.
       |                               ^
checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup?
    71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1.
       |                                                               ^
checkRd: (-1) dcatState1Alive2Dead.Rd:36: Lost braces; missing escapes or markup?
    36 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState1Alive2Dead.Rd:38: Lost braces; missing escapes or markup?
    38 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup?
    92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup?
    92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |                                                                                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup?
    94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). 
       |                                                                                                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup?
    94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). 
       |                                                                                                                                                                                          ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |                                                                                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup?
    97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1.
       |                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup?
    97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1.
       |                                                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:48: Lost braces; missing escapes or markup?
    48 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:50: Lost braces; missing escapes or markup?
    50 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dpoisppLocalDetection_normal.Rd:148-152: Lost braces
   148 | for(i in 1:nrow(x)){
       |                    ^
checkRd: (-1) sampler_categorical_general.Rd:19: Lost braces
    19 | The \code{categorical_general} sampler operates within \code{nimble}'s MCMC engine to perform Gibbs sampling for a single node, which must in essence follow a categorical distribution.  However, the prior distribution need not be \code{nimble}'s \code{dcat} distribution, but rather can be any (potentially user-defined) distribution which has the same support as a standard categorical (\code{dcat}) distribution.  Specifically: the distribution must define a discrete random variable, which can only attain values from the set {1, 2, 3, ..., \code{numCategories}}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^

Rd files

checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup?
    59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3
       |      ^
checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup?
    59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3
       |                                                          ^
checkRd: (-1) dcatState1Alive1Dead.Rd:60: Lost braces; missing escapes or markup?
    60 | Individuals in dead states (z_{i,t} = 3 ) remain in that state with probability 1, the absorbing state.
       |                               ^
checkRd: (-1) dcatState1Alive1Dead.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState1Alive1Dead.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup?
    68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup?
    68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |      ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |                                                                                                     ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup?
    71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1.
       |                               ^
checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup?
    71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1.
       |                                                               ^
checkRd: (-1) dcatState1Alive2Dead.Rd:36: Lost braces; missing escapes or markup?
    36 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState1Alive2Dead.Rd:38: Lost braces; missing escapes or markup?
    38 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup?
    92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup?
    92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |                                                                                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup?
    94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). 
       |                                                                                                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup?
    94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). 
       |                                                                                                                                                                                          ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |                                                                                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup?
    97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1.
       |                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup?
    97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1.
       |                                                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:48: Lost braces; missing escapes or markup?
    48 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:50: Lost braces; missing escapes or markup?
    50 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dpoisppLocalDetection_normal.Rd:148-152: Lost braces
   148 | for(i in 1:nrow(x)){
       |                    ^
checkRd: (-1) sampler_categorical_general.Rd:19: Lost braces
    19 | The \code{categorical_general} sampler operates within \code{nimble}'s MCMC engine to perform Gibbs sampling for a single node, which must in essence follow a categorical distribution.  However, the prior distribution need not be \code{nimble}'s \code{dcat} distribution, but rather can be any (potentially user-defined) distribution which has the same support as a standard categorical (\code{dcat}) distribution.  Specifically: the distribution must define a discrete random variable, which can only attain values from the set {1, 2, 3, ..., \code{numCategories}}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^

Rd files

checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup?
    59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3
       |      ^
checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup?
    59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3
       |                                                          ^
checkRd: (-1) dcatState1Alive1Dead.Rd:60: Lost braces; missing escapes or markup?
    60 | Individuals in dead states (z_{i,t} = 3 ) remain in that state with probability 1, the absorbing state.
       |                               ^
checkRd: (-1) dcatState1Alive1Dead.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState1Alive1Dead.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup?
    68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup?
    68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |      ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |                                                                                                     ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup?
    71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1.
       |                               ^
checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup?
    71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1.
       |                                                               ^
checkRd: (-1) dcatState1Alive2Dead.Rd:36: Lost braces; missing escapes or markup?
    36 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState1Alive2Dead.Rd:38: Lost braces; missing escapes or markup?
    38 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup?
    92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup?
    92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |                                                                                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup?
    94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). 
       |                                                                                                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup?
    94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). 
       |                                                                                                                                                                                          ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |                                                                                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup?
    97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1.
       |                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup?
    97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1.
       |                                                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:48: Lost braces; missing escapes or markup?
    48 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:50: Lost braces; missing escapes or markup?
    50 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dpoisppLocalDetection_normal.Rd:148-152: Lost braces
   148 | for(i in 1:nrow(x)){
       |                    ^
checkRd: (-1) sampler_categorical_general.Rd:19: Lost braces
    19 | The \code{categorical_general} sampler operates within \code{nimble}'s MCMC engine to perform Gibbs sampling for a single node, which must in essence follow a categorical distribution.  However, the prior distribution need not be \code{nimble}'s \code{dcat} distribution, but rather can be any (potentially user-defined) distribution which has the same support as a standard categorical (\code{dcat}) distribution.  Specifically: the distribution must define a discrete random variable, which can only attain values from the set {1, 2, 3, ..., \code{numCategories}}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^

Rd files

checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup?
    58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup?
    59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3
       |      ^
checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup?
    59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3
       |                                                          ^
checkRd: (-1) dcatState1Alive1Dead.Rd:60: Lost braces; missing escapes or markup?
    60 | Individuals in dead states (z_{i,t} = 3 ) remain in that state with probability 1, the absorbing state.
       |                               ^
checkRd: (-1) dcatState1Alive1Dead.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState1Alive1Dead.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup?
    68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup?
    68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |      ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |                                                                                                     ^
checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup?
    69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup?
    71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1.
       |                               ^
checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup?
    71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1.
       |                                                               ^
checkRd: (-1) dcatState1Alive2Dead.Rd:36: Lost braces; missing escapes or markup?
    36 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState1Alive2Dead.Rd:38: Lost braces; missing escapes or markup?
    38 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup?
    92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup?
    92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited.
       |                                                                                                         ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |                                                                                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup?
    93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup?
    94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). 
       |                                                                                                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup?
    94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). 
       |                                                                                                                                                                                          ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |      ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |                                                                                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup?
    95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. 
       |                                                                                                                                                                                                ^
checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup?
    97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1.
       |                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup?
    97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1.
       |                                                               ^
checkRd: (-1) dcatState2Alive2Dead.Rd:48: Lost braces; missing escapes or markup?
    48 | \item{x}{Scalar, individual state z_{i,t+1}.}
       |                                     ^
checkRd: (-1) dcatState2Alive2Dead.Rd:50: Lost braces; missing escapes or markup?
    50 | \item{z}{Scalar, initial individual state z_{i,t}.}
       |                                             ^
checkRd: (-1) dpoisppLocalDetection_normal.Rd:148-152: Lost braces
   148 | for(i in 1:nrow(x)){
       |                    ^
checkRd: (-1) sampler_categorical_general.Rd:19: Lost braces
    19 | The \code{categorical_general} sampler operates within \code{nimble}'s MCMC engine to perform Gibbs sampling for a single node, which must in essence follow a categorical distribution.  However, the prior distribution need not be \code{nimble}'s \code{dcat} distribution, but rather can be any (potentially user-defined) distribution which has the same support as a standard categorical (\code{dcat}) distribution.  Specifically: the distribution must define a discrete random variable, which can only attain values from the set {1, 2, 3, ..., \code{numCategories}}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^