MCMCtreeR

Prepare MCMCtree Analyses and Plot Bayesian Divergence Time Analyses Estimates on Trees

v1.1 · May 21, 2019 · GPL (>= 2)

Description

Provides functions to prepare time priors for 'MCMCtree' analyses in the 'PAML' software from Yang (2007)<doi:10.1093/molbev/msm088> and plot time-scaled phylogenies from any Bayesian divergence time analysis. Most time-calibrated node prior distributions require user-specified parameters. The package provides functions to refine these parameters, so that the resulting prior distributions accurately reflect confidence in known, usually fossil, time information. These functions also enable users to visualise distributions and write 'MCMCtree' ready input files. Additionally, the package supplies flexible functions to visualise age uncertainty on a plotted tree with using node bars, using branch widths proportional to the age uncertainty, or by plotting the full posterior distributions on nodes. Time-scaled phylogenetic plots can be visualised with absolute and geological timescales . All plotting functions are applicable with output from any Bayesian software, not just 'MCMCtree'.

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14 NOTE

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Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	NOTE	78.1s
r-devel-linux-x86_64-debian-gcc	NOTE	57.3s
r-devel-linux-x86_64-fedora-clang	NOTE	121.8s
r-devel-linux-x86_64-fedora-gcc	NOTE	152.1s
r-devel-macos-arm64	NOTE	31s
r-devel-windows-x86_64	NOTE	119s
r-oldrel-macos-arm64	NOTE
r-oldrel-macos-x86_64	NOTE	80s
r-oldrel-windows-x86_64	NOTE	143s
r-patched-linux-x86_64	NOTE	74.7s
r-release-linux-x86_64	NOTE	71.5s
r-release-macos-arm64	NOTE
r-release-macos-x86_64	NOTE	110s
r-release-windows-x86_64	NOTE	117s

Check details (19 non-OK)

NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Mark Puttick <mark.puttick@bristol.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Mark",
                      family = "Puttick",
                      role = c("aut", "cre"),
                      email = "mark.puttick@bristol.ac.uk"),
               person(given = "Pascal",
                      family = "Title",
                      role = "ctb"))
as necessary.

NOTE r-devel-linux-x86_64-debian-clang

Rd files

checkRd: (-1) MCMCtreePhy.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:44: Lost braces in \itemize; \valu
...[truncated]...
ost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Mark Puttick <mark.puttick@bristol.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Mark",
                      family = "Puttick",
                      role = c("aut", "cre"),
                      email = "mark.puttick@bristol.ac.uk"),
               person(given = "Pascal",
                      family = "Title",
                      role = "ctb"))
as necessary.

NOTE r-devel-linux-x86_64-debian-gcc

Rd files

checkRd: (-1) MCMCtreePhy.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:44: Lost braces in \itemize; \valu
...[truncated]...
ost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-devel-linux-x86_64-fedora-clang

Rd files

checkRd: (-1) MCMCtreePhy.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:44: Lost braces in \itemize; \valu
...[truncated]...
ost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-devel-linux-x86_64-fedora-gcc

Rd files

checkRd: (-1) MCMCtreePhy.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:44: Lost braces in \itemize; \valu
...[truncated]...
ost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-devel-macos-arm64

Rd files

checkRd: (-1) MCMCtreePhy.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:44: Lost braces in \itemize; \valu
...[truncated]...
ost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-devel-windows-x86_64

Rd files

checkRd: (-1) MCMCtreePhy.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:44: Lost braces in \itemize; \valu
...[truncated]...
ost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-oldrel-macos-arm64

Rd files

checkRd: (-1) MCMCtreePhy.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:44: Lost braces in \itemize; \valu
...[truncated]...
ost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-oldrel-macos-arm64

installed package size

installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb

NOTE r-oldrel-macos-x86_64

Rd files

checkRd: (-1) MCMCtreePhy.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:44: Lost braces in \itemize; \valu
...[truncated]...
ost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-oldrel-macos-x86_64

installed package size

installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb

NOTE r-oldrel-windows-x86_64

Rd files

checkRd: (-1) MCMCtreePhy.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:44: Lost braces in \itemize; \valu
...[truncated]...
ost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-oldrel-windows-x86_64

installed package size

installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb

NOTE r-patched-linux-x86_64

Rd files

checkRd: (-1) MCMCtreePhy.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:44: Lost braces in \itemize; \valu
...[truncated]...
ost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-release-linux-x86_64

Rd files

checkRd: (-1) MCMCtreePhy.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:44: Lost braces in \itemize; \valu
...[truncated]...
ost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-release-macos-arm64

Rd files

checkRd: (-1) MCMCtreePhy.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:44: Lost braces in \itemize; \valu
...[truncated]...
ost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-release-macos-x86_64

Rd files

checkRd: (-1) MCMCtreePhy.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:44: Lost braces in \itemize; \valu
...[truncated]...
ost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-release-windows-x86_64

Rd files

checkRd: (-1) MCMCtreePhy.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateBound.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateCauchy.Rd:44: Lost braces in \itemize; \valu
...[truncated]...
ost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateSkewT.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimateUpper.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly

Check History

NOTE 0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026

NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Mark Puttick <mark.puttick@bristol.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Mark",
                      family = "Puttick",
                      role = c("aut", "cre"),
                      email = "mark.puttick@bristol.ac.uk"),
               person(given = "Pascal",
                      family = "Title",
                      role = "ctb"))
as necessary.

NOTE r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Mark Puttick <mark.puttick@bristol.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Mark",
                      family = "Puttick",
                      role = c("aut", "cre"),
                      email = "mark.puttick@bristol.ac.uk"),
               person(given = "Pascal",
                      family = "Title",
                      role = "ctb"))
as necessary.

NOTE r-devel-linux-x86_64-fedora-clang

Rd files

checkRd: (-1) MCMCtreePhy.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:70: Lost braces in \itemize; \value h
...[truncated]...
: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-devel-linux-x86_64-fedora-gcc

Rd files

checkRd: (-1) MCMCtreePhy.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:70: Lost braces in \itemize; \value h
...[truncated]...
: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-devel-macos-arm64

Rd files

checkRd: (-1) MCMCtreePhy.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:70: Lost braces in \itemize; \value h
...[truncated]...
: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-devel-windows-x86_64

Rd files

checkRd: (-1) MCMCtreePhy.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:70: Lost braces in \itemize; \value h
...[truncated]...
: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-patched-linux-x86_64

Rd files

checkRd: (-1) MCMCtreePhy.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:70: Lost braces in \itemize; \value h
...[truncated]...
: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-release-linux-x86_64

Rd files

checkRd: (-1) MCMCtreePhy.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:70: Lost braces in \itemize; \value h
...[truncated]...
: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-release-macos-arm64

Rd files

checkRd: (-1) MCMCtreePhy.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:70: Lost braces in \itemize; \value h
...[truncated]...
: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-release-macos-x86_64

Rd files

checkRd: (-1) MCMCtreePhy.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:70: Lost braces in \itemize; \value h
...[truncated]...
: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-release-windows-x86_64

Rd files

checkRd: (-1) MCMCtreePhy.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MCMCtreePhy.Rd:70: Lost braces in \itemize; \value h
...[truncated]...
: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) priorPosterior.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-oldrel-macos-arm64

installed package size

installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb

NOTE r-oldrel-macos-x86_64

installed package size

installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb

NOTE r-oldrel-windows-x86_64

installed package size

installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb

Dependency Network

Version History

new 1.1 Mar 10, 2026

updated 1.1 ← 1.0 diff May 21, 2019

updated 1.0 ← 0.1 diff May 19, 2019

new 0.1 Mar 23, 2019

Maintainer

Mark Puttick

Dependencies

Depends

R (>= 3.3) ape (>= 3.0-7) sn coda

Imports

methods utils stats grDevices graphics

Suggests

knitr rmarkdown

Compilation

No compilation needed

First Published

Mar 23, 2019

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