earlyR
Estimation of Transmissibility in the Early Stages of a Disease Outbreak
v0.0.5
·
Oct 27, 2020
·
MIT + file LICENSE
Description
Implements a simple, likelihood-based estimation of the reproduction number (R0) using a branching process with a Poisson likelihood. This model requires knowledge of the serial interval distribution, and dates of symptom onsets. Infectiousness is determined by weighting R0 by the probability mass function of the serial interval on the corresponding day. It is a simplified version of the model introduced by Cori et al. (2013) <doi:10.1093/aje/kwt133>.
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| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | NOTE |
| r-devel-linux-x86_64-debian-gcc | NOTE |
| r-devel-linux-x86_64-fedora-clang | NOTE |
| r-devel-linux-x86_64-fedora-gcc | NOTE |
| r-devel-macos-arm64 | NOTE |
| r-devel-windows-x86_64 | NOTE |
| r-oldrel-macos-arm64 | NOTE |
| r-oldrel-macos-x86_64 | NOTE |
| r-oldrel-windows-x86_64 | NOTE |
| r-patched-linux-x86_64 | NOTE |
| r-release-linux-x86_64 | NOTE |
| r-release-macos-arm64 | NOTE |
| r-release-macos-x86_64 | NOTE |
| r-release-windows-x86_64 | NOTE |
Check details (17 non-OK)
NOTE
r-devel-linux-x86_64-debian-clang
Rd files
checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
34 | if (require(incidence)) {
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r-devel-linux-x86_64-debian-gcc
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checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
34 | if (require(incidence)) {
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r-devel-linux-x86_64-fedora-clang
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checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
34 | if (require(incidence)) {
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r-devel-linux-x86_64-fedora-gcc
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checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
34 | if (require(incidence)) {
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r-devel-macos-arm64
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checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
34 | if (require(incidence)) {
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r-devel-windows-x86_64
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checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
34 | if (require(incidence)) {
| ^
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r-oldrel-macos-arm64
LazyData
'LazyData' is specified without a 'data' directory
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r-oldrel-macos-arm64
Rd files
checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
34 | if (require(incidence)) {
| ^
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r-oldrel-macos-x86_64
LazyData
'LazyData' is specified without a 'data' directory
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r-oldrel-macos-x86_64
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checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
34 | if (require(incidence)) {
| ^
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r-oldrel-windows-x86_64
LazyData
'LazyData' is specified without a 'data' directory
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r-oldrel-windows-x86_64
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checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
34 | if (require(incidence)) {
| ^
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r-patched-linux-x86_64
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checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
34 | if (require(incidence)) {
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r-release-linux-x86_64
Rd files
checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
34 | if (require(incidence)) {
| ^
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r-release-macos-arm64
Rd files
checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
34 | if (require(incidence)) {
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r-release-macos-x86_64
Rd files
checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
34 | if (require(incidence)) {
| ^
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r-release-windows-x86_64
Rd files
checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
34 | if (require(incidence)) {
| ^
Check History
NOTE 0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 9, 2026
NOTE
r-devel-linux-x86_64-debian-clang
Rd files
checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
34 | if (require(incidence)) {
| ^
NOTE
r-devel-linux-x86_64-debian-gcc
Rd files
checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
34 | if (require(incidence)) {
| ^
NOTE
r-devel-linux-x86_64-fedora-clang
Rd files
checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
34 | if (require(incidence)) {
| ^
NOTE
r-devel-linux-x86_64-fedora-gcc
Rd files
checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
34 | if (require(incidence)) {
| ^
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r-devel-macos-arm64
Rd files
checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
34 | if (require(incidence)) {
| ^
NOTE
r-devel-windows-x86_64
Rd files
checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
34 | if (require(incidence)) {
| ^
NOTE
r-patched-linux-x86_64
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checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
34 | if (require(incidence)) {
| ^
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r-release-linux-x86_64
Rd files
checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
34 | if (require(incidence)) {
| ^
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r-release-macos-arm64
Rd files
checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
34 | if (require(incidence)) {
| ^
NOTE
r-release-macos-x86_64
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checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
34 | if (require(incidence)) {
| ^
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r-release-windows-x86_64
Rd files
checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
34 | if (require(incidence)) {
| ^
NOTE
r-oldrel-macos-arm64
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checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
34 | if (require(incidence)) {
| ^
NOTE
r-oldrel-macos-x86_64
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checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
34 | if (require(incidence)) {
| ^
NOTE
r-oldrel-windows-x86_64
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checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
34 | if (require(incidence)) {
| ^
Dependency Network
Version History
new
0.0.5
Mar 9, 2026