EpiPvr
Estimating Plant Pathogen Epidemiology Parameters from Laboratory Assays
Description
Provides functions for estimating plant pathogen parameters from access period (AP) experiments. Separate functions are implemented for semi-persistently transmitted (SPT) and persistently transmitted (PT) pathogens. The common AP experiment exposes insect cohorts to infected source plants, healthy test plants, and intermediate plants (for PT pathogens). The package allows estimation of acquisition and inoculation rates during feeding, recovery rates, and latent progression rates (for PT pathogens). Additional functions support inference of epidemic risk from pathogen and local parameters, and also simulate AP experiment data. The functions implement probability models for epidemiological analysis, as derived in Donnelly et al. (2025), <doi:10.32942/X29K9P>. These models were originally implemented in the 'EpiPv' 'GitHub' package.
Downloads
245
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20268th
528
Last 90 days
1.6K
Last year
Trend: +114.9% (30d vs prior 30d)
24
Last 30 days
110
Last 90 days
307
Last year
Trend: -36.8% (30d vs prior 30d)
3
Last 7 days
15
Last 30 days
3
All-time
autoCRAN-only: this name is served only by autoCRAN, so the count is exact.
CRAN Check Status
Show all 13 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check History
OK 12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 25, 2026
NOTE 11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 22, 2026
installed package size
installed size is 54.3Mb
sub-directories of 1Mb or more:
libs 52.8Mb
installed package size
installed size is 56.2Mb
sub-directories of 1Mb or more:
libs 54.8Mb
for GNU extensions in Makefiles
GNU make is a SystemRequirements.
ERROR 10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 18, 2026
whether package can be installed
Installation failed. See 'd:/Rcompile/CRANpkg/local/4.6/EpiPvr.Rcheck/00install.out' for details.
installed package size
installed size is 54.3Mb
sub-directories of 1Mb or more:
libs 52.8Mb
installed package size
installed size is 56.2Mb
sub-directories of 1Mb or more:
libs 54.8Mb
for GNU extensions in Makefiles
GNU make is a SystemRequirements.
NOTE 11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
installed package size
installed size is 54.3Mb
sub-directories of 1Mb or more:
libs 52.8Mb
installed package size
installed size is 56.2Mb
sub-directories of 1Mb or more:
libs 54.8Mb
for GNU extensions in Makefiles
GNU make is a SystemRequirements.
Code & tests
Open call graph →Line coverage
–
Expression
–
Tests / Examples
–
Functions
13 4 exported
Complexity
8.6 avg / 16 max
Call network
13 nodes / 4 edges
Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.
Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
6,735
Files
66
Compiled share
58.6%
Has compiled src
Yes
Language breakdown
API
Exported functions
4
Internal functions
4
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.41
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Return-value doc rate
100%
\dontrun example ratio
0%
Roxygen coverage
100%
Has pkgdown
No
NEWS present
No
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
100%
Unsafe pattern score
0
Dep constraint coverage
57.1%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.5
System requirements
1
C++ standard
C++17
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
1
First release
2025-10-01
Latest release
2025-10-01
Avg cadence
–
Cold removal rate
–
Dep drift
0
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/cran-code-metrics.
Dependency Network
Version History
1 trackedR Observatory began tracking this package on Mar 10, 2026; it first appeared on CRAN Oct 1, 2025. Releases before tracking aren’t shown.