R Observatory: Metrics for landsepi version 1.5.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

landsepi

1.5.3Package record

Landscape Epidemiology and Evolution

0packages depend

6.7Kdownloads / year

13.1%test coverage

13/13flavors OK

Overview

About

Maintained by Jean-François ReyCRAN page ↗Repository ↗Website ↗Issues ↗

A stochastic, spatially-explicit, demo-genetic model simulating the spread and evolution of a plant pathogen in a heterogeneous landscape to assess resistance deployment strategies. It is based on a spatial geometry for describing the landscape and allocation of different cultivars, a dispersal kernel for the dissemination of the pathogen, and a SEIR ('Susceptible-Exposed-Infectious-Removed’) structure with a discrete time step. It provides a useful tool to assess the performance of a wide range of deployment options with respect to their epidemiological, evolutionary and economic outcomes. Loup Rimbaud, Julien Papaïx, Jean-François Rey, Luke G Barrett, Peter H Thrall (2018) doi:10.1371/journal.pcbi.1006067.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)

install.packages("landsepi", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-landsepi

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-landsepi

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 6.6 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18

Show 1 earlier changeHide 1 earlier change

NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.5.3

READMENoVignettesYes · 7 · dynamicNEWSYes · 100% structured · does not mention 1.5.3Citation fileYes · computed when R runs itWebsiteYes

Help pages: 85includes a package overview page
Examples that run: 31%19 run in a plain check · 42 never run
Exported functions with examples: 94%
Documented parameters: 98%
Return-value docs: 95%
Help pages citing references: 12%

Vignettes (7)

How these are measured

Downloads

6.7K

CRAN downloads in the past year

Rank #5,146 · ~18/day · ~555/mo

Releases R versions

Daily download trend is not available in this view yet.

64130 days

1.6K90 days

6.7K1 year

Compare downloads with other packages →

Also on418 r2u148 c2d4u

How downloads are counted

Repository

forge.inrae.fr/landsepi/landsepi ↗

0Stars

1Forks

0Open issues

0Open PRs

6Releases

997Commits

11Commit identities

R-packageEpidemiologymodellingR-Shiny

License file reads as GPL-2.0 · 997 commits · Last activity 2026-01-07

Responsiveness

How these are sampled

PRs merged (all time): 0%
Median days to close, 50 most recently updated closed issues: GitHub only
Median days to close, 50 most recently updated closed PRs: GitHub only

How these are measured

PracticesBeta

Repository forge.inrae.fr/landsepi/landsepi is linked, but repository-practices checks have not run for it yet. Checks are GitHub-only for now.

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Installing landsepi adds 56 packages (33 with compiled code, 48 MB of source tarballs). Heaviest: sf 9.3 MB, sp 4.3 MB, RSQLite 4.2 MB.

Depends (2)

R >= 4.2.0sp

Imports (17)

methodsutilsstatsgrDevicesgraphicsparallelRcpp Matrix (>= 1.3-0)mvtnorm fields splancs sf DBI RSQLite foreach doParallel deSolve

LinkingTo (2)

Rcpp testthat

Suggests (6)

testthat shiny shinyjs DT knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (6)

Jean-François Rey

Author, Maintainer · added in 1.1.0

Julien Papaix

Author

Loup Rimbaud

Author

Marta Zaffaroni

Author · added in 1.2.0

Manon Couty

Contributor · added in 1.4.0

Jean-Loup Gaussen

Contributor · added in 1.0.0

Maintainer since 0.0.2 (2018)

Listed in earlier versions (1)

Jean-Francois Rey

no longer listed · 0.0.2 to 1.0.2

Releases (25)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.5.3Latest
record
2026-01-07 · current release · diff ↗
1.5.2
record
2025-07-31 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.5.1
record
2024-09-23 · diff ↗
1.5.0
record
2024-09-03 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.4.0
record
2024-03-12 · diff ↗ ·
removed 1 export
setReproSexProb

added 9 exports
getMatrixCroptypePatho, getMatrixCultivarPatho, getMatrixGenePatho, getMatrixPolyPatho, inoculumToMatrix, loadInoculum, survivalProbToMatrix, updateReproSexProb, updateSurvivalProb
1.3.0
record
2023-07-19 · diff ↗ ·
removed 2 exports
getGPKGArea, getGPKGRotation
R
R 4.3.0 released · 2023-04-21
unarchivedReturned to CRAN
2023-02-27
1.2.5
record
2023-02-27 · diff ↗ ·
added 2 exports
compute_audpc100S, price_reduction
archivedRemoved from CRAN
2023-02-18
configure issues were not corrected in time 'CXX' not set correctly
1.2.4
record
2023-01-16 · diff ↗
1.2.3
record
2023-01-16 · diff ↗
1.2.2
record
2022-10-06 · diff ↗

Show 21 earlier eventsHide 21 earlier events

1.2.1
record
2022-10-06 · diff ↗
1.2.0
record
2022-10-05 · diff ↗ ·
added 4 exports
antideriv_verhulst, loadTreatment, setReproSexProb, setTreatment
R
R 4.2.0 released · 2022-04-22
1.1.2
record
2022-03-02 · diff ↗
1.1.1
record
2021-10-05 · diff ↗
1.1.0
record
2021-07-26 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0.2
record
2020-12-01 · diff ↗
1.0.1
record
2020-07-02 · diff ↗
1.0.0
record
2020-07-01 · diff ↗ ·
removed 2 exports
HLIRdynamics, plotevolQR

added 41 exports
allocateCroptypeCultivars, allocateCultivarGenes, allocateLandscapeCroptypes, checkSimulParams, createSimulParams, epid_output, evol_output, getGPKGArea, getGPKGRotation, is.in.01, is.positive, is.strict.positive, is.wholenumber, loadCroptypes, loadCultivar, loadDispersalHost, loadDispersalPathogen, loadGene, loadLandscape, loadOutputs, loadPathogen, loadSimulParams, plot_allocation, plot_freqPatho, runShinyApp, runSimul, saveDeploymentStrategy, setCroptypes, setCultivars, setDispersalHost and 11 more
R
R 4.0.0 released · 2020-04-24
0.0.8
record
2019-10-05 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.0.7
record
2019-01-14 · diff ↗
0.0.6
record
2019-01-09 · diff ↗ ·
removed 1 export
modelLandsEPI

added 1 export
model_landsepi
0.0.5
record
2018-11-27 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.0.4
record
2018-04-10 · diff ↗
0.0.3
record
2018-04-09 · diff ↗
0.0.2
record
2018-03-26
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2018-03-26
Total releases: 25 / 8 yrs
License: GPL (>= 2) | file LICENSE OSI
Minimum R: ≥ 4.2.0
Bundled data: 939 KB / 2 files
Download size: 4.3 MB

Appears in task views

Agricultural Science

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("landsepi")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for landsepi version 1.5.3 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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