cran-task-views / agriculture Goto Github PK

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Not sure i could give my two cents, but anyway here are.
I would suggest some packages for your consideration:
https://cran.r-project.org/package=FielDHub /
https://github.com/DidierMurilloF/FielDHub A shiny design of
experiments (DOE) app that aids in the creation of traditional,
un-replicated, augmented and partially-replicated designs applied to
agriculture, plant breeding, forestry, animal and biological sciences.
*Category: Experimental design

***Not on CRAN / *https://github.com/OpenDroneMap/FIELDimageR *
FIELDimageR: A Tool to Analyze Images From Agricultural Field Trials and
Lab in R. Manipulation of Multispectral images, plant part count.
*Category: High throughput phenotyping (HTP)

***https://cran.r-project.org/package=photosynthesis /
https://github.com/cdmuir/photosynthesis package with modeling tools
for C3 photosynthesis, as well as analytical tools for curve-fitting
plant ecophysiology responses. *Category: Crop growth models & crop
modelling

***https://cran.r-project.org/package=tealeaves /
https://github.com/cdmuir/tealeaves package to model leaf
temperature using leaf energy balance, companion of photosynthesis
*Category: Crop growth models & crop modelling

***https://cran.r-project.org/package=plantecophys /
https://github.com/remkoduursma/plantecophys package that bundles a
number of tools to analyze and model leaf gas exchange data. *Category:
Crop growth models & crop modelling

***Not on CRAN / https://github.com/jstinzi/plantecowrap add to
capabilities to 'plantecophys' include temperature responses of
mesophyll conductance (gm, gmeso), apparent Michaelis-Menten constant
for rubisco carboxylation in air (Km, Kcair),and photorespiratory CO2
compensation point (GammaStar) for fitting A-Ci or A-Cc curves for C3
plants, ability to fit the Arrhenius and modified Arrhenius temperature
response functions for maximum rubisco carboxylation rates (Vcmax) and
maximum electron transport rates (Jmax)
*Category: Crop growth models & crop modelling

***https://cran.r-project.org/package=bigleaf /
https://bitbucket.org/juergenknauer/bigleaf/src/master/ package for
the calculation of physical (e.g. aerodynamic conductance, surface
temperature) and physiological (e.g. canopy conductance, water-use
efficiency) ecosystem properties from eddy covariance data and
accompanying meteorological measurements *Category: Crop growth models &
crop modelling

***Not on CRAN / https://github.com/rasenior/ThermStats and
**https://cran.us.r-project.org/package=Thermimage /
https://github.com/gtatters/Thermimage *First *is R package addresses
current constraints on applying thermography in ecology, by speeding up
and simplifying the extraction of data from (FLIR) thermal images, and
by facilitating the calculation of different metrics of thermal
heterogeneity for any gridded temperature data. *Second *is a collection
of functions for assisting in converting extracted raw data from
infrared thermal images and converting them to estimated temperatures
using standard equations in thermography. Provides an open source proxy
tool for assisting with infrared thermographic analysis. Both require
the external software ExifTool or, easier for R newbie IMHO,
*https://github.com/JoshOBrien/exiftoolr **Category: Crop growth models
& crop modelling

***Not on CRAN / https://github.com/poppinace/tasselnetv2plus A Fast
Implementation for High-Throughput Plant Counting from High-Resolution
RGB Imagery. Some functionalities could be similar to FILEDimageR, but
with completely different approach. *Category: High throughput
phenotyping (HTP)
*
**https://cran.r-project.org/package=DataExplorer /
https://github.com/boxuancui/DataExplorer Exploratory Data Analysis
(EDA) Category: Trial analysis

*https://cran.r-project.org/package=ggstatsplot /
*https://github.com/IndrajeetPatil/ggstatsplot
*Not on CRAN / *https://easystats.r-universe.dev/ui#packages
*https://cran.r-project.org/package=rstatix /
*https://github.com/kassambara/rstatix
all 3 above pkgs for simple and intuitive pipe-friendly framework,
coherent with the ‘tidyverse’ design philosophy Category: Trial analysis

Hope it helps
Massimiliano

First, this is a great initiative! Thank you for starting this, I’m excited to see it.

I see entomology listed, I’d like to see plant pathology and weed science included as well or maybe just a broader “crop protection” category with some of these as possible examples?

od
DiGGer

Simplace is now on CRAN. Proposed new language from package author:

The modelling framework Simplace (Scientificmpact assessment and Modelling Platform for Advanced Crop and Ecosystem management) can be accessed using r pkg("simplace"). r github("gk-crop/simplaceUtil") provides additional utility functions that make the setup and handling of simulations more convenient.

https://cran.r-project.org/package=XPolaris

Package febr is currently listed in CRAN Task View Agriculture but the package has actually been archived for more than 60 days on CRAN. Often this indicates that the package is currently not sufficiently actively maintained and should be excluded from the task view.

Alternatively, you might also consider reaching out to the authors of the package and encourage (or even help) them to bring the package back to CRAN. See the section on CRAN package archivals in the maintenance guidelines for more details.

In any case, the situation should be resolved in the next four weeks. If the package does not seem to be brought back to CRAN, please exclude it from the task view.

What constitute the most important packages for agriculture science, broadly speaking or discipline-specific.

Feedback from twitter:
https://twitter.com/SeedsAndBreeds/status/1529083494474735616

• Agricolae
• FedData, cdlTools, soilDB

1. Which package would you like to suggest? What features does it provide?
   soiltestcorr is a compilation of functions designed to assist users on the correlation analysis of crop yield and soil test values.

2. Please provide the link to CRAN by appending the package name
   (case-sensitive) to the end of the URL below:

https://cran.r-project.org/package=soiltestcorr

3. Which category do you think is the best fit for the package:
   Soil Science

PRISM: climate data (not sure if this on CRAN)
MoPBS: plant breeding simulation

1. Which package would you like to suggest? What features does it provide?

pestr: Interface to Download Data on Pests and Hosts from 'EPPO'

2. Please provide the link to CRAN by appending the package name
   (case-sensitive) to the end of the URL below:

https://cran.r-project.org/package=pestr

3. Which category do you think is the best fit for the package:

(Delete those categories which do not apply)

• Agricultural & landuse databases

1. Which package would you like to suggest? What features does it provide?

cropdatape provides peruvian agricultural production data from the Agriculture Minestry of Peru (MINAGRI).

2. Please provide the link to CRAN by appending the package name
   (case-sensitive) to the end of the URL below:

https://cran.r-project.org/package=cropdatape

3. Which category do you think is the best fit for the package:

(Delete those categories which do not apply)

• General Packages
  • Agricultural data sets

@adamhsparks and @janetw

A draft of the CRAN task view is avaiable for feedback (The file called "Agriculture.md"). It's following the expected format for these task views.

Most (all?) other task views use a bulleted format, so I switched to that from the paragraphs (although, there a few paragraphs to consolidate information).

Can you please look at this, largely with copy editing in mind (e.g. misspellings, incorrect grammar, inconsistent style choices)? If you see a more substantial error, however, please bring it up.

Adam - can you please check the plant pathology section carefully? I made a few decisions about organization of that section that should be checked by an expert.

In the meantime, I will submit what is done thus far so the CTV committee can have a look. I created a new file for additional links so we can add them in the future. My plan is the delete the file called "draft_agriculture_ctv.md" because I don't want to maintain it. However, a close copy of that file is on the agstats.io website, which I plan to maintain for the foreseeable future.

Thank you!

1. ascotraceR

2. https://cran.r-project.org/package=ascotraceR

3. Which category do you think is the best fit for the package: Plant Pathology

1. Which package would you like to suggest? What features does it provide?

PesticideLoadIndicator
Computes the Danish Pesticide Load Indicator

2. Please provide the link to CRAN by appending the package name
   (case-sensitive) to the end of the URL below:

https://cran.r-project.org/package=PesticideLoadIndicator

3. Which category do you think is the best fit for the package:

(Delete those categories which do not apply)

• General Packages

Package CropScapeR is currently listed in CRAN Task View Agriculture but the package has actually been archived for more than 60 days on CRAN. Often this indicates that the package is currently not sufficiently actively maintained and should be excluded from the task view.

Alternatively, you might also consider reaching out to the authors of the package and encourage (or even help) them to bring the package back to CRAN.

In any case, the situation should be resolved in the next four weeks. If the package does not seem to be brought back to CRAN, please exclude it from the task view.

1. Which package would you like to suggest? What features does it provide?

nasapower, a client for 'NASA' 'POWER' global meteorology, surface solar energy and climatology data 'API'. 'POWER' (Prediction Of Worldwide Energy Resource) data are freely available for download with varying spatial resolutions dependent on the original data and with several temporal resolutions depending on the POWER parameter and community.

2. Please provide the link to CRAN by appending the package name
   (case-sensitive) to the end of the URL below:

https://cran.r-project.org/package=nasapower

3. Which category do you think is the best fit for the package:

(Delete those categories which do not apply)

• General Packages
  • Agrometeorology

If we have rnoaa back in the mix, I'd suggest this one as well. The APSIMX package already has it as a dependency. It has a specific "Ag" community with weather and climate parameters for agrometeorology, which is why I wrote the package to start with.

Not all of these are on CRAN, but here is a list to get started. Some of these are fringe or narrow-interest and should be deleted.

desplot is useful for plotting the plan for field experiments

agridat - datasets from agricultural experiments (mostly related to plant breeding)

agriCensData

https://github.com/OnofriAndreaPG/agriCensData

Three datasets with censored observations for the paper "Analyzing interval-censored data in agricultural research: A review with examples and software tips".

agriTutorial

https://myaseen208.github.io/agriTutorial/

Five datasets used to illustrate analyses.

agricolae

Has assorted data and functions for analysis of agricultural data.

agroBioData

https://github.com/OnofriAndreaPG/agroBioData

Datasets for agriculture and applied biology. Referenced by this blog: https://www.statforbiology.com/

BGLR - Bayesian Generalized Linear Regression.

Has an A matrix (but no pedigree) for 499 genotypes at 4 locations.

BLR - Bayesian Linear Regression.

Has an A matrix (but no pedigree) for 499 genotypes at 4 locations.

BSagri

Safety assessment in agriculture trials

cropcc - Climate change on crops

https://r-forge.r-project.org/projects/cropcc/

drc - Dose response curves

Has nice herbicide dose response curves and germination data for mungbean, rice, wheat.

FW - Finlay-Wilkinson regression

https://github.com/lian0090/FW/

Has phenotype data and marker data for 599 wheat lines in 4 environments.

ggenealogy

https://www.jstatsoft.org/article/view/v089i13

Data sbGeneal contains a soybean pedigree with 230 varieties.

gRbase

Data gRbase::carcass: thickness of meat and fat on slaughter pigs

lmDiallel

https://github.com/OnofriAndreaPG/lmDiallel/tree/master/data

lmtest

Data lmtest::ChickEgg time series of annual chicken and egg production in the United States 1930-1983.

nlraa

Miguez. Non-linear models in agriculture.
nlraa::sm = agridat::miguez.biomass
Vignettes and functions for working with (non)linear mixed models

plantbreeding

https://r-forge.r-project.org/projects/plantbreeding/

Data: fulldial
Data: linetester
Data: peanut same as agridat::kang.peanut

soilDB

https://ncss-tech.github.io/AQP/soilDB/soilDB-Intro.html
Soil database interface.

sommer - Solving mixed model equations in R

Data: h2. Modest-sized GxE experiment in potato Data: cornHybrid. Yield/PLTHT for 100 hybrids from 20 inbred * 20 inbred, 4 locs. Phenotype and relationship matrix.

Data: wheatLines CIMMYT wheat data for 599 lines. Phenotype and relationship data.

Data: RICE

Data: FDdata taken from agridat::bond.diallel

Data: Technow_data. AF=Additive Flint. AD=Additive Dent. MF=Marker Flint. MD=Marker Dent. pheno=phenotype data for 1254 hybrids (GY=yield, GM=moisture). This data is from Technow et al:
http://www.genetics.org/content/197/4/1343.supplemental

SoyNAM - Soybean nested association mapping

Dataset with phenotype data 3 yr, 9 locations, 18 environments, 60 thousand observations for height, maturity, lodging, moisture, protein, oil, fiber, seed size. There are 5000+ strains, 40 families.

Data formatted for the analysis of the NAM package is available with the following command: SoyNAM::ENV().

spdep

Has a vignette 'The Problem of Spatial Autocorrelation: forty years on' that examines agriculture in Irish counties.
See also the data ade4::irishdata

StatForBiology

https://www.statforbiology.com/

Blog posts with example analyses.

statgenSTA

https://CRAN.R-project.org/package=statgenSTA
See vignette: Modeling field trials using statgenSTA

statgenGWAS

https://CRAN.R-project.org/package=statgenGWAS

Includes a worked example with data from:
https://data.inra.fr/dataset.xhtml?persistentId=doi:10.15454/IASSTN

st4gi - Stat for genetic improvement

https://github.com/reyzaguirre/st4gi

1. Which package would you like to suggest? What features does it provide?

Pergola - linkage mapping for polyploids

2. Please provide the link to CRAN by appending the package name
   (case-sensitive) to the end of the URL below:

https://cran.r-project.org/package=pergola

3. Which category do you think is the best fit for the package:

(Delete those categories which do not apply)

* Linkage mapping & QTL analysis   

Some years ago I was involved in writing a set of course materials for self-instruction or classroom that demonstrate epidemiological concepts in R for plant pathologists.

This would be a nice addition to the “Links”, I think.

https://www.apsnet.org/edcenter/disimpactmngmnt/topc/EcologyAndEpidemiologyInR/Pages/default.aspx

Package isqg is currently listed in CRAN Task View Agriculture but the package has actually been archived for more than 60 days on CRAN. Often this indicates that the package is currently not sufficiently actively maintained and should be excluded from the task view.

Alternatively, you might also consider reaching out to the authors of the package and encourage (or even help) them to bring the package back to CRAN.

In any case, the situation should be resolved in the next four weeks. If the package does not seem to be brought back to CRAN, please exclude it from the task view.

1. Which package would you like to suggest? What features does it provide?

GAPIT

2. Please provide the link to CRAN by appending the package name
   (case-sensitive) to the end of the URL below:

https://www.zzlab.net/GAPIT/

3. Which category do you think is the best fit for the package:

   • GWAS
   • Genomic prediction

*Note: this is not a package - it's a collection of .R files that can be used to load other packages and conduct GWAS. *

MegaLMM is not really a GWAS tool – it’s more for genomic prediction. For GWAS you could instead include GridLMM: https://github.com/deruncie/GridLMM, https://doi.org/10.1371/journal.pgen.1007978 which is a GWAS tool and allows you to include multiple random effects to account for multiple sources of confounders. I think MegaLMM would best be described as a tool for multi-trait and/or multi-environment genomic prediction following our paper here: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02416-w

r github("deruncie/GridLMM") provides functions to run GWAS in models that require 2+ random effects (e.g. additive and dominance kinship matrices, or kinship and spatial covariance matrices)

(within Multiple environments and traits:) r github("deruncie/MegaLMM") implements multivariate genomic prediction with very large numbers of traits (up to several thousand) using several Bayesian genomic prediction models.

add:

kinship2
coxme

1. Which package would you like to suggest? What features does it provide?

ag5Tools

2. Please provide the link to CRAN by appending the package name
   (case-sensitive) to the end of the URL below:

https://cran.r-project.org/package=ag5Tools

3. Which category do you think is the best fit for the package:

• General Packages
  • Agricultural data sets

I think this is the most appropriate for it, but am open for discussion, so I didn't make this one a PR

Package agroclim is currently listed in CRAN Task View Agriculture but the package has actually been archived for more than 60 days on CRAN. Often this indicates that the package is currently not sufficiently actively maintained and should be excluded from the task view.

Alternatively, you might also consider reaching out to the authors of the package and encourage (or even help) them to bring the package back to CRAN.

In any case, the situation should be resolved in the next four weeks. If the package does not seem to be brought back to CRAN, please exclude it from the task view.

1. Which package would you like to suggest? What features does it provide?
   ALUES: Agricultural Land Use Evaluation System

Evaluates land suitability for different crops production. The package is based on the Food and Agriculture Organization (FAO) and the International Rice Research Institute (IRRI) methodology for land evaluation. Development of ALUES is inspired by similar tool for land evaluation, Land Use Suitability Evaluation Tool (LUSET). The package uses fuzzy logic approach to evaluate land suitability of a particular area based on inputs such as rainfall, temperature, topography, and soil properties. The membership functions used for fuzzy modeling are the following: Triangular, Trapezoidal and Gaussian. The methods for computing the overall suitability of a particular area are also included, and these are the Minimum, Maximum and Average. Finally, ALUES is a highly optimized library with core algorithms written in C++.

2. Please provide the link to CRAN by appending the package name
   (case-sensitive) to the end of the URL below:

https://cran.r-project.org/package=ALUES

3. Which category do you think is the best fit for the package:

General Agriculture

"CropDetectR" and "isqg" have both been archived.

1. Which package would you like to suggest? What features does it provide?

landsepi
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.

2. Please provide the link to CRAN by appending the package name
   (case-sensitive) to the end of the URL below:

https://cran.r-project.org/package=landsepi

3. Which category do you think is the best fit for the package:

Plant Pathology

book: https://www.statforbiology.com/_statbookeng/
same book in Italian: https://www.statforbiology.com/_statbook/

blog by same author: https://www.statforbiology.com/

despite blog name, it appears to be focused on agriculture.

hello everyone, as discussed in a previous e-mail, I add a table containing some package that are not covered in this CRAN Task View.

I downloaded all packages Descriptions from CRAN and searched for the following three substrings with grep:

1. agric
2. crop
3. agron

I can also provide a list with more agriculture related words, one can use to search some package descriptions. So in case I can use these stemmed strings to search more deeply.

1. Which package would you like to suggest? What features does it provide?

https://github.com/INTA-Suelos/SISINTAR

Allow access to the soil profile of INTA in Argentina. Also, allow handling of the soil data.

2. Please provide the link to CRAN by appending the package name
   (case-sensitive) to the end of the URL below:

There is not on CRAN (yet), but I suggest it because on the R-Ladies Community Slack was a request to suggest packages even if they aren't on CRAN.

3. Which category do you think is the best fit for the package:

Soil Science

1. fix issue templates
2. add suggestion from here.

Package BMTME is currently listed in CRAN Task View Agriculture but the package has actually been archived for more than 60 days on CRAN. Often this indicates that the package is currently not sufficiently actively maintained and should be excluded from the task view.

Alternatively, you might also consider reaching out to the authors of the package and encourage (or even help) them to bring the package back to CRAN. See the section on CRAN package archivals in the maintenance guidelines for more details.

In any case, the situation should be resolved in the next four weeks. If the package does not seem to be brought back to CRAN, please exclude it from the task view.

packages to add:

• AGPRIS
• agricolaeplotr
• agrifeatures
• agrostab
• AgroTech
• biotools
• cropdatape
• cropDemand
• CropDetecR
• cropgrowdays
• cropZoning
• grapesAgri1
• resevol
• rPAex
• Evapotranspiration
• KenSyn
• ZeBook
• Bsagri

1. Which package would you like to suggest? What features does it provide?

AlphaSimR for quantitative genetics and breeding simulations

2. Please provide the link to CRAN by appending the package name
   (case-sensitive) to the end of the URL below:

https://cran.r-project.org/package=AlphaSimR

3. Which category do you think is the best fit for the package:

General Agriculture,
Soil Science,
Agronomic Trials,

• Plant Breeding and Genetics,
  Entomology,
  Animal Science,
  Food Science,
  Rural Sociology,
  Agricultural Economics

https://r4pde.netlify.app/

1. Which package would you like to suggest? What features does it provide?

The {agromet} package includes a series of functions to calculate climatic and hydrological indices and statistics from tidy data. For example, umbrales() allow counting the number of observations that meet a certain condition, and dias_promedios() returns the first and last day of the average year of occurrence of an event.

Other functions such as spi() work as wrappers of functions from other packages and are intended to be compatible with tidy data management.

Finally, the package includes a geo-referenced data plotting function map() with INTA's own style and logo.

2. Please provide the link to CRAN by appending the package name
   (case-sensitive) to the end of the URL below:
   It is not in CRAN, yet, but I suggest it because in the R-Ladies Slack was a request about packages related to agriculture even if not in CRAN.

https://github.com/AgRoMeteorologiaINTA/agromet

3. Which category do you think is the best fit for the package:

Agrometerology

(found from searching the CRAN package list using keywords)

1. Which package would you like to suggest? What features does it provide?
   mvngGrAd
   Package for moving grid adjustment in plant breeding field trials.

2. Please provide the link to CRAN by appending the package name
   (case-sensitive) to the end of the URL below:

https://cran.r-project.org/package=mvngGrAd

3. Which category do you think is the best fit for the package:

Plant Breeding and Genetics

The GitHub repo doesn't appear to be in sync with CRAN, but it just got an update today, presumably removing {rgdal}, {rgeos}, and {rmaptools} since I only see {terra} in the Imports.

https://cran.r-project.org/web/packages/agriwater/index.html

I'll send through a PR

1. Which package would you like to suggest? What features does it provide?
   AgroReg
   Linear and nonlinear regression analysis common in agricultural science articles (Archontoulis & Miguez (2015). <doi:10.2134/agronj2012.0506>). The package includes polynomial, exponential, gaussian, logistic, logarithmic, segmented, non-parametric models, among others. The functions return the model coefficients and their respective p values, coefficient of determination, root mean square error, AIC, BIC, as well as graphs with the equations automatically.

2. Please provide the link to CRAN by appending the package name
   (case-sensitive) to the end of the URL below:

https://cran.r-project.org/package=AgroReg

3. Which category do you think is the best fit for the package:

Agronomic Trials (design and analysis)

Package CropDetectR is currently listed in CRAN Task View Agriculture but the package has actually been archived for more than 60 days on CRAN. Often this indicates that the package is currently not sufficiently actively maintained and should be excluded from the task view.

Alternatively, you might also consider reaching out to the authors of the package and encourage (or even help) them to bring the package back to CRAN.

In any case, the situation should be resolved in the next four weeks. If the package does not seem to be brought back to CRAN, please exclude it from the task view.

1. Which package would you like to suggest? What features does it provide?

cropdatape provides peruvian agricultural production data from the Agriculture Minestry of Peru (MINAGRI).

2. Please provide the link to CRAN by appending the package name
   (case-sensitive) to the end of the URL below:

https://cran.r-project.org/package=cropdatape

3. Which category do you think is the best fit for the package:

(Delete those categories which do not apply)

• General Packages
  • Agricultural data sets

https://github.com/luansheng/visPedigree

new package for consideration: AquaBEHER

Computes and integrates daily reference 'evapotranspiration' ('Eto') into a water balance model, to estimate the calendar of wet-season (Onset, Cessation and Duration) based on 'agroclimatic' approach, for further information please refer to Allen 'et al.' (1998, ISBN:92-5-104219-5), Allen (2005, ISBN:9780784408056), 'Doorenbos' and Pruitt (1975, ISBN:9251002797) 'Guo et al.' (2016) <doi:10.1016/j.envsoft.2015.12.019>, Hargreaves and 'Samani' (1985) <doi:10.13031/2013.26773>, Priestley and Taylor (1972) https://journals.ametsoc.org/downloadpdf/journals/mwre/100/2/1520-0493_1972_100_0081_otaosh_2_3_co_2.pdf.

Perhaps it fits in the Agrometeorology section?

See https://twitter.com/gregorgorjanc/status/1527726953985454080?s=21&t=hXmAo0eQUSJ5LZdl_YODmA

1. Which package would you like to suggest? What features does it provide?
   metrica is a compilation of more than 40 functions designed to evaluate prediction performance of point-forecast models (e.g. Machine Learning, APSIM, DSSAT) accounting for different aspects of the agreement between predicted and observed values. It includes error metrics (e.g. MAE, RMSE), model efficiencies (e.g. NSE, KGE), indices of agreement (e.g. d, RAC), goodness of fit (e.g. r, R2), concordance correlation (e.g. CCC), error decomposition (e.g. lack of accuracy-precision), and plots the visualize agreement. It also includes functions to open APSIM output files from APSIM Classic and APSIM NextGen.

2. Please provide the link to CRAN by appending the package name
   (case-sensitive) to the end of the URL below:

https://cran.r-project.org/package=metrica

3. Which category do you think is the best fit for the package:

General Agriculture,
Agronomic Trials

Package RGISTools is currently listed in CRAN Task View Agriculture but the package has actually been archived for more than 60 days on CRAN. Often this indicates that the package is currently not sufficiently actively maintained and should be excluded from the task view.

Alternatively, you might also consider reaching out to the authors of the package and encourage (or even help) them to bring the package back to CRAN.

In any case, the situation should be resolved in the next four weeks. If the package does not seem to be brought back to CRAN, please exclude it from the task view.

@emdelponte has a very nice open textbook for using R in botanical epidemiology that would be a good addition to the "Links" section, I think.

https://r4pde.netlify.app

Package for consideration: drcte

A specific and comprehensive framework for the analyses of time-to-event data in agriculture. Fit non-parametric and parametric time-to-event models. Compare time-to-event curves for different experimental groups. Plots and other displays. It is particularly tailored to the analyses of data from germination and emergence assays. The methods are described in Onofri et al. (2020) "A unified framework for the analysis of germination, emergence, and other time-to-event data in weed science"", Weed Science, 70, 259-271 <doi:10.1017/wsc.2022.8>

Would probably go in the Weed Science section.