cran-task-views / agriculture Goto Github PK
View Code? Open in Web Editor NEWCRAN Task View: Agricultural Science
Home Page: https://CRAN.R-project.org/view=Agriculture
CRAN Task View: Agricultural Science
Home Page: https://CRAN.R-project.org/view=Agriculture
@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.
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.
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.
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
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.
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
Agronomic Trials (design and analysis)
PRISM: climate data (not sure if this on CRAN)
MoPBS: plant breeding simulation
Package RGISTools is currently listed in CRAN Task View Agriculture but the package has actually been archived for more than 60 days on CRAN.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.
PesticideLoadIndicator
Computes the Danish Pesticide Load Indicator
https://cran.r-project.org/package=PesticideLoadIndicator
(Delete those categories which do not apply)
Pergola - linkage mapping for polyploids
https://cran.r-project.org/package=pergola
(Delete those categories which do not apply)
* Linkage mapping & QTL analysis
od
DiGGer
What constitute the most important packages for agriculture science, broadly speaking or discipline-specific.
Feedback from twitter:
https://twitter.com/SeedsAndBreeds/status/1529083494474735616
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.
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.
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)
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".
https://myaseen208.github.io/agriTutorial/
Five datasets used to illustrate analyses.
Has assorted data and functions for analysis of agricultural data.
https://github.com/OnofriAndreaPG/agroBioData
Datasets for agriculture and applied biology. Referenced by this blog: https://www.statforbiology.com/
Has an A matrix (but no pedigree) for 499 genotypes at 4 locations.
Has an A matrix (but no pedigree) for 499 genotypes at 4 locations.
Safety assessment in agriculture trials
https://r-forge.r-project.org/projects/cropcc/
Has nice herbicide dose response curves and germination data for mungbean, rice, wheat.
https://github.com/lian0090/FW/
Has phenotype data and marker data for 599 wheat lines in 4 environments.
https://www.jstatsoft.org/article/view/v089i13
Data sbGeneal
contains a soybean pedigree with 230 varieties.
Data gRbase::carcass
: thickness of meat and fat on slaughter pigs
https://github.com/OnofriAndreaPG/lmDiallel/tree/master/data
Data lmtest::ChickEgg
time series of annual chicken and egg production in the United States 1930-1983.
Miguez. Non-linear models in agriculture.
nlraa::sm
= agridat::miguez.biomass
Vignettes and functions for working with (non)linear mixed models
https://r-forge.r-project.org/projects/plantbreeding/
Data: fulldial
Data: linetester
Data: peanut same as agridat::kang.peanut
https://ncss-tech.github.io/AQP/soilDB/soilDB-Intro.html
Soil database interface.
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
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()
.
Has a vignette 'The Problem of Spatial Autocorrelation: forty years on' that examines agriculture in Irish counties.
See also the data ade4::irishdata
https://www.statforbiology.com/
Blog posts with example analyses.
https://CRAN.R-project.org/package=statgenSTA
See vignette: Modeling field trials using statgenSTA
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
ascotraceR
Which category do you think is the best fit for the package: Plant Pathology
(found from searching the CRAN package list using keywords)
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?
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++.
https://cran.r-project.org/package=ALUES
General Agriculture
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.
https://cran.r-project.org/package=nasapower
(Delete those categories which do not apply)
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.
GAPIT
Which category do you think is the best fit for the package:
*Note: this is not a package - it's a collection of .R files that can be used to load other packages and conduct GWAS. *
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?
@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!
add:
kinship2
coxme
cropdatape provides peruvian agricultural production data from the Agriculture Minestry of Peru (MINAGRI).
https://cran.r-project.org/package=cropdatape
(Delete those categories which do not apply)
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:
Package | Description | |
---|---|---|
737 | AutoWeatherIndices | Weather indices are formed from weather variables in this package. The users can input any number of weather variables recorded over any number of weeks. This package has no restriction on the number of weeks and weather variables to be taken as input.The details of the method can be seen (i)'Joint effects of weather variables on rice yields' by R. Agrawal, R. C. Jain and M. P. Jha in Mausam, vol. 34, pp. 189-194, 1983,<doi:10.54302/mausam.v34i2.2392>,(ii)'Improved weather indices based Bayesian regression model for forecasting crop yield' by M. Yeasin, K. N. Singh, A. Lama and B. Gurung in Mausam, vol. 72, pp.879-886, 2021,<doi:10.54302/mausam.v72i4.670>. |
1334 | biometryassist | Provides functions to aid in the design and analysis of agronomic and agricultural experiments through easy access to documentation and helper functions, especially for users who are learning these concepts. |
1597 | BrazilMet | A compilation of functions to download and processing AWS data of INMET-Brazil, with the purpose of reference evapotranspiration (ETo) estimation. The package aims to make meteorological and agricultural data analysis more parsimonious. |
1624 | briskaR | A spatio-temporal exposure-hazard model for assessing biological risk and impact. The model is based on stochastic geometry for describing the landscape and the exposed individuals, a dispersal kernel for the dissemination of contaminants, a set of tools to handle spatio-temporal dataframe and ecotoxicological equations. Walker E, Leclerc M, Rey JF, Beaudouin R, Soubeyrand S, and Messean A, (2017), A Spatio-Temporal Exposure-Hazard Model for Assessing Biological Risk and Impact, Risk Analysis, <doi:10.1111/risa.12941>. Leclerc M, Walker E, Messean A, Soubeyrand S (2018), Spatial exposure-hazard and landscape models for assessing the impact of GM crops on non-target organisms, Science of the Total Environment, 624, 470-479. |
2284 | climatrends | Supports analysis of trends in climate change, ecological and crop modelling. |
2820 | cosinor | A set of simple functions that transforms longitudinal data to estimate the cosinor linear model as described in Tong (1976). Methods are given to summarize the mean, amplitude and acrophase, to predict the mean annual outcome value, and to test the coefficients. |
2988 | crop | A device closing function which is able to crop graphics (e.g., PDF, PNG files) on Unix-like operating systems with the required underlying command-line tools installed. |
2989 | cropcircles | Images are cropped to a circle with a transparent background. The function takes a vector of images, either local or from a link, and circle crops the image. Paths to the cropped image are returned for plotting with 'ggplot2'. |
3053 | CSIndicators | Set of generalised tools for the flexible computation of climate related indicators defined by the user. Each method represents a specific mathematical approach which is combined with the possibility to select an arbitrary time period to define the indicator. This enables a wide range of possibilities to tailor the most suitable indicator for each particular climate service application (agriculture, food security, energy, water management…). This package is intended for sub-seasonal, seasonal and decadal climate predictions, but its methods are also applicable to other time-scales, provided the dimensional structure of the input is maintained. Additionally, the outputs of the functions in this package are compatible with 'CSTools'. This package was developed in the context of H2020 MED-GOLD (776467) and S2S4E (776787) projects. Lledó et al. (2019) <doi:10.1016/j.renene.2019.04.135>. |
3244 | Dasst | Provides methods for reading, displaying, processing and writing files originally arranged for the 'DSSAT-CSM' fixed width format. The 'DSSAT-CSM' cropping system model is described at J.W. Jones, G. Hoogenboomb, C.H. Porter, K.J. Boote, W.D. Batchelor, L.A. Hunt, P.W. Wilkens, U. Singh, A.J. Gijsman, J.T. Ritchie (2003) <doi:10.1016/S1161-0301(02)00107-7>. |
3910 | doolkit | Tools for exploring the topography of 3d triangle meshes. The functions were developed with dental surfaces in mind, but could be applied to any triangle mesh of class 'mesh3d'. More specifically, 'doolkit' allows to isolate the border of a mesh, or a subpart of the mesh using the polygon networks method; crop a mesh; compute basic descriptors (elevation, orientation, footprint area); compute slope, angularity and relief index (Ungar and Williamson (2000) <https://palaeo-electronica.org/2000_1/gorilla/issue1_00.htm>; Boyer (2008) <doi:10.1016/j.jhevol.2008.08.002>), inclination and occlusal relief index or gamma (Guy et al. (2013) <doi:10.1371/journal.pone.0066142>), OPC (Evans et al. (2007) <doi:10.1038/nature05433>), OPCR (Wilson et al. (2012) <doi:10.1038/nature10880>), DNE (Bunn et al. (2011) <doi:10.1002/ajpa.21489>; Pampush et al. (2016) <doi:10.1007/s10914-016-9326-0>), form factor (Horton (1932) <doi:10.1029/TR013i001p00350>), basin elongation (Schum (1956) <doi:10.1130/0016-7606(1956)67[597:EODSAS]2.0.CO;2>), lemniscate ratio (Chorley et al; (1957) <doi:10.2475/ajs.255.2.138>), enamel-dentine distance (Guy et al. (2015) <doi:10.1371/journal.pone.0138802>; Thiery et al. (2017) <doi:10.3389/fphys.2017.00524>), absolute crown strength (Schwartz et al. (2020) <doi:10.1098/rsbl.2019.0671>), relief rate (Thiery et al. (2019) <doi:10.1002/ajpa.23916>) and area-relative curvature; draw cumulative profiles of a topographic variable; and map a variable over a 3d triangle mesh. |
4723 | europepmc | An R Client for the Europe PubMed Central RESTful Web Service (see <https://europepmc.org/RestfulWebService> for more information). It gives access to both metadata on life science literature and open access full texts. Europe PMC indexes all PubMed content and other literature sources including Agricola, a bibliographic database of citations to the agricultural literature, or Biological Patents. In addition to bibliographic metadata, the client allows users to fetch citations and reference lists. Links between life-science literature and other EBI databases, including ENA, PDB or ChEMBL are also accessible. No registration or API key is required. See the vignettes for usage examples. |
4957 | FAO56 | Calculation of Evapotranspiration by FAO Penman-Monteith equation based on Allen, R. G., Pereira, L. S., Raes, D., Smith, M. (1998, ISBN:92-5-104219-5) "Crop evapotranspiration - Guidelines for computing crop water requirements - FAO Irrigation and drainage paper 56". |
5180 | 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. |
5347 | fluoSurv | Use spectrophotometry measurements performed on insects as a way to infer pathogens virulence. Insect movements cause fluctuations in fluorescence signal, and functions are provided to estimate when the insect has died as the moment when variance in autofluorescence signal drops to zero. The package provides functions to obtain this estimate together with functions to import spectrophotometry data from a Biotek microplate reader. Details of the method are given in Parthuisot et al. (2018) <doi:10.1101/297929>. |
5399 | forceR | For cleaning and analyses of animal closing force measurements. 'forceR' was initially written and optimized to deal with insect bite force measurements, but can be used for any time series. Includes a full workflow to load, plot and crop data, correct amplifier and baseline drifts, identify individual peak shapes (bites), rescale (normalize) peak curves, and find best polynomial fits to describe and analyze force curve shapes. |
5546 | fruclimadapt | Climate is a critical component limiting growing range of plant species, which also determines cultivar adaptation to a region. The evaluation of climate influence on fruit production is critical for decision-making in the design stage of orchards and vineyards and in the evaluation of the potential consequences of future climate. Bio- climatic indices and plant phenology are commonly used to describe the suitability of climate for growing quality fruit and to provide temporal and spatial information about regarding ongoing and future changes. 'fruclimadapt' streamlines the assessment of climate adaptation and the identification of potential risks for grapevines and fruit trees. Procedures in the package allow to i) downscale daily meteorological variables to hourly values (Forster et al (2016) <doi:10.5194/gmd-9-2315-2016>), ii) estimate chilling and forcing heat accumulation (Miranda et al (2019) <https://ec.europa.eu/eip/agriculture/sites/agri-eip/files/fg30_mp5_phenology_critical_temperatures.pdf>), iii) estimate plant phenology (Schwartz (2012) <doi:10.1007/978-94-007-6925-0>), iv) calculate bioclimatic indices to evaluate fruit tree and grapevine adaptation (e.g. Badr et al (2017) <doi:10.3354/cr01532>), v) estimate the incidence of weather-related disorders in fruits (e.g. Snyder and de Melo-Abreu (2005, ISBN:92-5-105328-6) and vi) estimate plant water requirements (Allen et al (1998, ISBN:92-5-104219-5)). |
5801 | gdalcubes | Processing collections of Earth observation images as on-demand multispectral, multitemporal raster data cubes. Users define cubes by spatiotemporal extent, resolution, and spatial reference system and let 'gdalcubes' automatically apply cropping, reprojection, and resampling using the 'Geospatial Data Abstraction Library' ('GDAL'). Implemented functions on data cubes include reduction over space and time, applying arithmetic expressions on pixel band values, moving window aggregates over time, filtering by space, time, bands, and predicates on pixel values, exporting data cubes as 'netCDF' or 'GeoTIFF' files, plotting, and extraction from spatial and or spatiotemporal features. All computational parts are implemented in C++, linking to the 'GDAL', 'netCDF', 'CURL', and 'SQLite' libraries. See Appel and Pebesma (2019) <doi:10.3390/data4030092> for further details. |
5845 | gen5helper | A collection of functions for processing 'Gen5' 2.06 exported data. 'Gen5' is an essential data analysis software for BioTek plate readers <https://www.biotek.com/products/software-robotics-software/gen5-microplate-reader-and-imager-software/>. This package contains functions for data cleaning, modeling and plotting using exported data from 'Gen5' version 2.06. It exports technically correct data defined in (Edwin de Jonge and Mark van der Loo (2013) <https://cran.r-project.org/doc/contrib/de_Jonge+van_der_Loo-Introduction_to_data_cleaning_with_R.pdf>) for customized analysis. It contains Boltzmann fitting for general kinetic analysis. See <https://www.github.com/yanxianUCSB/gen5helper> for more information, documentation and examples. |
5884 | geneticae | Data from multi environment agronomic trials, which are often carried out by plant breeders, can be analyzed with the tools offered by this package such as the Additive Main effects and Multiplicative Interaction model or 'AMMI' ('Gauch' 1992, ISBN:9780444892409) and the Site Regression model or 'SREG' ('Cornelius' 1996, <doi:10.1201/9780367802226>). Since these methods present a poor performance under the presence of outliers and missing values, this package includes robust versions of the 'AMMI' model ('Rodrigues' 2016, <doi:10.1093/bioinformatics/btv533>), and also imputation techniques specifically developed for this kind of data ('Arciniegas-Alarcón' 2014, <doi:10.2478/bile-2014-0006>). |
5946 | GeoFIS | Methods for processing spatial data for decision-making. This package is an R implementation of methods provided by the open source software GeoFIS <https://www.geofis.org> (Leroux et al. 2018) <doi:10.3390/agriculture8060073>. The main functionalities are the management zone delineation (Pedroso et al. 2010) <doi:10.1016/j.compag.2009.10.007> and data aggregation (Mora-Herrera et al. 2020) <doi:10.1016/j.compag.2020.105624>. |
6423 | gnm | Functions to specify and fit generalized nonlinear models, including models with multiplicative interaction terms such as the UNIDIFF model from sociology and the AMMI model from crop science, and many others. Over-parameterized representations of models are used throughout; functions are provided for inference on estimable parameter combinations, as well as standard methods for diagnostics etc. |
6745 | gvcR | Functionalities to compute model based genetic components i.e. genotypic variance, phenotypic variance and heritability for given traits of different genotypes from replicated data using methodology explained by Burton, G. W. & Devane, E. H. (1953) (<doi:10.2134/agronj1953.00021962004500100005x>) and Allard, R.W. (2010, ISBN:8126524154). |
7420 | IIProductionUnknown | The Importance Index (I.I.) can determine the loss and solution sources for a system in certain knowledge areas (e.g., agronomy), when production (e.g., fruits) is known (Demolin-Leite, 2021). Events (e.g., agricultural pest) can have different magnitudes (numerical measurements), frequencies, and distributions (aggregate, random, or regular) of event occurrence, and I.I. bases in this triplet (Demolin-Leite, 2021) <https://cjascience.com/index.php/CJAS/article/view/1009/1319>. Usually, the higher the magnitude and frequency of aggregated distribution, the greater the problem or the solution (e.g., natural enemies versus pests) for the system (Demolin-Leite, 2021). However, the final production of the system is not always known or is difficult to determine (e.g., degraded area recovery). A derivation of the I.I. is the percentage of Importance Index-Production Unknown (% I.I.-PU) that can detect the loss or solution sources, when production is unknown for the system (Demolin-Leite, 2024) <DOI:10.1590/1519-6984.253218>. |
8088 | kgc | Aids in identifying the Koeppen-Geiger (KG) climatic zone for a given location. The Koeppen-Geiger climate zones were first published in 1884, as a system to classify regions of the earth by their relative heat and humidity through the year, for the benefit of human health, plant and agriculture and other human activity [1]. This climate zone classification system, applicable to all of the earths surface, has continued to be developed by scientists up to the present day. Recently one of use (FZ) has published updated, higher accuracy KG climate zone definitions [2]. In this package we use these updated high-resolution maps as the data source [3]. We provide functions that return the KG climate zone for a given longitude and lattitude, or for a given United States zip code. In addition the CZUncertainty() function will check climate zones nearby to check if the given location is near a climate zone boundary. In addition an interactive shiny app is provided to define the KG climate zone for a given longitude and lattitude, or United States zip code. Digital data, as well as animated maps, showing the shift of the climate zones are provided on the following website <http://koeppen-geiger.vu-wien.ac.at>. This work was supported by the DOE-EERE SunShot award DE-EE-0007140. [1] W. Koeppen, (2011) <doi:10.1127/0941-2948/2011/105>. [2] F. Rubel and M. Kottek, (2010) <doi:10.1127/0941-2948/2010/0430>. [3] F. Rubel, K. Brugger, K. Haslinger, and I. Auer, (2016) <doi:10.1127/metz/2016/0816>. |
8437 | lemna | The reference implementation of model equations and default parameters for the toxicokinetic-toxicodynamic (TKTD) model of the Lemna (duckweed) aquatic plant. Lemna is a standard test macrophyte used in ecotox effect studies. The model was described and published by the SETAC Europe Interest Group Effect Modeling. It is a refined description of the Lemna TKTD model published by Schmitt et al. (2013) <doi:10.1016/j.ecolmodel.2013.01.017>. |
8855 | lue | Contains LUE_BIOMASS(),LUE_BIOMASS_VPD(), LUE_YIELD() and LUE_YIELD_VPD() to estimate aboveground biomass and crop yield firstly by calculating the Absorbed Photosynthetically Active Radiation (APAR) and secondly the actual values of light use efficiency with and without vapour presure deficit Shi et al.(2007) <doi:10.2134/agronj2006.0260>. |
8912 | magick | Bindings to 'ImageMagick': the most comprehensive open-source image processing library available. Supports many common formats (png, jpeg, tiff, pdf, etc) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All operations are vectorized via the Magick++ STL meaning they operate either on a single frame or a series of frames for working with layers, collages, or animation. In RStudio images are automatically previewed when printed to the console, resulting in an interactive editing environment. The latest version of the package includes a native graphics device for creating in-memory graphics or drawing onto images using pixel coordinates. |
9393 | metan | Performs stability analysis of multi-environment trial data using parametric and non-parametric methods. Parametric methods includes Additive Main Effects and Multiplicative Interaction (AMMI) analysis by Gauch (2013) <doi:10.2135/cropsci2013.04.0241>, Ecovalence by Wricke (1965), Genotype plus Genotype-Environment (GGE) biplot analysis by Yan & Kang (2003) <doi:10.1201/9781420040371>, geometric adaptability index by Mohammadi & Amri (2008) <doi:10.1007/s10681-007-9600-6>, joint regression analysis by Eberhart & Russel (1966) <doi:10.2135/cropsci1966.0011183X000600010011x>, genotypic confidence index by Annicchiarico (1992), Murakami & Cruz's (2004) method, power law residuals (POLAR) statistics by Doring et al. (2015) <doi:10.1016/j.fcr.2015.08.005>, scale-adjusted coefficient of variation by Doring & Reckling (2018) <doi:10.1016/j.eja.2018.06.007>, stability variance by Shukla (1972) <doi:10.1038/hdy.1972.87>, weighted average of absolute scores by Olivoto et al. (2019a) <doi:10.2134/agronj2019.03.0220>, and multi-trait stability index by Olivoto et al. (2019b) <doi:10.2134/agronj2019.03.0221>. Non-parametric methods includes superiority index by Lin & Binns (1988) <doi:10.4141/cjps88-018>, nonparametric measures of phenotypic stability by Huehn (1990) <https://link.springer.com/article/10.1007/BF00024241>, TOP third statistic by Fox et al. (1990) <doi:10.1007/BF00040364>. Functions for computing biometrical analysis such as path analysis, canonical correlation, partial correlation, clustering analysis, and tools for inspecting, manipulating, summarizing and plotting typical multi-environment trial data are also provided. |
9435 | MeTo | Meteorological Tools following the FAO56 irrigation paper of Allen et al. (1998) [1]. Functions for calculating: reference evapotranspiration (ETref), extraterrestrial radiation (Ra), net radiation (Rn), saturation vapor pressure (satVP), global radiation (Rs), soil heat flux (G), daylight hours, and more. [1] Allen, R. G., Pereira, L. S., Raes, D., & Smith, M. (1998). Crop evapotranspiration-Guidelines for computing crop water requirements-FAO Irrigation and drainage paper 56. FAO, Rome, 300(9). |
9541 | microplot | The microplot function writes a set of R graphics files to be used as microplots (sparklines) in tables in either 'LaTeX', 'HTML', 'Word', or 'Excel' files. For 'LaTeX', we provide methods for the Hmisc::latex() generic function to construct 'latex' tabular environments which include the graphs. These can be used directly with the operating system 'pdflatex' or 'latex' command, or by using one of 'Sweave', 'knitr', 'rmarkdown', or 'Emacs org-mode' as an intermediary. For 'MS Word', the msWord() function uses the 'flextable' package to construct 'Word' tables which include the graphs. There are several distinct approaches for constructing HTML files. The simplest is to use the msWord() function with argument filetype="html". Alternatively, use either 'Emacs org-mode' or the htmlTable::htmlTable() function to construct an 'HTML' file containing tables which include the graphs. See the documentation for our as.htmlimg() function. For 'Excel' use on 'Windows', the file examples/irisExcel.xls includes 'VBA' code which brings the individual panels into individual cells in the spreadsheet. Examples in the examples and demo subdirectories are shown with 'lattice' graphics, 'ggplot2' graphics, and 'base' graphics. Examples for 'LaTeX' include 'Sweave' (both 'LaTeX'-style and 'Noweb'-style), 'knitr', 'emacs org-mode', and 'rmarkdown' input files and their 'pdf' output files. Examples for 'HTML' include 'org-mode' and 'Rmd' input files and their webarchive 'HTML' output files. In addition, the as.orgtable() function can display a data.frame in an 'org-mode' document. The examples for 'MS Word' (with either filetype="docx" or filetype="html") work with all operating systems. The package does not require the installation of 'LaTeX' or 'MS Word' to be able to write '.tex' or '.docx' files. |
10643 | NiLeDAM | Th-U-Pb electron microprobe age dating of monazite, as originally described in <doi:10.1016/0009-2541(96)00024-1>. |
10936 | OBIC | The Open Bodem Index (OBI) is a method to evaluate the quality of soils of agricultural fields in The Netherlands and the sustainability of the current agricultural practices. The OBI score is based on four main criteria: chemical, physical, biological and management, which consist of more than 21 indicators. By providing results of a soil analysis and management info the 'OBIC' package can be use to calculate he scores, indicators and derivatives that are used by the OBI. More information about the Open Bodem Index can be found at <https://www.openbodemindex.nl/>. |
11535 | PBIBD | The PBIB designs are important type of incomplete block designs having wide area of their applications for example in agricultural experiments, in plant breeding, in sample surveys etc. This package constructs various series of PBIB designs and assists in checking all the necessary conditions of PBIB designs and the association scheme on which these designs are based on. It also assists in calculating the efficiencies of PBIB designs with any number of associate classes. The package also constructs Youden-m square designs which are Row-Column designs for the two-way elimination of heterogeneity. The incomplete columns of these Youden-m square designs constitute PBIB designs. With the present functionality, the package will be of immense importance for the researchers as it will help them to construct PBIB designs, to check if their PBIB designs and association scheme satisfy various necessary conditions for the existence, to calculate the efficiencies of PBIB designs based on any association scheme and to construct Youden-m square designs for the two-way elimination of heterogeneity. R. C. Bose and K. R. Nair (1939) <http://www.jstor.org/stable/40383923>. |
12052 | pmetar | Allows to download current and historical METAR weather reports extract and parse basic parameters and present main weather information. Current reports are downloaded from Aviation Weather Center <https://www.aviationweather.gov/metar> and historical reports from Iowa Environmental Mesonet web page of Iowa State University ASOS-AWOS-METAR <http://mesonet.agron.iastate.edu/AWOS/>. |
12191 | PopVar | The main attribute of 'PopVar' is the prediction of genetic variance in bi-parental populations, from which the package derives its name. 'PopVar' contains a set of functions that use phenotypic and genotypic data from a set of candidate parents to 1) predict the mean, genetic variance, and superior progeny value of all, or a defined set of pairwise bi-parental crosses, and 2) perform cross-validation to estimate genome-wide prediction accuracy of multiple statistical models. More details are available in Mohammadi, Tiede, and Smith (2015, <doi:10.2135/cropsci2015.01.0030>). A dataset 'think_barley.rda' is included for reference and examples. |
12807 | quadcleanR | A tool that can be customized to aid in the clean up of ecological data collected using quadrats and can crop quadrats to ensure comparability between quadrats collected under different methodologies. |
13842 | RGISTools | Downloading, customizing, and processing time series of satellite images for a region of interest. 'RGISTools' functions allow a unified access to multispectral images from Landsat, MODIS and Sentinel repositories. 'RGISTools' also offers capabilities for customizing satellite images, such as tile mosaicking, image cropping and new variables computation. Finally, 'RGISTools' covers the processing, including cloud masking, compositing and gap-filling/smoothing time series of images (Militino et al., 2018 <doi:10.3390/rs10030398> and Militino et al., 2019 <doi:10.1109/TGRS.2019.2904193>). |
14823 | saemix | The 'saemix' package implements the Stochastic Approximation EM algorithm for parameter estimation in (non)linear mixed effects models. The SAEM algorithm (i) computes the maximum likelihood estimator of the population parameters, without any approximation of the model (linearisation, quadrature approximation,...), using the Stochastic Approximation Expectation Maximization (SAEM) algorithm, (ii) provides standard errors for the maximum likelihood estimator (iii) estimates the conditional modes, the conditional means and the conditional standard deviations of the individual parameters, using the Hastings-Metropolis algorithm (see Comets et al. (2017) <doi:10.18637/jss.v080.i03>). Many applications of SAEM in agronomy, animal breeding and PKPD analysis have been published by members of the Monolix group. The full PDF documentation for the package including references about the algorithm and examples can be downloaded on the github of the IAME research institute for 'saemix': <https://github.com/iame-researchCenter/saemix/blob/7638e1b09ccb01cdff173068e01c266e906f76eb/docsaem.pdf>. |
14919 | satellite | Herein, we provide a broad variety of functions which are useful for handling, manipulating, and visualizing satellite-based remote sensing data. These operations range from mere data import and layer handling (eg subsetting), over Raster* typical data wrangling (eg crop, extend), to more sophisticated (pre-)processing tasks typically applied to satellite imagery (eg atmospheric and topographic correction). This functionality is complemented by a full access to the satellite layers' metadata at any stage and the documentation of performed actions in a separate log file. Currently available sensors include Landsat 4-5 (TM), 7 (ETM+), and 8 (OLI/TIRS Combined), and additional compatibility is ensured for the Landsat Global Land Survey data set. |
15090 | SDAR | A fast, consistent tool for plotting and facilitating the analysis of stratigraphic and sedimentological data. Taking advantage of the flexible plotting tools available in R, 'SDAR' uses stratigraphic and sedimentological data to produce detailed graphic logs for outcrop sections and borehole logs. These logs can include multiple features (e.g., bed thickness, lithology, samples, sedimentary structures, colors, fossil content, bioturbation index, gamma ray logs) (Johnson, 1992, <ISSN 0037-0738>). |
16164 | spectralR | Tools for obtaining, processing, and visualizing spectral reflectance data for the user-defined land or water surface classes for visual exploring in which wavelength the classes differ. Input should be a shapefile with polygons of surface classes (it might be different habitat types, crops, vegetation, etc.). The Sentinel-2 L2A satellite mission optical bands pixel data are obtained through the Google Earth Engine service (<https://earthengine.google.com/>) and used as a source of spectral data. |
16291 | sprtt | The seq_ttest() function is the implementation of Abraham Wald’s (1947) <doi:10.2134/agronj1947.00021962003900070011x> Sequential Probability Ratio Test (SPRT) for the test of a normal mean (difference) with unknown variance in R (R Core Team, 2018). It performs sequential t tests developed by Rushton (1950) <doi:10.2307/2332385>, Rushton (1952) <doi:10.2307/2334026> and Hajnal (1961) <doi:10.2307/2333131>, based on the SPRT. Specifically, seq_ttest() performs one-sample, two-sample, and paired t tests for testing one- and two-sided hypotheses. The test is to be applied to the data during the sampling process, ideally after each observation. At any stage, it will return a decision to either continue sampling or terminate and accept one of the specified hypotheses. For more information on the SPRT t test, see Schnuerch & Erdfelder (2019) <doi:10.1037/met0000234>. |
16396 | stability | Functionalities to perform Stability Analysis of Genotype by Environment Interaction (GEI) to identify superior and stable genotypes under diverse environments. It performs Eberhart & Russel's ANOVA (1966) (<doi:10.2135/cropsci1966.0011183X000600010011x>), Finlay and Wilkinson (1963) Joint Linear Regression (<doi:10.1071/AR9630742>), Wricke (1962, 1964) Ecovalence, Shukla's stability variance parameter (1972) (<doi:10.1038/hdy.1972.87>) and Kang's (1991) (<doi:10.2134/agronj1991.00021962008300010037x>) simultaneous selection for high yielding and stable parameter. |
17424 | toolStability | Tools to calculate stability indices with parametric, non-parametric and probabilistic approaches. The basic data format requirement for 'toolStability' is a data frame with 3 columns including numeric trait values, genotype,and environmental labels. Output format of each function is the dataframe with chosen stability index for each genotype. Function "table_stability" offers the summary table of all stability indices in this package. Sample dataset in this package is from: Casadebaig P, Zheng B, Chapman S et al. (2016) <doi: 10.1371/journal.pone.0146385>. Indices used in this package are from: Döring TF, Reckling M (2018) <doi: 10.1016/j.eja.2018.06.007>. Eberhart SA, Russell WA (1966) <doi: 10.2135/cropsci1966.0011183X000600010011x>. Eskridge KM (1990) <doi: 10.2135/cropsci1990.0011183X003000020025x>. Finlay KW, Wilkinson GN (1963) <doi: 10.1071/AR9630742>. Hanson WD (1970) Genotypic stability. <doi: 10.1007/BF00285245>. Lin CS, Binns MR (1988) <https://cdnsciencepub.com/doi/abs/10.4141/cjps88-018>. Nassar R, Hühn M (1987). Pinthus MJ (1973) <doi: 10.1007/BF00021563>. Römer T (1917). Shukla GK (1972). Wricke G (1962). |
18257 | warabandi | It generates the roster of turn for an outlet which is flowing (water) 24X7 or 168 hours towards the area under command or agricutural area (to be irrigated). The area under command is differentially owned by different individual farmers. The Outlet runs for free of cost to irrigate the area under command 24X7. So, flow time of the outlet has to be divided based on an area owned by an individual farmer and the location of his land or farm. This roster is known as 'warabandi' and its generation in agriculture practices is a very tedious task. Calculations of time in microseconds are more error-prone, especially whenever it is performed by hands. That division of flow time for an individual farmer can be calculated by 'warabandi'. However, it generates a full publishable report for an outlet and all the farmers who have farms subjected to be irrigated. It reduces error risk and makes a more reproducible roster. For more details about warabandi system you can found elsewhere in Bandaragoda DJ(1995) <https://publications.iwmi.org/pdf/H_17571i.pdf>. |
18311 | weaana | Functions are collected to analyse weather data for agriculture purposes including to read weather records in multiple formats, calculate extreme climate index. |
18705 | zoomGroupStats | Provides utilities for processing and analyzing the files that are exported from a recorded 'Zoom' Meeting. This includes analyzing data captured through video cameras and microphones, the text-based chat, and meta-data. You can analyze aspects of the conversation among meeting participants and their emotional expressions throughout the meeting. |
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.
word | freq | |
---|---|---|
function | function | 66 |
use | use | 65 |
data | data | 62 |
model | model | 59 |
packag | packag | 51 |
analysi | analysi | 35 |
https | https | 31 |
provid | provid | 30 |
agricultur | agricultur | 29 |
estim | estim | 29 |
base | base | 27 |
soil | soil | 26 |
also | also | 25 |
method | method | 23 |
statist | statist | 23 |
plant | plant | 22 |
genet | genet | 21 |
includ | includ | 20 |
calcul | calcul | 19 |
design | design | 18 |
tool | tool | 18 |
crop | crop | 18 |
inform | inform | 18 |
develop | develop | 18 |
perform | perform | 17 |
implement | implement | 16 |
experi | experi | 16 |
select | select | 16 |
see | see | 15 |
genom | genom | 15 |
obtain | obtain | 15 |
regress | regress | 15 |
variabl | variabl | 14 |
comput | comput | 14 |
simul | simul | 14 |
breed | breed | 14 |
differ | differ | 14 |
sever | sever | 13 |
plot | plot | 13 |
avail | avail | 13 |
mix | mix | 13 |
predict | predict | 13 |
test | test | 12 |
linear | linear | 12 |
algorithm | algorithm | 12 |
approach | approach | 12 |
map | map | 12 |
describ | describ | 12 |
analys | analys | 11 |
dataset | dataset | 11 |
support | support | 11 |
set | set | 11 |
evalu | evalu | 11 |
allow | allow | 11 |
one | one | 11 |
fit | fit | 11 |
download | download | 10 |
product | product | 10 |
field | field | 10 |
paramet | paramet | 10 |
applic | applic | 10 |
spatial | spatial | 10 |
trait | trait | 10 |
interfac | interfac | 10 |
exampl | exampl | 9 |
addit | addit | 9 |
contain | contain | 9 |
experiment | experiment | 9 |
nation | nation | 9 |
research | research | 9 |
ag5Tools
https://cran.r-project.org/package=ag5Tools
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.
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.
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.
https://github.com/AgRoMeteorologiaINTA/agromet
Agrometerology
https://github.com/INTA-Suelos/SISINTAR
Allow access to the soil profile of INTA in Argentina. Also, allow handling of the soil data.
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.
Soil Science
packages to add:
Which package would you like to suggest? What features does it provide?
mvngGrAd
Package for moving grid adjustment in plant breeding field trials.
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
Plant Breeding and Genetics
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.
pestr: Interface to Download Data on Pests and Hosts from 'EPPO'
https://cran.r-project.org/package=pestr
(Delete those categories which do not apply)
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.
"CropDetectR" and "isqg" have both been archived.
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.
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.
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.
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
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.
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
General Agriculture,
Agronomic Trials
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
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.
https://cran.r-project.org/package=landsepi
Plant Pathology
AlphaSimR for quantitative genetics and breeding simulations
https://cran.r-project.org/package=AlphaSimR
General Agriculture,
Soil Science,
Agronomic Trials,
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
cropdatape provides peruvian agricultural production data from the Agriculture Minestry of Peru (MINAGRI).
https://cran.r-project.org/package=cropdatape
(Delete those categories which do not apply)
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.