Package: DImodels 1.3.2

Rafael de Andrade Moral

DImodels: Diversity-Interactions (DI) Models

The 'DImodels' package is suitable for analysing data from biodiversity and ecosystem function studies using the Diversity-Interactions (DI) modelling approach introduced by Kirwan et al. (2009) <doi:10.1890/08-1684.1>. Suitable data will contain proportions for each species and a community-level response variable, and may also include additional factors, such as blocks or treatments. The package can perform data manipulation tasks, such as computing pairwise interactions (the DI_data() function), can perform an automated model selection process (the autoDI() function) and has the flexibility to fit a wide range of user-defined DI models (the DI() function).

Authors:Rafael de Andrade Moral [aut, cre], John Connolly [aut], Rishabh Vishwakarma [ctb], Caroline Brophy [aut]

DImodels_1.3.2.tar.gz
DImodels_1.3.2.tar.gz(r-4.5-noble)DImodels_1.3.2.tar.gz(r-4.4-noble)
DImodels_1.3.2.tgz(r-4.4-emscripten)DImodels_1.3.2.tgz(r-4.3-emscripten)
DImodels.pdf |DImodels.html
DImodels/json (API)

# Install 'DImodels' in R:
install.packages('DImodels', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • Bell - The "Bell" Dataset
  • Switzerland - The "Switzerland" Dataset
  • design_a - The "design_a" Dataset
  • design_b - The "design_b" Dataset
  • sim0 - The Simulated "sim0" Dataset
  • sim0_design - The "sim0_design" Dataset
  • sim1 - The Simulated "sim1" Dataset
  • sim2 - The Simulated "sim2" Dataset
  • sim3 - The Simulated "sim3" Dataset
  • sim4 - The Simulated "sim4" Dataset
  • sim5 - The Simulated "sim5" Dataset

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

4.67 score 2 packages 52 scripts 310 downloads 15 exports 37 dependencies

Last updated 8 months agofrom:a12ca89ce0. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 28 2024
R-4.5-linuxOKOct 28 2024

Exports:autoDIcontrasts_DIdescribe_modelDIDI_compareDI_dataDI_data_ADDDI_data_E_AVDI_data_FGDI_data_fullpairwiseDI_data_prepareextractrichness_vs_DItheta_CIupdate_DI

Dependencies:clicodetoolscolorspacefansifarverggplot2gluegtablehnpisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmultcompmunsellmvtnormnlmepillarpkgconfigR6RColorBrewerrlangrootSolvesandwichscalessurvivalTH.datatibbleutf8vctrsviridisLitewithrzoo

DImodels

Rendered fromDImodels.Rmdusingknitr::rmarkdownon Oct 28 2024.

Last update: 2024-01-25
Started: 2023-05-22

Readme and manuals

Help Manual

Help pageTopics
Diversity-Interactions (DI) ModelsDImodels-package DImodels
Automated Diversity-Interactions Model FittingautoDI
The "Bell" DatasetBell
Compute contrasts for Diversity Interactions (DI) modelscontrasts_DI
Describe DI modelsdescribe_model
The "design_a" Datasetdesign_a
The "design_b" Datasetdesign_b
Diversity-Interactions Model FittingDI DI_ADD DI_ADD_treat DI_AV DI_AV_treat DI_CUSTOM DI_E DI_E_treat DI_FG DI_FG_treat DI_FULL DI_FULL_treat DI_ID DI_ID_treat DI_STR DI_STR_treat DI_theta
Compare a Fitted Diversity-Interactions Model to the Reference ModelDI_compare
Data manipulation functionDI_data DI_data_ADD DI_data_E_AV DI_data_FG DI_data_fullpairwise DI_data_manipulation DI_data_prepare
Methods for 'DI' ObjectsAIC.DI AICc.DI anova.DI BIC.DI BICc.DI fortify.DI logLik.DI
Internal Functionsadd_name_check AIC2 AICc AICc.default AICcsel_autoDI AICsel_autoDI anovaDIglm anova_glmlist autoDI_step0 autoDI_step1 autoDI_step2 autoDI_step3 autoDI_step4 BIC2 BICc BICc.default BICcsel_autoDI BICsel_autoDI DI_matrix_check DI_reference get_community get_P_indices get_theta_cols namesub_autoDI namesub_DI proflik_theta reftest_autoDI test_autoDI theta_index_matching
Extract terms from a DI or autoDI model objectextract extract.autoDI extract.DI
Predict Method for Diversity-Interactions (DI) Modelspredict.DI
Comparing the Richness Model with DI Alternativesrichness_vs_DI
The Simulated "sim0" Datasetsim0
The "sim0_design" Datasetsim0_design
The Simulated "sim1" Datasetsim1
The Simulated "sim2" Datasetsim2
The Simulated "sim3" Datasetsim3
The Simulated "sim4" Datasetsim4
The Simulated "sim5" Datasetsim5
The "Switzerland" DatasetSwitzerland
Compute Confidence Interval for Thetatheta_CI
Update DI function callupdate_DI