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:
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')) |
- 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.
Last updated 9 months agofrom:a12ca89ce0. Checks:OK: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 28 2024 |
| R-4.5-linux | OK | Oct 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
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Diversity-Interactions (DI) Models | DImodels-package DImodels |
| Automated Diversity-Interactions Model Fitting | autoDI |
| The "Bell" Dataset | Bell |
| Compute contrasts for Diversity Interactions (DI) models | contrasts_DI |
| Describe DI models | describe_model |
| The "design_a" Dataset | design_a |
| The "design_b" Dataset | design_b |
| Diversity-Interactions Model Fitting | DI 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 Model | DI_compare |
| Data manipulation function | DI_data DI_data_ADD DI_data_E_AV DI_data_FG DI_data_fullpairwise DI_data_manipulation DI_data_prepare |
| Methods for 'DI' Objects | AIC.DI AICc.DI anova.DI BIC.DI BICc.DI fortify.DI logLik.DI |
| Internal Functions | add_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 object | extract extract.autoDI extract.DI |
| Predict Method for Diversity-Interactions (DI) Models | predict.DI |
| Comparing the Richness Model with DI Alternatives | richness_vs_DI |
| The Simulated "sim0" Dataset | sim0 |
| The "sim0_design" Dataset | sim0_design |
| The Simulated "sim1" Dataset | sim1 |
| The Simulated "sim2" Dataset | sim2 |
| The Simulated "sim3" Dataset | sim3 |
| The Simulated "sim4" Dataset | sim4 |
| The Simulated "sim5" Dataset | sim5 |
| The "Switzerland" Dataset | Switzerland |
| Compute Confidence Interval for Theta | theta_CI |
| Update DI function call | update_DI |