Files in ghislainv/jSDM
Joint Species Distribution Models
.Rbuildignore
.github/.gitignore
.github/workflows/check-standard.yaml
.github/workflows/pkgdown.yaml
.github/workflows/test-coverage.yaml
.gitignore
DESCRIPTION
NAMESPACE
NEWS.md
R/RcppExports.R
R/get_enviro_cor.R
R/get_residual_cor.R
R/hidden.R
R/jSDM-package.R
R/jSDM_binomial_logit.R
R/jSDM_binomial_probit.R
R/jSDM_binomial_probit_long_format.R
R/jSDM_binomial_probit_sp_constrained.R
R/jSDM_gaussian.R
R/jSDM_poisson_log.R
R/logit.R
R/plot_associations.R
R/plot_residual_cor.R
R/predict.jSDM.R
R/zzz.R
README.Rmd
README.md
cleanup
codecov.yml
cran-comments.md
data/aravo.rda
data/birds.rda
data/eucalypts.rda
data/frogs.rda
data/fungi.rda
data/madagascar.rda
data/mites.rda
data/mosquitos.rda
logos/A_gran.png
logos/PhyloPic_Apiformes_Megachilidae.png
logos/bea_eater.svg
logos/beeeater.png
logos/jSDM.png
logos/jSDM_beeeater_color.png
logos/jSDM_beeeater_grey.png
logos/jSDM_wide.png
logos/logo_grey.png
logos/logos/logo-cirad.png
logos/make_hex.R
man/aravo.Rd
man/birds.Rd
man/eucalypts.Rd
man/figures/logo-cirad.svg
man/figures/logo.png
man/frogs.Rd
man/fungi.Rd
man/get_enviro_cor.Rd
man/get_residual_cor.Rd
man/inv_logit.Rd
man/jSDM-package.Rd
man/jSDM_binomial_logit.Rd
man/jSDM_binomial_probit.Rd
man/jSDM_binomial_probit_long_format.Rd
man/jSDM_binomial_probit_sp_constrained.Rd
man/jSDM_gaussian.Rd
man/jSDM_poisson_log.Rd
man/logit.Rd
man/madagascar.Rd
man/mites.Rd
man/mosquitos.Rd
man/plot_associations.Rd
man/plot_residual_cor.Rd
man/predict.jSDM.Rd
pkgdown/_pkgdown.yml
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/Rcpp_jSDM_binomial_logit.cpp
src/Rcpp_jSDM_binomial_logit_fixed_site.cpp
src/Rcpp_jSDM_binomial_logit_fixed_site_lv.cpp
src/Rcpp_jSDM_binomial_logit_lv.cpp
src/Rcpp_jSDM_binomial_logit_rand_site.cpp
src/Rcpp_jSDM_binomial_logit_rand_site_lv.cpp
src/Rcpp_jSDM_binomial_logit_traits.cpp
src/Rcpp_jSDM_binomial_logit_traits_fixed_site.cpp
src/Rcpp_jSDM_binomial_logit_traits_fixed_site_lv.cpp
src/Rcpp_jSDM_binomial_logit_traits_lv.cpp
src/Rcpp_jSDM_binomial_logit_traits_rand_site.cpp
src/Rcpp_jSDM_binomial_logit_traits_rand_site_lv.cpp
src/Rcpp_jSDM_binomial_probit.cpp
src/Rcpp_jSDM_binomial_probit_fixed_site.cpp
src/Rcpp_jSDM_binomial_probit_fixed_site_long_format.cpp
src/Rcpp_jSDM_binomial_probit_fixed_site_lv.cpp
src/Rcpp_jSDM_binomial_probit_fixed_site_lv_long_format.cpp
src/Rcpp_jSDM_binomial_probit_long_format.cpp
src/Rcpp_jSDM_binomial_probit_lv.cpp
src/Rcpp_jSDM_binomial_probit_lv_long_format.cpp
src/Rcpp_jSDM_binomial_probit_rand_site.cpp
src/Rcpp_jSDM_binomial_probit_rand_site_long_format.cpp
src/Rcpp_jSDM_binomial_probit_rand_site_lv.cpp
src/Rcpp_jSDM_binomial_probit_rand_site_lv_long_format.cpp
src/Rcpp_jSDM_binomial_probit_traits.cpp
src/Rcpp_jSDM_binomial_probit_traits_fixed_site.cpp
src/Rcpp_jSDM_binomial_probit_traits_fixed_site_long_format.cpp
src/Rcpp_jSDM_binomial_probit_traits_fixed_site_lv.cpp
src/Rcpp_jSDM_binomial_probit_traits_fixed_site_lv_long_format.cpp
src/Rcpp_jSDM_binomial_probit_traits_long_format.cpp
src/Rcpp_jSDM_binomial_probit_traits_lv.cpp
src/Rcpp_jSDM_binomial_probit_traits_lv_long_format.cpp
src/Rcpp_jSDM_binomial_probit_traits_rand_site.cpp
src/Rcpp_jSDM_binomial_probit_traits_rand_site_long_format.cpp
src/Rcpp_jSDM_binomial_probit_traits_rand_site_lv.cpp
src/Rcpp_jSDM_binomial_probit_traits_rand_site_lv_long_format.cpp
src/Rcpp_jSDM_gaussian.cpp
src/Rcpp_jSDM_gaussian_fixed_site.cpp
src/Rcpp_jSDM_gaussian_fixed_site_lv.cpp
src/Rcpp_jSDM_gaussian_lv.cpp
src/Rcpp_jSDM_gaussian_rand_site.cpp
src/Rcpp_jSDM_gaussian_rand_site_lv.cpp
src/Rcpp_jSDM_gaussian_traits.cpp
src/Rcpp_jSDM_gaussian_traits_fixed_site.cpp
src/Rcpp_jSDM_gaussian_traits_fixed_site_lv.cpp
src/Rcpp_jSDM_gaussian_traits_lv.cpp
src/Rcpp_jSDM_gaussian_traits_rand_site.cpp
src/Rcpp_jSDM_gaussian_traits_rand_site_lv.cpp
src/Rcpp_jSDM_poisson_log.cpp
src/Rcpp_jSDM_poisson_log_fixed_site.cpp
src/Rcpp_jSDM_poisson_log_fixed_site_lv.cpp
src/Rcpp_jSDM_poisson_log_lv.cpp
src/Rcpp_jSDM_poisson_log_rand_site.cpp
src/Rcpp_jSDM_poisson_log_rand_site_lv.cpp
src/Rcpp_jSDM_poisson_log_traits.cpp
src/Rcpp_jSDM_poisson_log_traits_fixed_site.cpp
src/Rcpp_jSDM_poisson_log_traits_fixed_site_lv.cpp
src/Rcpp_jSDM_poisson_log_traits_lv.cpp
src/Rcpp_jSDM_poisson_log_traits_rand_site.cpp
src/Rcpp_jSDM_poisson_log_traits_rand_site_lv.cpp
src/Rcpp_jSDM_useful.cpp
src/Rcpp_jSDM_useful.h
tests/testthat.R
tests/testthat/test-get_enviro_cor.R
tests/testthat/test-get_residual_cor.R
tests/testthat/test-hidden.R
tests/testthat/test-inv_logit.R
tests/testthat/test-jSDM_binomial_logit.R
tests/testthat/test-jSDM_binomial_probit.R
tests/testthat/test-jSDM_binomial_probit_long_format.R
tests/testthat/test-jSDM_binomial_probit_sp_constrained.R
tests/testthat/test-jSDM_gaussian.R
tests/testthat/test-jSDM_poisson_log.R
tests/testthat/test-logit.R
tests/testthat/test-predict.jSDM.R
vignettes/.gitignore
vignettes/Code_of_conduct.Rmd
vignettes/Contributing.Rmd
vignettes/Madagascar.Rmd
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vignettes/SDM_JSDM.Rmd
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vignettes/jSDM.Rmd
vignettes/jSDM_Hmsc.Rmd
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vignettes/jSDM_binomial_probit_sp_constrained_files/figure-html/plot-results-probit-ord-34.png
vignettes/jSDM_binomial_probit_sp_constrained_files/figure-html/plot-results-probit-ord-35.png
vignettes/jSDM_binomial_probit_sp_constrained_files/figure-html/plot-results-probit-ord-36.png
vignettes/jSDM_binomial_probit_sp_constrained_files/figure-html/plot-results-probit-ord-4.png
vignettes/jSDM_binomial_probit_sp_constrained_files/figure-html/plot-results-probit-ord-5.png
vignettes/jSDM_binomial_probit_sp_constrained_files/figure-html/plot-results-probit-ord-6.png
vignettes/jSDM_binomial_probit_sp_constrained_files/figure-html/plot-results-probit-ord-7.png
vignettes/jSDM_binomial_probit_sp_constrained_files/figure-html/plot-results-probit-ord-8.png
vignettes/jSDM_binomial_probit_sp_constrained_files/figure-html/plot-results-probit-ord-9.png
vignettes/jSDM_boral.Rmd
vignettes/jSDM_boral_files/figure-html/boral-simulation-plot-1.png
vignettes/jSDM_boral_files/figure-html/boral-simulation-plot-2.png
vignettes/jSDM_boral_files/figure-html/boral-simulation-plot-3.png
vignettes/jSDM_boral_files/figure-html/boral-simulation-plot-4.png
vignettes/jSDM_boral_files/figure-html/boral-simulation-plot-5.png
vignettes/jSDM_boral_files/figure-html/boral-simulation-plot-6.png
vignettes/jSDM_boral_files/figure-html/boral-simulation-plot-7.png
vignettes/jSDM_boral_files/figure-html/boral-simulation-plot-8.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-Eucalypts-1.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-Eucalypts-2.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-Eucalypts-3.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-Eucalypts-4.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-birds-1.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-birds-2.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-birds-3.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-birds-4.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-birds-5.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-birds-6.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-frogs-1.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-frogs-2.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-frogs-3.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-frogs-4.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-fungi-1.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-fungi-2.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-fungi-3.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-fungi-4.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-mites-1.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-mites-2.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-mites-3.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-mites-4.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-mosquitos-1.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-mosquitos-2.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-mosquitos-3.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-mosquitos-4.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-simulation-1.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-simulation-2.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-simulation-3.png
vignettes/jSDM_boral_files/figure-html/jSDM-boral-simulation-4.png
vignettes/jSDM_boral_files/figure-html/jSDM-simulation-plot-1.png
vignettes/jSDM_boral_files/figure-html/jSDM-simulation-plot-10.png
vignettes/jSDM_boral_files/figure-html/jSDM-simulation-plot-2.png
vignettes/jSDM_boral_files/figure-html/jSDM-simulation-plot-3.png
vignettes/jSDM_boral_files/figure-html/jSDM-simulation-plot-4.png
vignettes/jSDM_boral_files/figure-html/jSDM-simulation-plot-5.png
vignettes/jSDM_boral_files/figure-html/jSDM-simulation-plot-6.png
vignettes/jSDM_boral_files/figure-html/jSDM-simulation-plot-7.png
vignettes/jSDM_boral_files/figure-html/jSDM-simulation-plot-8.png
vignettes/jSDM_boral_files/figure-html/jSDM-simulation-plot-9.png
vignettes/jSDM_boral_files/jSDM-boral-comparison.rda
vignettes/jSDM_gaussian.Rmd
vignettes/jSDM_in_parallel.Rmd
vignettes/jSDM_in_parallel_files/figure-html/MCMC-convergence-randsite-lv-1.png
vignettes/jSDM_in_parallel_files/figure-html/est-probit-1.png
vignettes/jSDM_in_parallel_files/figure-html/est-probit-2.png
vignettes/jSDM_in_parallel_files/figure-html/est-probit-3.png
vignettes/jSDM_in_parallel_files/figure-html/est-probit-4.png
vignettes/jSDM_in_parallel_files/figure-html/est-probit-5.png
vignettes/jSDM_in_parallel_files/figure-html/est-probit-6.png
vignettes/jSDM_in_parallel_files/figure-html/est-probit-7.png
vignettes/jSDM_in_parallel_files/figure-html/est-probit-8.png
vignettes/jSDM_in_parallel_files/figure-html/est-probit-9.png
vignettes/jSDM_in_parallel_files/figure-html/obs-fitted-1.png
vignettes/jSDM_in_parallel_files/figure-html/obs-fitted-2.png
vignettes/jSDM_in_parallel_files/figure-html/obs-fitted-3.png
vignettes/jSDM_in_parallel_files/figure-html/obs-fitted-4.png
vignettes/jSDM_in_parallel_files/output.rda
vignettes/jSDM_poisson_log.Rmd
vignettes/jSDM_with_traits.Rmd
vignettes/proof.Rmd
