Files in dbystrova/GJAM_clust
Generalized Joint Attribute Modeling
.Rhistory
.gitattributes
.gitignore
Bauges/Bauges.zone.env.stk.CALIB.RData
Bauges/Bauges.zone.env.stk.PROJ.RData
Bauges/DB.XY.RData
Bauges/DOM.mat.sites.species.PA.RData
Bauges/DOM.mat.sites.species.abund.RData
Bauges/ENV_VARIABLES/EOBS_1970_2005/aspect.tif
Bauges/ENV_VARIABLES/EOBS_1970_2005/bio_10_0.tif
Bauges/ENV_VARIABLES/EOBS_1970_2005/bio_11_0.tif
Bauges/ENV_VARIABLES/EOBS_1970_2005/bio_12_0.tif
Bauges/ENV_VARIABLES/EOBS_1970_2005/bio_13_0.tif
Bauges/ENV_VARIABLES/EOBS_1970_2005/bio_14_0.tif
Bauges/ENV_VARIABLES/EOBS_1970_2005/bio_15_0.tif
Bauges/ENV_VARIABLES/EOBS_1970_2005/bio_16_0.tif
Bauges/ENV_VARIABLES/EOBS_1970_2005/bio_17_0.tif
Bauges/ENV_VARIABLES/EOBS_1970_2005/bio_18_0.tif
Bauges/ENV_VARIABLES/EOBS_1970_2005/bio_19_0.tif
Bauges/ENV_VARIABLES/EOBS_1970_2005/bio_1_0.tif
Bauges/ENV_VARIABLES/EOBS_1970_2005/bio_2_0.tif
Bauges/ENV_VARIABLES/EOBS_1970_2005/bio_3_0.tif
Bauges/ENV_VARIABLES/EOBS_1970_2005/bio_4_0.tif
Bauges/ENV_VARIABLES/EOBS_1970_2005/bio_5_0.tif
Bauges/ENV_VARIABLES/EOBS_1970_2005/bio_6_0.tif
Bauges/ENV_VARIABLES/EOBS_1970_2005/bio_7_0.tif
Bauges/ENV_VARIABLES/EOBS_1970_2005/bio_8_0.tif
Bauges/ENV_VARIABLES/EOBS_1970_2005/bio_9_0.tif
Bauges/ENV_VARIABLES/EOBS_1970_2005/dem.tif
Bauges/ENV_VARIABLES/EOBS_1970_2005/slope.tif
Bauges/ENV_VARIABLES/EOBS_1970_2005/tave_summer_0.tif
Bauges/ENV_VARIABLES/EOBS_1970_2005/tave_winter_0.tif
Bauges/MASK_100m.tif
Bauges/PFG.mat.traits.pfg.RData
Bauges/PFG.mat.traits.sp.RData
Bauges/PFG_Bauges_Description_2017.csv
Bauges/mat.traits.sp.RData
Bauges/traitsBauges.RData
Bauges_dataset/PA_data_clean.RData
Bauges_dataset/PA_data_clean_PCA.RData
Bauges_dataset/PCAtrain_ind.Rds
Bauges_dataset/TrainTest/TrainTestPCA/test.Rdata
Bauges_dataset/TrainTest/TrainTestPCA/train.Rdata
Bauges_dataset/TrainTest10/PA_data_10.Rdata
Bauges_dataset/TrainTest10/PA_test_10.Rdata
Bauges_dataset/TrainTest10/PA_train_10.Rdata
Bauges_dataset/TrainTest20/PA_data_20.Rdata
Bauges_dataset/TrainTest20/PA_test_20.Rdata
Bauges_dataset/TrainTest20/PA_train_20.Rdata
Bauges_dataset/TrainTest30/PA_data_30.Rdata
Bauges_dataset/TrainTest30/PA_test_30.Rdata
Bauges_dataset/TrainTest30/PA_train_30.Rdata
Bauges_dataset/TrainTest40/PA_data_40.Rdata
Bauges_dataset/TrainTest40/PA_test_40.Rdata
Bauges_dataset/TrainTest40/PA_train_40.Rdata
Bauges_dataset/TrainTest50/PA_data_50.Rdata
Bauges_dataset/TrainTest50/PA_test_50.Rdata
Bauges_dataset/TrainTest50/PA_train_50.Rdata
Bauges_dataset/TrainTestPCA10/PA_pcadata_10.Rdata
Bauges_dataset/TrainTestPCA10/PA_pcatest_10.Rdata
Bauges_dataset/TrainTestPCA10/PA_pcatrain_10.Rdata
Bauges_dataset/TrainTestPCA20/PA_pcadata_20.Rdata
Bauges_dataset/TrainTestPCA20/PA_pcatest_20.Rdata
Bauges_dataset/TrainTestPCA20/PA_pcatrain_20.Rdata
DESCRIPTION
IJulia_part/.ipynb_checkpoints/Cnk_matrix-checkpoint.ipynb
IJulia_part/.ipynb_checkpoints/Plots_GJAM-checkpoint.ipynb
IJulia_part/C_nk_matrix/Cnk_mat_112_025.Rdata
IJulia_part/C_nk_matrix/Cnk_mat_112_05.Rdata
IJulia_part/C_nk_matrix/Cnk_mat_112_08.Rdata
IJulia_part/C_nk_matrix/Cnk_mat_112_09.Rdata
IJulia_part/C_nk_matrix/Cnk_mat_112_H025.Rdata
IJulia_part/C_nk_matrix/Cnk_mat_112_H05.Rdata
IJulia_part/C_nk_matrix/Cnk_mat_112_H08.Rdata
IJulia_part/C_nk_matrix/Cnk_mat_112_H09.Rdata
IJulia_part/Cnk_matrix.ipynb
IJulia_part/DPM_prior/DPM_original_prior.Rdata
IJulia_part/DPM_prior/DPM_prior16_fixed.Rdata
IJulia_part/DPM_prior/DPM_prior56.Rdata
IJulia_part/DPM_prior/DPM_prior_16.Rdata
IJulia_part/Plots_GJAM.ipynb
IJulia_part/plots/Priors_k_16.png
MD5
NAMESPACE
PCA_analysis/.gitattributes
PCA_analysis/PCA_plot.R
PCA_analysis/alpha/aDP16.Rdata
PCA_analysis/alpha/aDP1_56.Rdata
PCA_analysis/alpha/aDP1_8.Rdata
PCA_analysis/create_dataset_PCA.R
PCA_analysis/different_r/df_DIC_10.Rdata
PCA_analysis/different_r/df_DIC_15.Rdata
PCA_analysis/different_r/df_DIC_20.Rdata
PCA_analysis/r5/Clusters/Clusters_all_1.Rdata
PCA_analysis/r5/Clusters/Clusters_all_1_old.Rdata
PCA_analysis/r5/Clusters/Clusters_all_2.Rdata
PCA_analysis/r5/Clusters/Clusters_all_2_old.Rdata
PCA_analysis/r5/Conv_beta_DP.Rdata
PCA_analysis/r5/DP1_analysis/Cluster_DP1_1.Rdata
PCA_analysis/r5/DP1_analysis/Cluster_DP1_2.Rdata
PCA_analysis/r5/DP1_analysis/Clustering_gre_diff_sp_DP1.Rdata
PCA_analysis/r5/DP1_analysis/Clustering_mcclust_diff_sp_DP1.Rdata
PCA_analysis/r5/DP1_analysis/Conv_beta_DP1.Rdata
PCA_analysis/r5/DP1_analysis/Conv_sigma_DP1.Rdata
PCA_analysis/r5/DP1_analysis/CorDP1_prediction.Rdata
PCA_analysis/r5/DP1_analysis/DP1_k_chains.Rdata
PCA_analysis/r5/DP1_analysis/DP1_pars.Rdata
PCA_analysis/r5/DP1_analysis/DP1_post_clust16.Rdata
PCA_analysis/r5/DP1_analysis/DP1_post_clust_56.Rdata
PCA_analysis/r5/DP1_analysis/DP1_prediction.Rdata
PCA_analysis/r5/DP1_analysis/Fin_tabDP1_r5.Rdata
PCA_analysis/r5/DP1_analysis/GRE_tab_DP1.Rdata
PCA_analysis/r5/DP1_analysis/GR_value_beta_DP1.Rdata
PCA_analysis/r5/DP1_analysis/GR_value_sigma_DP1.Rdata
PCA_analysis/r5/DP1_analysis/SW_tab_DP1.Rdata
PCA_analysis/r5/DP_analysis/Cluster_DP_1.Rdata
PCA_analysis/r5/DP_analysis/Cluster_DP_2.Rdata
PCA_analysis/r5/DP_analysis/Clustering_gre_diff_sp_DP.Rdata
PCA_analysis/r5/DP_analysis/Clustering_mcclust_diff_sp_DP.Rdata
PCA_analysis/r5/DP_analysis/Conv_beta_DP.Rdata
PCA_analysis/r5/DP_analysis/Conv_sigma_DP.Rdata
PCA_analysis/r5/DP_analysis/CorDP_prediction.Rdata
PCA_analysis/r5/DP_analysis/DP_k_chains.Rdata
PCA_analysis/r5/DP_analysis/DP_post_clust.Rdata
PCA_analysis/r5/DP_analysis/DP_prediction.Rdata
PCA_analysis/r5/DP_analysis/GRE_tab_DP.Rdata
PCA_analysis/r5/DP_analysis/GR_value_beta_DP.Rdata
PCA_analysis/r5/DP_analysis/GR_value_sigma_DP.Rdata
PCA_analysis/r5/DP_analysis/SW_tab_DP.Rdata
PCA_analysis/r5/DP_analysis/prob_clustDP.Rdata
PCA_analysis/r5/PY_analysis/Cluster_PY1_1.Rdata
PCA_analysis/r5/PY_analysis/Cluster_PY1_2.Rdata
PCA_analysis/r5/PY_analysis/Clustering__PY1_v1.Rdata
PCA_analysis/r5/PY_analysis/Clustering_gre_diff_sp_DP1_56.Rdata
PCA_analysis/r5/PY_analysis/Clustering_gre_diff_sp_PY1.Rdata
PCA_analysis/r5/PY_analysis/Clustering_gre_diff_sp_PY_56.Rdata
PCA_analysis/r5/PY_analysis/Clustering_mcclust_diff_sp_PY1.Rdata
PCA_analysis/r5/PY_analysis/Conv_beta_PY1.Rdata
PCA_analysis/r5/PY_analysis/Conv_sigma_PY1.Rdata
PCA_analysis/r5/PY_analysis/CorPY1_prediction.Rdata
PCA_analysis/r5/PY_analysis/Fin_tabPY_r5.Rdata
PCA_analysis/r5/PY_analysis/GRE_tab_PY1.Rdata
PCA_analysis/r5/PY_analysis/GR_value_beta_PY1.Rdata
PCA_analysis/r5/PY_analysis/GR_value_sigma_PY1.Rdata
PCA_analysis/r5/PY_analysis/PY1_k_chains.Rdata
PCA_analysis/r5/PY_analysis/PY1_prediction.Rdata
PCA_analysis/r5/PY_analysis/PY_pars.Rdata
PCA_analysis/r5/PY_analysis/PY_post_clust16.Rdata
PCA_analysis/r5/PY_analysis/SW_tab_PY1.Rdata
PCA_analysis/r5/PY_analysis/WP_56_DP1.Rdata
PCA_analysis/r5/PY_analysis/WP_56_PY.Rdata
PCA_analysis/r5/PY_analysis/aDP1_56.Rdata
PCA_analysis/r5/PY_analysis/df_trace_wp_56.Rdata
PCA_analysis/r5/PY_analysis/prob_clust_PY_56.Rdata
PCA_analysis/r_wp/wp_56/Clustering_gre_diff_sp_DP1_56.Rdata
PCA_analysis/r_wp/wp_56/Clustering_gre_diff_sp_PY_56.Rdata
PCA_analysis/r_wp/wp_56/DP1_post_clust_56.Rdata
PCA_analysis/r_wp/wp_56/WP_56_DP1.Rdata
PCA_analysis/r_wp/wp_56/WP_56_PY.Rdata
PCA_analysis/r_wp/wp_56/aDP1_56.Rdata
PCA_analysis/r_wp/wp_56/df_trace_wp_56.Rdata
PCA_analysis/r_wp/wp_56/prob_clust_PY_56.Rdata
PCA_analysis/r_wp/wp_8/DP1/DP1_clust_8.Rdata
PCA_analysis/r_wp/wp_8/DP1/DP1_pars_8.Rdata
PCA_analysis/r_wp/wp_8/DP1/DP1_post_clust_8.Rdata
PCA_analysis/r_wp/wp_8/DP1/DPM_prior_16.Rdata
PCA_analysis/r_wp/wp_8/DP1/DPM_prior_8.Rdata
PCA_analysis/r_wp/wp_8/PY/PY_clust_8.Rdata
PCA_analysis/r_wp/wp_8/PY/PY_k_chains8.Rdata
PCA_analysis/r_wp/wp_8/PY/PY_pars_8.Rdata
PCA_analysis/r_wp/wp_8/PY/PY_post_clust_8.Rdata
Plots/Beta_ESS.pdf
Plots/Correlation_matrix_DP.pdf
Plots/Correlation_matrix_DP1.pdf
Plots/Correlation_matrix_PY.pdf
Plots/DIC.pdf
Plots/DP1_Rhat_large_beta_rs.pdf
Plots/DP1_Rhat_large_sigma_rs.pdf
Plots/DP1_alpha_posterior.pdf
Plots/DP1_alpha_posterior_16.pdf
Plots/DP1_alpha_posterior_56.pdf
Plots/DP1_alpha_posterior_K16.pdf
Plots/DP1_alpha_posterior_K56.pdf
Plots/DP1_alpha_posterior_K8.pdf
Plots/DP1_alpha_prior_8.pdf
Plots/ESS.pdf
Plots/ESS_all.pdf
Plots/Effective_size_beta.pdf
Plots/Effective_size_sigma.pdf
Plots/Final_cluster_distances_AR.pdf
Plots/Final_cluster_distances_between_models.pdf
Plots/Final_cluster_distances_random.pdf
Plots/Kn_posterior_trace_56.pdf
Plots/PCA_plot.pdf
Plots/PY1_Rhat_large_beta_rs.pdf
Plots/PY1_Rhat_large_sigma_rs.pdf
Plots/Posterior_for_DP1_parameters.pdf
Plots/Prior_16_specification.pdf
Plots/Prior_all_16.pdf
Plots/Prior_all_56.pdf
Plots/Prior_all_8.pdf
Plots/Rhat_all.pdf
Plots/Rhat_beta.pdf
Plots/Rhat_sigma.pdf
Plots/Sigma_ESS.pdf
Plots/Trace_plot_partitions.pdf
Plots/Wrong_prior.pdf
R/BNP_functions.R
R/RcppExports.R
R/gjam.r
R/gjamCensorY.r
R/gjamDeZero.r
R/gjamHfunctions.R
R/gjamIIE.r
R/gjamIIEplot.r
R/gjamOrdination.R
R/gjamPlot.r
R/gjamPoints2Grid.R
R/gjamPredict.r
R/gjamPriorTemplate.r
R/gjamReZero.r
R/gjamSimData.r
R/gjamSpec2Trait.r
R/gjamTrimY.r
R/rlaptrans.r
README.md
Readme.Rmd
analysis/an_wp_56.R
analysis/analysis.R
analysis/analysis_2chains.R
analysis/analysis_DP.R
analysis/analysis_DP1.R
analysis/analysis_PY1.R
analysis/analysis_all_models.R
analysis/analysis_functions.R
analysis/analysis_internal.R
build/vignette.rds
data/Bauges_data.Rdata
fit_script.R
fit_script_simulation.R
inst/CITATION
inst/doc/gjamVignette.R
inst/doc/gjamVignette.Rmd
inst/doc/gjamVignette.html
man/gjam-package.Rd
man/gjam.Rd
man/gjamCensorY.Rd
man/gjamDeZero.Rd
man/gjamFillMissingTimes.Rd
man/gjamIIE.Rd
man/gjamIIEplot.Rd
man/gjamOrdination.Rd
man/gjamPlot.Rd
man/gjamPoints2Grid.Rd
man/gjamPredict.Rd
man/gjamPriorTemplate.Rd
man/gjamReZero.Rd
man/gjamSensitivity.Rd
man/gjamSimData.Rd
man/gjamSpec2Trait.Rd
man/gjamTrimY.Rd
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/cppFns.cpp
src/user_fns.cpp
vignettes/gjamVignette.Rmd
