Data and codes for manuscript: Environmental and functional niches complement phylogeny

# scripts for Chapter 2# Environmental and functional niches complement phylogeny in explaining intraspecific # trait-environment response of woody plants## =========================================================================## 0. Data preprocess and analyzing ------------------------------------------## =========================================================================### 0.1 Trait environmental data preprocess ------------------------------------source('./src/0_Preparing/Species_name.R')source('./src/0_Preparing/Trait_data_cleaning.R')source('./src/0_Preparing/Trait_env_data_merge.R')## 0.2 phylogenetic tree, trait plasticity and functional data calculation --------------source('./src/0_Preparing/Download_phylogenetic_tree.R')source('./src/0_Preparing/functional_niches.R')source('./src/0_Preparing/habitat_niches.R')source('./src/0_Preparing/spatial_distance.R')## 0.3 Trait environment response estimates --------------source('./src/0_Estimate_trait_environment_response/ITER_estimation_with_all_data.R')source('./src/0_Preparing/combined_trait_response_with_drivers.R')source('./src/0_Estimate_trait_environment_response/ITER_comparison_CHELSA_and_worldclimate.R')## =========================================================================## 1. Data overview ---------------------------------------------## =========================================================================##* Global map of trait measurementssource('./src/1_global_map_and_trait_response/Global_map_data_preprocess.R')source('./src/1_global_map_and_trait_response/Trait_response_along_gradients.R')source('./src/1_global_map_and_trait_response/Trait_response_at_Order_and_family_level.R')## =========================================================================## 2. Phylogenetic constraints on ITERs across lineage scales --------------## =========================================================================## source('./src/2_phylgenetic_signal_along_linages/Lambda_at_different_level.R') # run oncesource('./src/2_phylgenetic_signal_along_linages/Figure_brm_lambda_and_tree_plot.R')source('./src/2_phylgenetic_signal_along_linages/Figure_of_all_lambda_in_sub_clades.R')## =========================================================================## 3. The effects of potential drivers on ITERs -------------------## =========================================================================##* the effects of trait plasticity and functional niche under phylogenetic controls. source('./src/3_Combined_analysis/Figure_main_driver_effects_brm.R')source('./src/3_Combined_analysis/Relative_contribution_brm.R')source('./src/3_Combined_analysis/summary_brm.R')## =========================================================================## 4. Supplementary: -------------------## =========================================================================##* the effects of trait plasticity and functional niche under phylogenetic controls. # check the rhat and show the trace plotsource('./src/4_supplementary/rhat_and_trace_plot.R')source('./src/4_supplementary/morans_I.R')source('./src/4_supplementary/correlation_of_matrix.R')