2026-10-11T03:00:26Z https://api.figshare.com/v2/oai

oai:figshare.com:article/28921001 2026-09-28T11:36:16Z category_24217 item_type_3 month_year_09_2026

Data and codes for manuscript: Environmental and functional niches complement phylogeny Quan Pan (18764029) Community ecology (excl. invasive species ecology) intra specific plasticity <pre># scripts for Chapter 2<br><br># Environmental and functional niches complement phylogeny in explaining intraspecific <br># trait-environment response of woody plants<br><br>## =========================================================================#<br># 0. Data preprocess and analyzing ------------------------------------------<br>## =========================================================================#<br><br># ## 0.1 Trait environmental data preprocess ------------------------------------<br># source('./src/0_Preparing/Species_name.R')<br># source('./src/0_Preparing/Trait_data_cleaning.R') # ErrorRisk <= 2 <br># source('./src/0_Preparing/Trait_env_data_merge.R')<br># <br># ## 0.2 phylogenetic tree, trait plasticity and functional data calculation --------------<br># source('./src/0_Preparing/combined_trait_response_with_drivers.R')<br># source('./src/0_Preparing/Download_phylogenetic_tree.R')<br># source('./src/0_Preparing/spatial_distance.R')<br># <br># <br># ## 0.3 Trait environment response estimates --------------<br># source('./src/0_Estimate_trait_environment_response/ITER_estimation_with_all_data.R')<br># source('./src/0_Estimate_trait_environment_response/ITER_comparison_CHELSA_and_worldclimate.R')<br><br>## =========================================================================#<br># 1. Data overview ---------------------------------------------<br>## =========================================================================#<br><br>#* Global map of trait measurements<br>source('./src/1_global_map_and_trait_response/Global_map_data_preprocess.R')<br>#* Overview of trait responses<br>source('./src/1_global_map_and_trait_response/Trait_response_along_gradients.R')<br><br>## =========================================================================#<br># 2 (new). Phylogenetic constraints on ITERs --------------<br>## =========================================================================#<br>source('./src/2_phylgenetic_signal/phylosig_signals.R') # as a reference<br>source('./src/2_phylgenetic_signal/brm_signal_across_level.R') # run once<br>source('./src/2_phylgenetic_signal/brm_environment_traits.R') # run once</pre><p dir="ltr"># plot figures</p><p dir="ltr">source('./src/2_phylgenetic_signal/Figure_across_levels.R') # run once</p><p dir="ltr">source('./src/2_phylgenetic_signal/Figure_brm_lambda_and_tree_plot.R')</p><p dir="ltr">source('./src/2_phylgenetic_signal/Figure_of_all_lambda_in_sub_clades.R')</p><p><br></p><p>## =========================================================================#</p><p dir="ltr"># 3. The effects of potential drivers on ITERs -------------------</p><p>## =========================================================================#</p><p dir="ltr">#* the effects of trait plasticity and functional niche under phylogenetic controls. </p><p dir="ltr">source('./src/3_Combined_analysis/Figure_main_driver_effects_brm.R')</p><p dir="ltr">source('./src/3_Combined_analysis/Relative_contribution_brm.R')</p><p dir="ltr">source('./src/3_Combined_analysis/summary_brm.R')</p><p><br></p><p><br></p><p>## =========================================================================#</p><p dir="ltr"># 4. Supplementary: -------------------</p><p>## =========================================================================#</p><p dir="ltr">#* the effects of trait plasticity and functional niche under phylogenetic controls. </p><p dir="ltr"># check the rhat and show the trace plot</p><p dir="ltr">source('./src/4_supplementary/rhat_and_trace_plot.R')</p><p dir="ltr">source('./src/4_supplementary/morans_I.R')</p><p dir="ltr">source('./src/4_supplementary/correlation_of_matrix.R')</p><p dir="ltr">source('./src/4_supplementary/scatter_regression_for_brm_effects.R')</p><p dir="ltr"><br></p><p><br></p> 2025-05-02T15:31:33Z Dataset Dataset 10.6084/m9.figshare.28921001.v3 https://figshare.com/articles/dataset/Data_and_codes_for_manuscript_Functional_niche_and_trait_plasticity_complement_phylogeny_in_explaining_the_variance_of_intraspecific_trait-environment_response_in_woody_plants/28921001 CC BY 4.0