## Loadinga packages #************************************************************************************ library(nlme) library(bbmle) ## Loading data ##************************************************************************************* data <- read.csv("results_phylogenetic_metrics_compiled.csv", header = T, row.names = 1, sep = ",") head(data) ######################################## NRI ########################################### ######################################################################################## ## NRI REGIONS TOGETHER ##************************************************************************************* M1_NRI <- gls (NRI_ses ~ PC1.ATUAL, data = data, correlation = corExp (form = ~ Longitude + Latitude)) M2_NRI <- gls (NRI_ses ~ PC1.LGM, data = data, correlation = corExp (form = ~ Longitude + Latitude)) M3_NRI <- gls (NRI_ses ~ PC1.ALT, data = data, correlation = corExp (form = ~ Longitude + Latitude)) M4_NRI <- gls (NRI_ses ~ Region, data = data, correlation = corExp (form = ~ Longitude + Latitude)) M5_NRI <- gls (NRI_ses ~ 1, data = data, correlation = corExp (form = ~ Longitude + Latitude)) M6_NRI <- gls (NRI_ses ~ PC1.ATUAL + PC1.ALT, data = data, correlation = corExp (form = ~ Longitude + Latitude)) M7_NRI <- gls (NRI_ses ~ PC1.LGM + PC1.ALT, data = data, correlation = corExp (form = ~ Longitude + Latitude)) ## Model Selection ##********************************** AICc.NRI <- ICtab(M1_NRI, M2_NRI, M3_NRI, M4_NRI, M5_NRI, M6_NRI, M7_NRI, type = c("AICc"), base = TRUE, weights = TRUE, delta = TRUE, sort = TRUE, logLik = T, nobs= 14) AICc.NRI ## NRI INLAND SITES ##**************************************************************************************** M1_NRI_inland <- gls (NRI_pool_ses ~ PC1.ATUAL, data = data[1:7,], correlation = corExp (form = ~ Longitude + Latitude)) M2_NRI_inland <- gls (NRI_pool_ses ~ PC1.LGM, data = data[1:7,], correlation = corExp (form = ~ Longitude + Latitude)) M3_NRI_inland <- gls (NRI_pool_ses ~ PC1.ALT, data = data[1:7,], correlation = corExp (form = ~ Longitude + Latitude)) M4_NRI_inland <- gls (NRI_pool_ses ~ 1, data = data[1:7,], correlation = corExp (form = ~ Longitude + Latitude)) M5_NRI_inland <- gls (NRI_pool_ses ~ PC1.ATUAL + PC1.LGM, data = data[1:7,], correlation = corExp (form = ~ Longitude + Latitude)) M6_NRI_inland <- gls (NRI_pool_ses ~ PC1.ATUAL + PC1.ALT, data = data[1:7,], correlation = corExp (form = ~ Longitude + Latitude)) M7_NRI_inland <- gls (NRI_pool_ses ~ PC1.LGM + PC1.ALT, data = data[1:7,], correlation = corExp (form = ~ Longitude + Latitude)) ## Model selection ##********************************** AICc.NRI_inland <- ICtab(M1_NRI_inland, M2_NRI_inland, M3_NRI_inland, M4_NRI_inland, M5_NRI_inland, M6_NRI_inland, M7_NRI_inland, type = c("AICc"), base = TRUE, weights = TRUE, delta = TRUE, sort = TRUE, logLik = T, nobs= 7) AICc.NRI_inland ## NRI COASTAL SITES ##**************************************************************************************** M1_NRI_coastal <- gls (NRI_pool_ses ~ PC1.ATUAL, data = data[8:14,], correlation = corExp (form = ~ Longitude + Latitude)) M2_NRI_coastal <- gls (NRI_pool_ses ~ PC1.LGM, data = data[8:14,], correlation = corExp (form = ~ Longitude + Latitude)) M3_NRI_coastal <- gls (NRI_pool_ses ~ PC1.ALT, data = data[8:14,], correlation = corExp (form = ~ Longitude + Latitude)) M4_NRI_coastal <- gls (NRI_pool_ses ~ 1, data = data[8:14,], correlation = corExp (form = ~ Longitude + Latitude)) M5_NRI_coastal <- gls (NRI_pool_ses ~ PC1.ATUAL + PC1.LGM, data = data[8:14,], correlation = corExp (form = ~ Longitude + Latitude)) M6_NRI_coastal <- gls (NRI_pool_ses ~ PC1.ATUAL + PC1.ALT, data = data[8:14,], correlation = corExp (form = ~ Longitude + Latitude)) M7_NRI_coastal <- gls (NRI_pool_ses ~ PC1.LGM + PC1.ALT, data = data[8:14,], correlation = corExp (form = ~ Longitude + Latitude)) ## Model selection ##********************************** AICc.NRI_coastal <- ICtab(M1_NRI_coastal, M2_NRI_coastal, M3_NRI_coastal, M4_NRI_coastal, M5_NRI_coastal, M6_NRI_coastal, M7_NRI_coastal, type = c("AICc"), base = TRUE, weights = TRUE, delta = TRUE, sort = TRUE, logLik = T, nobs= 7) AICc.NRI_coastal ######################################## NTI ########################################### ######################################################################################## ## NTI REGIONS TOGETHER ##************************************************************************************** M1_NTI <- gls (NTI_ses ~ PC1.ATUAL, data = data, correlation = corExp (form = ~ Longitude + Latitude)) M2_NTI <- gls (NTI_ses ~ PC1.LGM, data = data, correlation = corExp (form = ~ Longitude + Latitude)) M3_NTI <- gls (NTI_ses ~ PC1.ALT, data = data, correlation = corExp (form = ~ Longitude + Latitude)) M4_NTI <- gls (NTI_ses ~ Region, data = data, correlation = corExp (form = ~ Longitude + Latitude)) M5_NTI <- gls (NTI_ses ~ 1, data = data, correlation = corExp (form = ~ Longitude + Latitude)) M6_NTI <- gls (NTI_ses ~ PC1.ATUAL + PC1.ALT, data = data, correlation = corExp (form = ~ Longitude + Latitude)) M7_NTI <- gls (NTI_ses ~ PC1.LGM + PC1.ALT, data = data, correlation = corExp (form = ~ Longitude + Latitude)) ## Model selection ##********************************** AICc.NTI <- ICtab(M1_NTI, M2_NTI, M3_NTI, M4_NTI, M5_NTI, M6_NTI, M7_NTI, type = c("AICc"), base = TRUE, weights = TRUE, delta = TRUE, sort = TRUE, logLik = T, nobs= 14) AICc.NTI ## NTI Inland ##****************************************************************************************** M1_NTI_inland <- gls (NTI_pool_ses ~ PC1.ATUAL, data = data[1:7,], correlation = corExp (form = ~ Longitude + Latitude)) M2_NTI_inland <- gls (NTI_pool_ses ~ PC1.LGM, data = data[1:7,], correlation = corExp (form = ~ Longitude + Latitude)) M3_NTI_inland <- gls (NTI_pool_ses ~ PC1.ALT, data = data[1:7,], correlation = corExp (form = ~ Longitude + Latitude)) M4_NTI_inland <- gls (NTI_pool_ses ~ 1, data = data[1:7,], correlation = corExp (form = ~ Longitude + Latitude)) M5_NTI_inland <- gls (NTI_pool_ses ~ PC1.ATUAL + PC1.LGM, data = data[1:7,], correlation = corExp (form = ~ Longitude + Latitude)) M6_NTI_inland <- gls (NTI_pool_ses ~ PC1.ATUAL + PC1.ALT, data = data[1:7,], correlation = corExp (form = ~ Longitude + Latitude)) M7_NTI_inland <- gls (NTI_pool_ses ~ PC1.LGM + PC1.ALT, data = data[1:7,], correlation = corExp (form = ~ Longitude + Latitude)) ## Selecionando o melhor modelo ##********************************** AICc.NTI_inland <- ICtab(M1_NTI_inland, M2_NTI_inland, M3_NTI_inland, M4_NTI_inland, M5_NTI_inland, M6_NTI_inland, M7_NTI_inland, type = c("AICc"), base = TRUE, weights = TRUE, delta = TRUE, sort = TRUE, logLik = T, nobs= 7) AICc.NTI_inland ## NTI Coastal ##************************************************************************************** M1_NTI_coastal <- gls (NTI_pool_ses ~ PC1.ATUAL, data = data[8:14,], correlation = corExp (form = ~ Longitude + Latitude)) M2_NTI_coastal <- gls (NTI_pool_ses ~ PC1.LGM, data = data[8:14,], correlation = corExp (form = ~ Longitude + Latitude)) M3_NTI_coastal <- gls (NTI_pool_ses ~ PC1.ALT, data = data[8:14,], correlation = corExp (form = ~ Longitude + Latitude)) M4_NTI_coastal <- gls (NTI_pool_ses ~ 1, data = data[8:14,], correlation = corExp (form = ~ Longitude + Latitude)) M5_NTI_coastal <- gls (NTI_pool_ses ~ PC1.ATUAL + PC1.LGM, data = data[8:14,], correlation = corExp (form = ~ Longitude + Latitude)) M6_NTI_coastal <- gls (NTI_pool_ses ~ PC1.ATUAL + PC1.ALT, data = data[8:14,], correlation = corExp (form = ~ Longitude + Latitude)) M7_NTI_coastal <- gls (NTI_pool_ses ~ PC1.LGM + PC1.ALT, data = data[8:14,], correlation = corExp (form = ~ Longitude + Latitude)) ## Model selection ##********************************** AICc.NTI_coastal <- ICtab(M1_NTI_coastal, M2_NTI_coastal, M3_NTI_coastal, M4_NTI_coastal, M5_NTI_coastal, M6_NTI_coastal, M7_NTI_coastal, type = c("AICc"), base = TRUE, weights = TRUE, delta = TRUE, sort = TRUE, logLik = T, nobs= 7) AICc.NTI_coastal