Updated R scripts

Reeg_et_al_2021/Scripts/(2) Final_figures_without_Fig3.R

@@ -403,3 +403,48 @@ dev.off()
 # This figure was generated within the BiTZ SA R-project (file "(2) Figures")
 #
 #####
+
+#####
+#
+# Statistical analyses of quasi extinction risk
+# using an ANOVA
+#
+#####
+
+extinction_risk$TZ<-factor(extinction_risk$TZ)
+extinction_risk$Cluster<-factor(extinction_risk$Cluster)
+
+# summary(extinction_risk)
+
+two.way <- aov(ext.prob ~ TZ + Cluster, data = extinction_risk)
+kruskal1 <- kruskal.test(ext.prob ~ TZ, data = extinction_risk[Cluster==1])
+kruskal2 <- kruskal.test(ext.prob ~ TZ, data = extinction_risk[Cluster==2])
+kruskal3 <- kruskal.test(ext.prob ~ TZ, data = extinction_risk[Cluster==3])
+kruskal4 <- kruskal.test(ext.prob ~ TZ, data = extinction_risk[Cluster==4])
+
+Cl1 <- extinction_risk[Cluster==1]
+pairwise.wilcox.test(Cl1$ext.prob, Cl1$TZ,
+                     p.adjust.method = "BH")
+
+one.way <- aov(ext.prob ~ TZ, data = extinction_risk[Cluster==1])
+
+# multiple linear regression
+model <- lm(ext.prob~TZ+Cluster,data=extinction_risk)
+summary(model)
+
+hist(rstandard(model))
+hist(residuals(model))
+qqnorm(rstandard(model))
+qqline(rstandard(model))
+shapiro.test(rstandard(model))
+
+
+#1
+plot(model, 1)
+
+#2
+plot(fitted.values(model), rstandard(model))
+
+par(mfrow=c(2,2))
+plot(two.way)
+par(mfrow=c(1,1))

Reeg_et_al_2021/Scripts/(8) Figures_local_sensitivity_analysis.R

@@ -106,6 +106,39 @@ Landscape_mean$Parameter <- factor(Landscape_mean$Parameter,
                                               'disturbance_eff',
                                               'trans_effect_nest', 'trans_effect_res', 'trans_effect_nest_res'))
 
+# Rename
+Landscape_mean[Parameter=="weather_std"]$Parameter <- "standard deviation \n weather"
+Landscape_mean[Parameter=="disturbance_prob"]$Parameter <- "disturbance \n probability"
+Landscape_mean[Parameter=="dispersal_tries"]$Parameter <- "dispersal \n tries"
+Landscape_mean[Parameter=="competition_strength"]$Parameter <- "competition \n strength"
+Landscape_mean[Parameter=="growth_rate"]$Parameter <- "growth rate"
+Landscape_mean[Parameter=="nest_suitability"]$Parameter <- "nesting site \n suitability"
+Landscape_mean[Parameter=="res_suitability"]$Parameter <- "resource \n suitability"
+Landscape_mean[Parameter=="dispersal_mean"]$Parameter <- "mean dispersal"
+Landscape_mean[Parameter=="dispersal_sd"]$Parameter <- "standard deviation \n dispersal"
+Landscape_mean[Parameter=="emigration_mu"]$Parameter <- "emigration \n parameter mu"
+Landscape_mean[Parameter=="emigration_omega"]$Parameter <- "emigration \n parameter omega"
+Landscape_mean[Parameter=="disturbance_eff"]$Parameter <- "disturbance \n effect"
+Landscape_mean[Parameter=="trans_effect_nest"]$Parameter <- "effect of ABZs \n on nesting site"
+Landscape_mean[Parameter=="trans_effect_res"]$Parameter <- "effect of ABZs  \n on resources"
+Landscape_mean[Parameter=="trans_effect_nest_res"]$Parameter <- "effect of ABZs \n on nesting site \n and resources"
+
+Landscape_Shannon_all[Parameter=="weather_std"]$Parameter <- "standard deviation \n weather"
+Landscape_Shannon_all[Parameter=="disturbance_prob"]$Parameter <- "disturbance \n probability"
+Landscape_Shannon_all[Parameter=="dispersal_tries"]$Parameter <- "dispersal \n tries"
+Landscape_Shannon_all[Parameter=="competition_strength"]$Parameter <- "competition \n strength"
+Landscape_Shannon_all[Parameter=="growth_rate"]$Parameter <- "growth rate"
+Landscape_Shannon_all[Parameter=="nest_suitability"]$Parameter <- "nesting site \n suitability"
+Landscape_Shannon_all[Parameter=="res_suitability"]$Parameter <- "resource \n suitability"
+Landscape_Shannon_all[Parameter=="dispersal_Shannon_all"]$Parameter <- "mean dispersal"
+Landscape_Shannon_all[Parameter=="dispersal_sd"]$Parameter <- "standard deviation \n dispersal"
+Landscape_Shannon_all[Parameter=="emigration_mu"]$Parameter <- "emigration \n parameter mu"
+Landscape_Shannon_all[Parameter=="emigration_omega"]$Parameter <- "emigration \n parameter omega"
+Landscape_Shannon_all[Parameter=="disturbance_eff"]$Parameter <- "disturbance \n effect"
+Landscape_Shannon_all[Parameter=="trans_effect_nest"]$Parameter <- "effect of ABZs \n on nesting site"
+Landscape_Shannon_all[Parameter=="trans_effect_res"]$Parameter <- "effect of ABZs  \n on resources"
+Landscape_Shannon_all[Parameter=="trans_effect_nest_res"]$Parameter <- "effect of ABZs \n on nesting site \n and resources"
+
 
 #####
 # Figure F.3