underlying data model

00-scripts/step5/figures/figure3.R

@@ -133,6 +133,19 @@ modAutocovF=lm(acinv2a~SST+nb_species+nb_indv_mean+regions+Alt+SlopeAvg,data= en
 ## residuals (part of spatial autocorrelation not explained by the model)
 autocor=residuals(modAutocovF)
 
+## underlying data fig 3c
+underlying_data_fig3c=data.frame(
+  x=env2$x,
+  y=env2$y,
+  mean_genetic_diversity=env2$GD_mean,
+  regional_temperature=env2$SST,
+  regions=env2$regions,
+  number_of_species=env2$nb_species,
+  number_of_sequences=env2$nb_indv_mean,
+  autocor=autocor
+)
+write.table(underlying_data_fig3c,"14-tables/figure_3c_underlying_data.tsv",col.names=T,row.names=F,sep="\t")
+
 
 ##########################################################################
 ## step AIC with term of spatial autocorrelation
@@ -172,7 +185,7 @@ p_ic_F=p_ic_F+theme(plot.title = element_text(size = 24),
                     panel.border=element_rect(fill=NA,size=1),
                     panel.background = element_blank())+ggtitle("(c)")
 ## underlying data
-sink("14-tables/figure_3c_underlying_data.tsv")
+sink("13-analysis/freshwater_summary_lm.txt")
 print(summary(modclimF.autof))
 sink()
 
@@ -259,6 +272,18 @@ dcM.r4<-data.frame(x=dcM.r3$x,
 ### Missing value distance to the coast : 2 missing values
 dcM.r4$distanceFromShore[c(139,337)]=mean(na.omit(dcM.r4)$distanceFromShore)
 
+underlying_data_fig3a=data.frame(
+  x=dcM.r4$x,
+  y=dcM.r4$y,
+  mean_genetic_diversity=dcM.r4$GD_mean,
+  sea_surface_temperature=dcM.r4$SST,
+  regions=dcM.r4$regions,
+  number_of_species=dcM.r4$nb_species,
+  number_of_sequences=dcM.r4$nb_indv_mean
+)
+write.table(underlying_data_fig3a,"14-tables/figure_3a_underlying_data.tsv",col.names=T,row.names=F,sep="\t")
+
+
 
 ##########################################################################
 ## Selection top 200 cells
@@ -333,7 +358,7 @@ p_ic_M=p_ic_M+theme(plot.title = element_text(size = 24),
                     panel.border=element_rect(fill=NA,size=1),
                     panel.background = element_blank())+ggtitle("(a)")
 ## underlying data
-sink("14-tables/figure_3a_underlying_data.tsv")
+sink("13-analysis/marine_summary_lm.txt")
 print(summary(modclimM.autof))
 sink()
 

13-analysis/freshwater_summary_lm.txt

+
+Call:
+lm(formula = GD_mean ~ SST + scale(SlopeAvg) + regions + scale(autocor) + 
+    nb_species + nb_indv_mean, data = env2)
+
+Residuals:
+     Min       1Q   Median       3Q      Max 
+-2.77334 -0.53425  0.04287  0.58127  2.23167 
+
+Coefficients:
+                            Estimate Std. Error t value Pr(>|t|)    
+(Intercept)                -0.602047   0.150004  -4.014 7.37e-05 ***
+Mean regional\ntemperature  0.134435   0.058521   2.297   0.0222 *  
+Average slope              -0.225852   0.050788  -4.447 1.18e-05 ***
+Regions                     0.121156   0.028227   4.292 2.31e-05 ***
+Autocor                     0.237272   0.048076   4.935 1.26e-06 ***
+Number of species           0.004486   0.005001   0.897   0.3703    
+Number of sequences         0.020028   0.048674   0.411   0.6810    
+---
+Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
+
+Residual standard error: 0.893 on 339 degrees of freedom
+Multiple R-squared:  0.2081,	Adjusted R-squared:  0.1941 
+F-statistic: 14.85 on 6 and 339 DF,  p-value: 4.382e-15
+

13-analysis/marine_summary_lm.txt

+
+Call:
+lm(formula = GD_mean ~ SST + regions + scale(autocor) + nb_species + 
+    nb_indv_mean, data = dcM.r4)
+
+Residuals:
+    Min      1Q  Median      3Q     Max 
+-3.1807 -0.5386 -0.0072  0.5799  3.5761 
+
+Coefficients:
+                          Estimate Std. Error t value Pr(>|t|)    
+(Intercept)              -0.138762   0.061680  -2.250  0.02489 *  
+Sea surface\ntemperature  0.341185   0.040324   8.461 2.84e-16 ***
+Regions                   0.221148   0.082181   2.691  0.00736 ** 
+Autocor                   0.076247   0.040835   1.867  0.06245 .  
+Number of species         0.002905   0.001370   2.120  0.03450 *  
+Number of sequences      -0.083582   0.043620  -1.916  0.05591 .  
+---
+Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
+
+Residual standard error: 0.9249 on 508 degrees of freedom
+Multiple R-squared:  0.168,	Adjusted R-squared:  0.1598 
+F-statistic: 20.51 on 5 and 508 DF,  p-value: < 2.2e-16
+