library(data.table)
library(glmmTMB)
library(ggplot2)
GI=fread("./VigieChiro/GIS/Capture/GI_site_capture_chiro.csv")
Capture=fread("./VigieChiro/GIS/Capture/data_2019-06-06_clean_loc_sunset.csv")
GIC=merge(GI,Capture,by="INSEE")
GIC$yday=yday(GIC$DATE_POSIX)
GIC$BCI=GIC$POIDS/(GIC$AB^2)
hist(GIC$BCI)
GIC$SR=(GIC$SEXE=="FEMELLE")
GIC_elevage=subset(GIC,(GIC$yday>190)&(GIC$yday<230))
GIC_repro=subset(GIC,(GIC$yday>140)&(GIC$yday<230))
GIC_rut=subset(GIC,(GIC$yday>=230))
GIC_repro_adulte=subset(GIC_repro,GIC_repro$AGE!="JUVENILE")
GIC_rut_adulte=subset(GIC_rut,GIC_rut$AGE!="JUVENILE")
#BCI
for (i in 1:nlevels(as.factor(GIC_repro_adulte$TAXON)))
{
GIC_Sp=subset(GIC_repro_adulte
,GIC_repro_adulte$TAXON==levels(as.factor(GIC_repro_adulte$TAXON))[i])
if(nrow(GIC_Sp)>1000)
{
m1=glm(GIC_Sp$BCI~GIC_Sp$SEXE*GIC_Sp$yday+GIC_Sp$SpHC1L
+GIC_Sp$SpHC21L+GIC_Sp$SpHC3L+GIC_Sp$SpHC4L+GIC_Sp$SpHC5L
+GIC_Sp$SpAltiL)
print(levels(as.factor(GIC_repro_adulte$TAXON))[i])
print(summary(m1))
}
}
#automne
for (i in 1:nlevels(as.factor(GIC_rut_adulte$TAXON)))
{
GIC_Sp=subset(GIC_rut_adulte
,GIC_rut_adulte$TAXON==levels(as.factor(GIC_rut_adulte$TAXON))[i])
if(nrow(GIC_Sp)>1000)
{
m1=glm(GIC_Sp$BCI~GIC_Sp$SEXE*GIC_Sp$yday+GIC_Sp$SpHC1L
+GIC_Sp$SpHC3L+GIC_Sp$SpHC4L+GIC_Sp$SpHC5L
+GIC_Sp$SpAltiL)
print(levels(as.factor(GIC_rut$TAXON))[i])
print(summary(m1))
}
}
#Sex-ratio
for (i in 1:nlevels(as.factor(GIC_repro_adulte$TAXON)))
{
GIC_Sp=subset(GIC_repro_adulte
,GIC_repro_adulte$TAXON==levels(as.factor(GIC_repro_adulte$TAXON))[i])
if(nrow(GIC_Sp)>1000)
{
m1=glmmTMB(GIC_Sp$SR~GIC_Sp$SpHC1L
+GIC_Sp$SpHC21L+GIC_Sp$SpHC3L+GIC_Sp$SpHC4L+GIC_Sp$SpHC5L
+GIC_Sp$SpAltiL,family="binomial")
print(levels(as.factor(GIC_repro_adulte$TAXON))[i])
print(summary(m1))
}
}
for (i in 1:nlevels(as.factor(GIC_rut_adulte$TAXON)))
{
GIC_Sp=subset(GIC_rut_adulte
,GIC_rut_adulte$TAXON==levels(as.factor(GIC_rut_adulte$TAXON))[i])
if(nrow(GIC_Sp)>1000)
{
m1=glmmTMB(GIC_Sp$SR~GIC_Sp$SpHC1L
+GIC_Sp$SpHC21L+GIC_Sp$SpHC3L+GIC_Sp$SpHC4L+GIC_Sp$SpHC5L
+GIC_Sp$SpAltiL,family="binomial")
print(levels(as.factor(GIC_rut_adulte$TAXON))[i])
print(summary(m1))
}
}
#time
for (i in 1:nlevels(as.factor(GIC_repro_adulte$TAXON)))
{
GIC_Sp=subset(GIC_repro_adulte
,GIC_repro_adulte$TAXON==levels(as.factor(GIC_repro_adulte$TAXON))[i])
GIC_Sp=subset(GIC_Sp,!is.na(GIC_Sp$SEXE))
if(nrow(GIC_Sp)>10)
{
Folder="./VigieChiro/GIS/Capture/PlotHeures"
dir.create(Folder)
png(paste0(Folder,"/",levels(as.factor(GIC_repro_adulte$TAXON))[i],"_repro.png")
,width = 480, height = 300)
print(
ggplot(GIC_Sp, aes(x=diff_sunset_heure,color=SEXE)) +
geom_histogram(binwidth=0.2,aes(y=..density..),color="black", fill="white") +
xlim(0,5)+
geom_density(alpha=.2, fill="#FF6666") +
labs(title=paste0(levels(as.factor(GIC_repro_adulte$TAXON))[i]
," (période de reproduction)"),
x ="Temps après le coucher du soleil (en h)", y = "FREQUENCE")
)
dev.off()
print(levels(as.factor(GIC_repro_adulte$TAXON))[i])
#print(hist(GIC_Sp$diff_sunset_heure
# ,main=paste0(levels(as.factor(GIC_repro_adulte$TAXON))[i])
# ,xlim=c(0,6),breaks=50))
}
}
for (i in 1:nlevels(as.factor(GIC_rut_adulte$TAXON)))
{
GIC_Sp=subset(GIC_rut_adulte
,GIC_rut_adulte$TAXON==levels(as.factor(GIC_rut_adulte$TAXON))[i])
GIC_Sp=subset(GIC_Sp,!is.na(GIC_Sp$SEXE))
if(nrow(GIC_Sp)>10)
{
Folder="./VigieChiro/GIS/Capture/PlotHeures"
dir.create(Folder)
png(paste0(Folder,"/",levels(as.factor(GIC_rut_adulte$TAXON))[i],"_rut.png")
,width = 480, height = 300)
print(
ggplot(GIC_Sp, aes(x=diff_sunset_heure,color=SEXE)) +
geom_histogram(binwidth=0.2,aes(y=..density..),color="black", fill="white") +
xlim(0,5)+
geom_density(alpha=.2, fill="#FF6666") +
labs(title=paste0(levels(as.factor(GIC_rut_adulte$TAXON))[i]
," (période de rut)"),
x ="Temps après le coucher du soleil (en h)", y = "FREQUENCE")
)
dev.off()
print(levels(as.factor(GIC_rut_adulte$TAXON))[i])
#print(hist(GIC_Sp$diff_sunset_heure
# ,main=paste0(levels(as.factor(GIC_rut_adulte$TAXON))[i])
# ,xlim=c(0,6),breaks=50))
}
}
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