misc/Trends/Contrib_Trends.R
In cesco-lab/Vigie-Chiro_scripts: Predict Distribution Of Chiropter
library(data.table)
library(glmmTMB)
Species="Nyclei"
Hab="No selection"
DataRP=fread("C:/Users/Yves Bas/Documents/GitHub/VigieChiro/data/data_vigieChiro_DataRP_SpTron_50_TronPoint_55sp_withAbs.csv")
DataPF=fread("C:/wamp64/www/SpNuit2_50_DataLP_PF_exportTot.csv")
SpeciesList=fread("SpeciesList.csv")
Particip=fread("C:/wamp64/www/p_export.csv",encoding="UTF-8")
SiteLoc=fread("C:/wamp64/www/sites_localites.txt")
Hab="All" #"No selection" if no filter "All" if running all habitats, name of the habitat otherwise
#Hab="Urbain"
#Hab="No selection"
#filter out unappropriate sample rates
DataRP=subset(DataRP,DataRP$SampleRate<=DataRP$seuilSR_sup)
DataRP=subset(DataRP,DataRP$SampleRate>=DataRP$seuilSR_inf)
if(!("nb_contacts" %in% names(DataRP)))
{
DataRP$nb_contacts=DataRP$nb_contacts_strict
DataRP=subset(DataRP,!is.na(DataRP$nb_contacts))
}
SumEsp=aggregate(DataRP$nb_contacts,by=list(DataRP$espece),FUN=sum)
SpeciesOrder=SumEsp$Group.1[order(SumEsp$x,decreasing=T)]
DataPF$year=as.numeric(substr(DataPF$Nuit,1,4))
table(DataPF$year)
DataPF=subset(DataPF,DataPF$year %in% YearsSelected)
SampleUnique=unique(subset(DataPF,select=c("participation","Nuit","num_micro","year")))
ParticipPF=subset(Particip,Particip$point!="")
SampleUniqueP=merge(SampleUnique,ParticipPF,by="participation")
PointAgg=aggregate(SampleUniqueP$participation
,by=list(SampleUniqueP$site,SampleUniqueP$point
,SampleUniqueP$year)
,FUN=length)
PointAggY=aggregate(PointAgg$Group.3
,by=list(PointAgg$Group.1,PointAgg$Group.2)
,FUN=length)
table(PointAggY$x) #number of years per points
PointsRepetes=subset(PointAggY,PointAggY$x>1)
Dep=substr(PointsRepetes$Group.1,25,26)
table(Dep)
ParticipRepetes=subset(ParticipPF,paste(ParticipPF$site,ParticipPF$point) %in%
paste(PointsRepetes$Group.1,PointsRepetes$Group.2))
DataPFrepetes=subset(DataPF,DataPF$participation %in% ParticipRepetes$participation)
SampleUniqueRep=unique(subset(DataPFrepetes,select=c("participation","Nuit","num_micro","year")))
table(SampleUniqueRep$year)
#SpeciesShort=subset(SpeciesList,SpeciesList$Group==GroupSel)
DataSp=rbind(subset(DataRP,select=c("espece","nb_contacts"))
,subset(DataPFrepetes,select=c("espece","nb_contacts")))
DataSp$espece[substr(DataSp$espece,1,3)=="Myo"]="Myospp"
NDataSp=aggregate(DataSp$nb_contacts,by=list(DataSp$espece),FUN=sum)
NDataSp=NDataSp[order(NDataSp$x,decreasing = T),]
colnames(NDataSp)=c("species","weight")
fwrite(NDataSp,"NDataSp.csv")
DataPFP=merge(DataPF,Particip,by="participation")
DataPFP$protocole=tstrsplit(DataPFP$site,split="-")[[2]]
DataRP$protocole=tstrsplit(DataRP$site,split="-")[[2]]
DataRP$protocole[DataRP$protocole=="chiro "]="Routier"
DataSp=rbind(subset(DataRP,select=c("espece","nb_contacts","protocole"))
,subset(DataPFP,select=c("espece"
,"nb_contacts","protocole")))
DataSpPos=subset(DataSp,DataSp$nb_contacts>0)
DataRPi=subset(DataRP,DataRP$espece==Species)
#DataRPi=merge(DataRPi,AnomWeather,by=c("participation"))
DataPFi=subset(DataPFrepetes,DataPFrepetes$espece==Species)
table(DataPFi$year)
DataPFi_w0=merge(DataPFi,SampleUniqueRep
,by=c("participation","Nuit","num_micro","year"),all.y=T)
ndata=nrow(DataPFi_w0)
DataPFi_w0=merge(DataPFi_w0,Particip,by="participation")
if(nrow(DataPFi_w0)<ndata)
{
#print(paste(ndata-nrow(DataPFi_w0)
# ,"données perdues car absentes de la table participation"))
ndata=nrow(DataPFi_w0)
}
DataPFi_w0=merge(DataPFi_w0,SiteLoc,by.x=c("site","point")
,by.y=c("site","nom"))
if(nrow(DataPFi_w0)<ndata)
{
#print(paste(ndata-nrow(DataPFi_w0)
# ,"données perdues car absentes de la table localites"))
ndata=nrow(DataPFi_w0)
}
backup=DataPFi_w0
DataPFi_w0=merge(DataPFi_w0,Bioclim,by.x=c("longitude","latitude")
,by.y=c("Group.1","Group.2"))
if(nrow(DataPFi_w0)<ndata)
{
#print(paste(ndata-nrow(DataPFi_w0)
# ,"données perdues car absentes de la table bioclim"))
Tot=merge(backup,Bioclim,by.x=c("longitude","latitude")
,by.y=c("Group.1","Group.2"),all.x=T)
test2=Tot$SpBioC1
test3=is.na(test2)
test=subset(Tot,test3)
#plot(test$longitude,test$latitude)
#print("Exemple :")
Exemple=test[sample.int(nrow(test),1),1:2]
#print(paste0(Exemple[1,2],",",Exemple[1,1]))
ndata=nrow(DataPFi_w0)
}
#DataPFi_w0=merge(DataPFi_w0,AnomWeather,by=c("participation","Nuit"))
#if(nrow(DataPFi_w0)<ndata)
#{
#print(paste(ndata-nrow(DataPFi_w0)
# ,"données perdues car absentes de la table anomalies"))
# ndata=nrow(DataPFi_w0)
#}
DataPFi_w0$nb_contacts[is.na(DataPFi_w0$nb_contacts)]=0
DataPFi_w0$espece=Species
DataPFi_w0$month=as.numeric(substr(DataPFi_w0$Nuit,6,7))
sum(is.na(DataPFi_w0$month))
#barplot(table(DataPFi_w0$month))
#boxplot(DataPFi_w0$nb_contacts~DataPFi_w0$month)
DataPFi_w0$julian <- yday(DataPFi_w0$Nuit)
#barplot(table(DataPFi_w0$julian))
#hist(DataPFi_w0$julian)
DataPFi_w0$sample_cat="point_fixe"
DataPFi_w0$expansion_direct="direct"
DataPFi_w0$temps_enr=360
DataPFi_w0$SampleRate=384000 #to be modified using SR values from tc but useless for now
DataPFi_w0$num_site=as.numeric(gsub("Vigiechiro - Point Fixe-",""
,DataPFi_w0$site))
DataPFi_w0$nb_Tron_strict=10
#fwrite(DataPFi_w0,paste0("./VigieChiro/Trends/DataPF/DataPFi_w0_"
# ,Species,".csv"),sep=";")
#add localities variable
DataRPi$siteloc=paste(DataRPi$num_site,DataRPi$Tron)
DataPFi_w0$siteloc=paste(DataPFi_w0$num_site,DataPFi_w0$point)
DataRPi_purge=subset(DataRPi
,select=(colnames(DataRPi) %in% colnames(DataPFi_w0)))
DataPFi_purge=subset(DataPFi_w0
,select=(colnames(DataPFi_w0) %in% colnames(DataRPi_purge)))
DataRPPF=rbindlist(list(DataRPi_purge,DataPFi_purge),use.names=T)
#for test
#DataRPPF=DataRPi_purge
#DataRPPF=DataPFi_purge
DataRPPF$mat=substr(DataRPPF$detecteur_enregistreur_type,1,4)
DataRPPF$micro0_type[DataRPPF$micro0_type=="SMX-U1"]="SMM-U1"
DataRPPF$micro0_type[DataRPPF$micro0_type=="Micro externe sans cornet"]=""
DataRPPF$micro0_type[DataRPPF$micro0_type=="Autre micro externe"]=""
DataRPPF$micro0_type[DataRPPF$micro0_type=="Micro interne"]=""
DataRPPF$micro0_type[DataRPPF$micro0_type=="SMX-U1"]="SMM-U1"
DataRPPF$micro0_type[!(DataRPPF$detecteur_enregistreur_type %in%
c("SM2BAT","SM2BAT+","SM4"))]=""
DataRPPF$mat=paste(DataRPPF$mat,substr(DataRPPF$micro0_type,1,6))
MatSum=aggregate(DataRPPF$participation,by=list(DataRPPF$mat), FUN=length)
MatSum=MatSum[order(MatSum$x,decreasing=T),]
MatSum$csx=cumsum(MatSum$x)
CommonMat=subset(MatSum$Group.1,MatSum$csx<0.95*max(MatSum$csx))
DataRPPF=subset(DataRPPF,DataRPPF$mat %in% CommonMat)
DataRPPF$nb_contacts_strict=DataRPPF$nb_contacts
DataRPPF$AnomClimateNight=apply(cbind(DataRPPF$TN_1_1,DataRPPF$TX_0_0)
,MARGIN=1,function(x) mean(x,na.rm=T))
DataRPPF$AnomTemperature=mapply(function(x,y) ifelse(is.na(x),y,x)
,DataRPPF$AnomClimateNight
,DataRPPF$NTempM_NCEP_0_0
)
DataRPPF$AnomTemperature[is.na(DataRPPF$AnomTemperature)]=0
DataRPPF$NWM_NCEP_0_0[is.na(DataRPPF$NWM_NCEP_0_0)]=0
if(Hab!="No selection")
{
DataRPPF=merge(DataRPPF,CoordHab,by.x=c("longitude.y","latitude.y")
,by.y=c("longitude","latitude"))
}
Save=DataRPPF
ListCir=unique(DataRPPF$site)
Tendance=vector()
Ndata=vector()
FYear=vector()
LYear=vector()
for (i in 1:length(ListCir))
{
EPPi=subset(DataRPPF,DataRPPF$site==ListCir[i])
modi=glmmTMB(EPPi$nb_contacts~EPPi$year,family=nbinom2)
Tendance[i]=summary(modi)$coefficients$cond[2,1]
Ndata[i]=nrow(EPPi)
FYear[i]=min(EPPi$year)
LYear[i]=max(EPPi$year)
if(i%%10==1){print(paste(i,length(ListCir),Sys.time()))}
}
Contrib=data.table(ListCir,Tendance,Ndata,FYear,LYear)
Contrib$Contrib=Contrib$Tendance*Contrib$Ndata
fwrite(Contrib,paste0("ContribTrends",substr(Sys.time(),1,10),".csv"),sep=";")
SiteTest="Vigiechiro - Pédestre-530699"
DataSub=subset(DataRPPF,DataRPPF$site==SiteTest)
boxplot(DataSub$nb_contacts~DataSub$year)
DataSub$Pass=paste(DataSub$expansion_direct,DataSub$year,DataSub$month)
boxplot(DataSub$nb_contacts~DataSub$Pass,las=2)
table(DataSub$Pass,DataSub$expansion_direct)
cesco-lab/Vigie-Chiro_scripts documentation built on Jan. 19, 2025, 6:11 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
library(data.table)
library(glmmTMB)
Species="Nyclei"
Hab="No selection"
DataRP=fread("C:/Users/Yves Bas/Documents/GitHub/VigieChiro/data/data_vigieChiro_DataRP_SpTron_50_TronPoint_55sp_withAbs.csv")
DataPF=fread("C:/wamp64/www/SpNuit2_50_DataLP_PF_exportTot.csv")
SpeciesList=fread("SpeciesList.csv")
Particip=fread("C:/wamp64/www/p_export.csv",encoding="UTF-8")
SiteLoc=fread("C:/wamp64/www/sites_localites.txt")
Hab="All" #"No selection" if no filter "All" if running all habitats, name of the habitat otherwise
#Hab="Urbain"
#Hab="No selection"
#filter out unappropriate sample rates
DataRP=subset(DataRP,DataRP$SampleRate<=DataRP$seuilSR_sup)
DataRP=subset(DataRP,DataRP$SampleRate>=DataRP$seuilSR_inf)
if(!("nb_contacts" %in% names(DataRP)))
{
DataRP$nb_contacts=DataRP$nb_contacts_strict
DataRP=subset(DataRP,!is.na(DataRP$nb_contacts))
}
SumEsp=aggregate(DataRP$nb_contacts,by=list(DataRP$espece),FUN=sum)
SpeciesOrder=SumEsp$Group.1[order(SumEsp$x,decreasing=T)]
DataPF$year=as.numeric(substr(DataPF$Nuit,1,4))
table(DataPF$year)
DataPF=subset(DataPF,DataPF$year %in% YearsSelected)
SampleUnique=unique(subset(DataPF,select=c("participation","Nuit","num_micro","year")))
ParticipPF=subset(Particip,Particip$point!="")
SampleUniqueP=merge(SampleUnique,ParticipPF,by="participation")
PointAgg=aggregate(SampleUniqueP$participation
,by=list(SampleUniqueP$site,SampleUniqueP$point
,SampleUniqueP$year)
,FUN=length)
PointAggY=aggregate(PointAgg$Group.3
,by=list(PointAgg$Group.1,PointAgg$Group.2)
,FUN=length)
table(PointAggY$x) #number of years per points
PointsRepetes=subset(PointAggY,PointAggY$x>1)
Dep=substr(PointsRepetes$Group.1,25,26)
table(Dep)
ParticipRepetes=subset(ParticipPF,paste(ParticipPF$site,ParticipPF$point) %in%
paste(PointsRepetes$Group.1,PointsRepetes$Group.2))
DataPFrepetes=subset(DataPF,DataPF$participation %in% ParticipRepetes$participation)
SampleUniqueRep=unique(subset(DataPFrepetes,select=c("participation","Nuit","num_micro","year")))
table(SampleUniqueRep$year)
#SpeciesShort=subset(SpeciesList,SpeciesList$Group==GroupSel)
DataSp=rbind(subset(DataRP,select=c("espece","nb_contacts"))
,subset(DataPFrepetes,select=c("espece","nb_contacts")))
DataSp$espece[substr(DataSp$espece,1,3)=="Myo"]="Myospp"
NDataSp=aggregate(DataSp$nb_contacts,by=list(DataSp$espece),FUN=sum)
NDataSp=NDataSp[order(NDataSp$x,decreasing = T),]
colnames(NDataSp)=c("species","weight")
fwrite(NDataSp,"NDataSp.csv")
DataPFP=merge(DataPF,Particip,by="participation")
DataPFP$protocole=tstrsplit(DataPFP$site,split="-")[[2]]
DataRP$protocole=tstrsplit(DataRP$site,split="-")[[2]]
DataRP$protocole[DataRP$protocole=="chiro "]="Routier"
DataSp=rbind(subset(DataRP,select=c("espece","nb_contacts","protocole"))
,subset(DataPFP,select=c("espece"
,"nb_contacts","protocole")))
DataSpPos=subset(DataSp,DataSp$nb_contacts>0)
DataRPi=subset(DataRP,DataRP$espece==Species)
#DataRPi=merge(DataRPi,AnomWeather,by=c("participation"))
DataPFi=subset(DataPFrepetes,DataPFrepetes$espece==Species)
table(DataPFi$year)
DataPFi_w0=merge(DataPFi,SampleUniqueRep
,by=c("participation","Nuit","num_micro","year"),all.y=T)
ndata=nrow(DataPFi_w0)
DataPFi_w0=merge(DataPFi_w0,Particip,by="participation")
if(nrow(DataPFi_w0)<ndata)
{
#print(paste(ndata-nrow(DataPFi_w0)
# ,"données perdues car absentes de la table participation"))
ndata=nrow(DataPFi_w0)
}
DataPFi_w0=merge(DataPFi_w0,SiteLoc,by.x=c("site","point")
,by.y=c("site","nom"))
if(nrow(DataPFi_w0)<ndata)
{
#print(paste(ndata-nrow(DataPFi_w0)
# ,"données perdues car absentes de la table localites"))
ndata=nrow(DataPFi_w0)
}
backup=DataPFi_w0
DataPFi_w0=merge(DataPFi_w0,Bioclim,by.x=c("longitude","latitude")
,by.y=c("Group.1","Group.2"))
if(nrow(DataPFi_w0)<ndata)
{
#print(paste(ndata-nrow(DataPFi_w0)
# ,"données perdues car absentes de la table bioclim"))
Tot=merge(backup,Bioclim,by.x=c("longitude","latitude")
,by.y=c("Group.1","Group.2"),all.x=T)
test2=Tot$SpBioC1
test3=is.na(test2)
test=subset(Tot,test3)
#plot(test$longitude,test$latitude)
#print("Exemple :")
Exemple=test[sample.int(nrow(test),1),1:2]
#print(paste0(Exemple[1,2],",",Exemple[1,1]))
ndata=nrow(DataPFi_w0)
}
#DataPFi_w0=merge(DataPFi_w0,AnomWeather,by=c("participation","Nuit"))
#if(nrow(DataPFi_w0)<ndata)
#{
#print(paste(ndata-nrow(DataPFi_w0)
# ,"données perdues car absentes de la table anomalies"))
# ndata=nrow(DataPFi_w0)
#}
DataPFi_w0$nb_contacts[is.na(DataPFi_w0$nb_contacts)]=0
DataPFi_w0$espece=Species
DataPFi_w0$month=as.numeric(substr(DataPFi_w0$Nuit,6,7))
sum(is.na(DataPFi_w0$month))
#barplot(table(DataPFi_w0$month))
#boxplot(DataPFi_w0$nb_contacts~DataPFi_w0$month)
DataPFi_w0$julian <- yday(DataPFi_w0$Nuit)
#barplot(table(DataPFi_w0$julian))
#hist(DataPFi_w0$julian)
DataPFi_w0$sample_cat="point_fixe"
DataPFi_w0$expansion_direct="direct"
DataPFi_w0$temps_enr=360
DataPFi_w0$SampleRate=384000 #to be modified using SR values from tc but useless for now
DataPFi_w0$num_site=as.numeric(gsub("Vigiechiro - Point Fixe-",""
,DataPFi_w0$site))
DataPFi_w0$nb_Tron_strict=10
#fwrite(DataPFi_w0,paste0("./VigieChiro/Trends/DataPF/DataPFi_w0_"
# ,Species,".csv"),sep=";")
#add localities variable
DataRPi$siteloc=paste(DataRPi$num_site,DataRPi$Tron)
DataPFi_w0$siteloc=paste(DataPFi_w0$num_site,DataPFi_w0$point)
DataRPi_purge=subset(DataRPi
,select=(colnames(DataRPi) %in% colnames(DataPFi_w0)))
DataPFi_purge=subset(DataPFi_w0
,select=(colnames(DataPFi_w0) %in% colnames(DataRPi_purge)))
DataRPPF=rbindlist(list(DataRPi_purge,DataPFi_purge),use.names=T)
#for test
#DataRPPF=DataRPi_purge
#DataRPPF=DataPFi_purge
DataRPPF$mat=substr(DataRPPF$detecteur_enregistreur_type,1,4)
DataRPPF$micro0_type[DataRPPF$micro0_type=="SMX-U1"]="SMM-U1"
DataRPPF$micro0_type[DataRPPF$micro0_type=="Micro externe sans cornet"]=""
DataRPPF$micro0_type[DataRPPF$micro0_type=="Autre micro externe"]=""
DataRPPF$micro0_type[DataRPPF$micro0_type=="Micro interne"]=""
DataRPPF$micro0_type[DataRPPF$micro0_type=="SMX-U1"]="SMM-U1"
DataRPPF$micro0_type[!(DataRPPF$detecteur_enregistreur_type %in%
c("SM2BAT","SM2BAT+","SM4"))]=""
DataRPPF$mat=paste(DataRPPF$mat,substr(DataRPPF$micro0_type,1,6))
MatSum=aggregate(DataRPPF$participation,by=list(DataRPPF$mat), FUN=length)
MatSum=MatSum[order(MatSum$x,decreasing=T),]
MatSum$csx=cumsum(MatSum$x)
CommonMat=subset(MatSum$Group.1,MatSum$csx<0.95*max(MatSum$csx))
DataRPPF=subset(DataRPPF,DataRPPF$mat %in% CommonMat)
DataRPPF$nb_contacts_strict=DataRPPF$nb_contacts
DataRPPF$AnomClimateNight=apply(cbind(DataRPPF$TN_1_1,DataRPPF$TX_0_0)
,MARGIN=1,function(x) mean(x,na.rm=T))
DataRPPF$AnomTemperature=mapply(function(x,y) ifelse(is.na(x),y,x)
,DataRPPF$AnomClimateNight
,DataRPPF$NTempM_NCEP_0_0
)
DataRPPF$AnomTemperature[is.na(DataRPPF$AnomTemperature)]=0
DataRPPF$NWM_NCEP_0_0[is.na(DataRPPF$NWM_NCEP_0_0)]=0
if(Hab!="No selection")
{
DataRPPF=merge(DataRPPF,CoordHab,by.x=c("longitude.y","latitude.y")
,by.y=c("longitude","latitude"))
}
Save=DataRPPF
ListCir=unique(DataRPPF$site)
Tendance=vector()
Ndata=vector()
FYear=vector()
LYear=vector()
for (i in 1:length(ListCir))
{
EPPi=subset(DataRPPF,DataRPPF$site==ListCir[i])
modi=glmmTMB(EPPi$nb_contacts~EPPi$year,family=nbinom2)
Tendance[i]=summary(modi)$coefficients$cond[2,1]
Ndata[i]=nrow(EPPi)
FYear[i]=min(EPPi$year)
LYear[i]=max(EPPi$year)
if(i%%10==1){print(paste(i,length(ListCir),Sys.time()))}
}
Contrib=data.table(ListCir,Tendance,Ndata,FYear,LYear)
Contrib$Contrib=Contrib$Tendance*Contrib$Ndata
fwrite(Contrib,paste0("ContribTrends",substr(Sys.time(),1,10),".csv"),sep=";")
SiteTest="Vigiechiro - Pédestre-530699"
DataSub=subset(DataRPPF,DataRPPF$site==SiteTest)
boxplot(DataSub$nb_contacts~DataSub$year)
DataSub$Pass=paste(DataSub$expansion_direct,DataSub$year,DataSub$month)
boxplot(DataSub$nb_contacts~DataSub$Pass,las=2)
table(DataSub$Pass,DataSub$expansion_direct)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.