misc/MergeProtocolsForTrends.R
In cesco-lab/Vigie-Chiro_scripts: Predict Distribution Of Chiropter
library(data.table)
library(raster)
GroupMyo=T
GroupPle=T
Annual=T
if(Annual)
{
source("GitHub/VigieChiro/main_glm.r")
}else{
source("GitHub/VigieChiro/simple_glm.r")
}
source("./GitHub/VigieChiro/script_trend.r")
GLM=F
#DataRP=fread("C:/Users/yvesb/Documents/GitHub/VigieChiro/data/data_vigieChiro_DataRP_SpTron_50_site_55sp_withAbs.csv")
DataRP=fread("C:/Users/yvesb/Documents/GitHub/VigieChiro/data/data_vigieChiro_DataRP_SpTron_50_TronPoint_55sp_withAbs.csv")
DataPF=fread("./www/SpNuit2_50_DataLP_PF_exportTot.csv")
TagData=c("50")
VarEffectI=c("year","poly(julian,2)","sample_cat"
#,"nb_Tron_strict"
,"temps_enr"
,"mat"
,"SpBioC1","SpBioC12"
,"expansion_direct"
,"AnomTemperature","NWM_NCEP_0_0"
)
SpeciesList=fread("SpeciesList.csv")
Particip=fread("./www/p_export_forLinux.csv",encoding="UTF-8")
SiteLoc=fread("./www/sites_localites.txt")
AnomWeather=fread("./VigieChiro/Weather/SLAll_W.csv")
YearsSelected=c(2006:2020)
Bioclim=fread("./www/GI_sites_localites.csv")
RandomEffectI="(1|siteloc)"
ClassHab=fread("./vrac_md_dell2021/Classes_coord.csv")
Hab="All" #"No selection" if no filter "All" if running all habitats, name of the habitat otherwise
#Hab="Urbain"
Hab="No selection"
PurgeZeros=F
TagSave=TagData
#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$nb_contacts))
}
if(GroupPle){DataRP$espece[substr(DataRP$espece,1,3)=="Ple"]="Plespp"}
if(GroupMyo){DataRP$espece[substr(DataRP$espece,1,3)=="Myo"]="Myospp"}
SumEsp=aggregate(DataRP$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")))
if(GroupMyo){DataSp$espece[substr(DataSp$espece,1,3)=="Myo"]="Myospp"}
if(GroupPle){DataSp$espece[substr(DataSp$espece,1,3)=="Ple"]="Plespp"}
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$protocole=="chiro "]="Routier"
fwrite(DataRP,"DataRP.csv",sep=";")
DataSpPos=subset(DataSp,DataSp$nb_contacts>0)
AbDataSp=aggregate(DataSpPos$nb_contacts,by=list(DataSpPos$espece)
,FUN=sum)
names(AbDataSp)[ncol(AbDataSp)]="NbContactsTot"
#OccDataSp=aggregate(DataSpPos$nb_contacts,by=list(DataSpPos$espece,DataSpPos$protocole)
# ,FUN=length)
#AbDataSp$NbOccurrences=OccDataSp$x
#head(AbDataSp)
#fwrite(AbDataSp,"GrandsTotauxSpProtocoles.csv",sep=";")
#SpeciesOrder=subset(SpeciesOrder,grepl("Myo",SpeciesOrder))
if(GroupMyo){DataPFrepetes$espece[substr(DataPFrepetes$espece,1,3)=="Myo"]="Myospp"}
if(GroupPle){DataPFrepetes$espece[substr(DataPFrepetes$espece,1,3)=="Ple"]="Plespp"}
if(Hab=="All")
{
ListHab=unique(ClassHab$Habitat)
}else{
ListHab=Hab
}
#subsetting
for (h in 1:length(ListHab))
{
if(Hab=="No selection")
{
CoordHab=ClassHab
TagData=TagSave
}else{
CoordHab=subset(ClassHab,ClassHab$Habitat==ListHab[h])
TagData=paste0(TagSave,"_",ListHab[h])
}
SpPZ=vector()
PZ=vector()
for (i in 1:length(SpeciesOrder))
#for (i in 1:3)
{
print(paste(SpeciesOrder[i],ListHab[h]))
DataRPi=subset(DataRP,DataRP$espece==SpeciesOrder[i])
DataRPi=merge(DataRPi,AnomWeather,by=c("participation"))
DataPFi=subset(DataPFrepetes,DataPFrepetes$espece==SpeciesOrder[i])
table(DataPFi$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$protocole=NULL
DataPFi_w0=merge(DataPFi_w0,Bioclim,by=c("longitude","latitude"))
#,by.y=c("Group.1","Group.2"))
if(nrow(DataPFi_w0)<ndata)
{
#print(paste(ndata-nrow(DataPFi_w0)
# ,"données perdues car absentes de la table bioclim"))
Tot=merge(backup,Bioclim,by=c("longitude","latitude"),all.x=T)
# ,by.y=c("Group.1","Group.2"),all.x=T)
test2=Tot$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$espece=SpeciesOrder[i]
DataPFi_w0$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_"
# ,SpeciesOrder[i],".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)))
table(names(DataPFi_purge))
dim(DataPFi_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"))
}else{
if(i==1)
{
ValidCir=aggregate(DataRPPF$participation
,by=c(list(DataRPPF$site),
list(DataRPPF$date_debut)
,list(DataRPPF$expansion_direct)
,list(DataRPPF$siteloc))
,FUN=length)
fwrite(ValidCir,"ValidCir.csv",sep=";")
}
}
if(PurgeZeros)
{
PropZeros=aggregate(DataRPPF$nb_contacts_strict,by=list(DataRPPF$siteloc)
,FUN=function(x) (sum(x==0))/length(x))
PZ_threshold=mean(PropZeros$x)+(1-mean(PropZeros$x))*0.9
SL_PZ=subset(PropZeros$Group.1,PropZeros$x<PZ_threshold)
#Excl_PZ=subset(PropZeros$Group.1,PropZeros$x>=PZ_threshold)
DataRPPF=subset(DataRPPF,DataRPPF$siteloc %in% SL_PZ)
SpPZ=c(SpPZ,SpeciesOrder[i])
PZ=c(PZ,PZ_threshold)
}
test=nrow(subset(DataRPPF,DataRPPF$nb_contacts_strict>0))
if(test>20)
{
#filtering locations makes models unstable
#NdataPerSite=aggregate(DataRPPF$nb_contacts,by=list(DataRPPF$siteloc)
# ,FUN=sum)
#SitePresence=subset(NdataPerSite$Group.1,NdataPerSite$x>0)
#DataRPPF=subset(DataRPPF,DataRPPF$siteloc %in% SitePresence)
fwrite(DataRPPF,paste0("./VigieChiro/Raw/forGLM/DataRPPF_",SpeciesOrder[i],".csv"))
if(GLM)
{
main.glm(id=paste0(Sys.Date(),"_",SpeciesOrder[i],"_",TagData)
,
donneesAll=list(DataRPPF)
,
donneesName=TagData
,
method="glmmTMB"
,
family="nbinom2"
,
#only_direct=""
only_direct=
,
only_exp=""
,
seuilOccu=2
,
col_sp="espece"
,
col_date_julien="julian"
,
col_site="site"
,
col_nbcontact="nb_contacts"
,
assessIC= TRUE
,
listSp=NULL
,
tabsp="SpeciesList.csv"
,
first_year=NULL
,
last_year=NULL
,
figure=TRUE
,
description=c("Abondances brutes","Occurrences","Proportion","Nombre de sites")
,
tendanceSurFigure=TRUE
,
tendanceGroupSpe = FALSE
,
seuilSignif=0.05
,
seuilAbond=NA
,
ecritureStepByStep=TRUE
,
doBeep=F
,
VarEffect=VarEffectI
,
RandomEffect=RandomEffectI
)
}
}
}
#beep()
}
cesco-lab/Vigie-Chiro_scripts documentation built on April 4, 2024, 4:27 a.m.
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library(data.table)
library(raster)
GroupMyo=T
GroupPle=T
Annual=T
if(Annual)
{
source("GitHub/VigieChiro/main_glm.r")
}else{
source("GitHub/VigieChiro/simple_glm.r")
}
source("./GitHub/VigieChiro/script_trend.r")
GLM=F
#DataRP=fread("C:/Users/yvesb/Documents/GitHub/VigieChiro/data/data_vigieChiro_DataRP_SpTron_50_site_55sp_withAbs.csv")
DataRP=fread("C:/Users/yvesb/Documents/GitHub/VigieChiro/data/data_vigieChiro_DataRP_SpTron_50_TronPoint_55sp_withAbs.csv")
DataPF=fread("./www/SpNuit2_50_DataLP_PF_exportTot.csv")
TagData=c("50")
VarEffectI=c("year","poly(julian,2)","sample_cat"
#,"nb_Tron_strict"
,"temps_enr"
,"mat"
,"SpBioC1","SpBioC12"
,"expansion_direct"
,"AnomTemperature","NWM_NCEP_0_0"
)
SpeciesList=fread("SpeciesList.csv")
Particip=fread("./www/p_export_forLinux.csv",encoding="UTF-8")
SiteLoc=fread("./www/sites_localites.txt")
AnomWeather=fread("./VigieChiro/Weather/SLAll_W.csv")
YearsSelected=c(2006:2020)
Bioclim=fread("./www/GI_sites_localites.csv")
RandomEffectI="(1|siteloc)"
ClassHab=fread("./vrac_md_dell2021/Classes_coord.csv")
Hab="All" #"No selection" if no filter "All" if running all habitats, name of the habitat otherwise
#Hab="Urbain"
Hab="No selection"
PurgeZeros=F
TagSave=TagData
#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$nb_contacts))
}
if(GroupPle){DataRP$espece[substr(DataRP$espece,1,3)=="Ple"]="Plespp"}
if(GroupMyo){DataRP$espece[substr(DataRP$espece,1,3)=="Myo"]="Myospp"}
SumEsp=aggregate(DataRP$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")))
if(GroupMyo){DataSp$espece[substr(DataSp$espece,1,3)=="Myo"]="Myospp"}
if(GroupPle){DataSp$espece[substr(DataSp$espece,1,3)=="Ple"]="Plespp"}
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$protocole=="chiro "]="Routier"
fwrite(DataRP,"DataRP.csv",sep=";")
DataSpPos=subset(DataSp,DataSp$nb_contacts>0)
AbDataSp=aggregate(DataSpPos$nb_contacts,by=list(DataSpPos$espece)
,FUN=sum)
names(AbDataSp)[ncol(AbDataSp)]="NbContactsTot"
#OccDataSp=aggregate(DataSpPos$nb_contacts,by=list(DataSpPos$espece,DataSpPos$protocole)
# ,FUN=length)
#AbDataSp$NbOccurrences=OccDataSp$x
#head(AbDataSp)
#fwrite(AbDataSp,"GrandsTotauxSpProtocoles.csv",sep=";")
#SpeciesOrder=subset(SpeciesOrder,grepl("Myo",SpeciesOrder))
if(GroupMyo){DataPFrepetes$espece[substr(DataPFrepetes$espece,1,3)=="Myo"]="Myospp"}
if(GroupPle){DataPFrepetes$espece[substr(DataPFrepetes$espece,1,3)=="Ple"]="Plespp"}
if(Hab=="All")
{
ListHab=unique(ClassHab$Habitat)
}else{
ListHab=Hab
}
#subsetting
for (h in 1:length(ListHab))
{
if(Hab=="No selection")
{
CoordHab=ClassHab
TagData=TagSave
}else{
CoordHab=subset(ClassHab,ClassHab$Habitat==ListHab[h])
TagData=paste0(TagSave,"_",ListHab[h])
}
SpPZ=vector()
PZ=vector()
for (i in 1:length(SpeciesOrder))
#for (i in 1:3)
{
print(paste(SpeciesOrder[i],ListHab[h]))
DataRPi=subset(DataRP,DataRP$espece==SpeciesOrder[i])
DataRPi=merge(DataRPi,AnomWeather,by=c("participation"))
DataPFi=subset(DataPFrepetes,DataPFrepetes$espece==SpeciesOrder[i])
table(DataPFi$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$protocole=NULL
DataPFi_w0=merge(DataPFi_w0,Bioclim,by=c("longitude","latitude"))
#,by.y=c("Group.1","Group.2"))
if(nrow(DataPFi_w0)<ndata)
{
#print(paste(ndata-nrow(DataPFi_w0)
# ,"données perdues car absentes de la table bioclim"))
Tot=merge(backup,Bioclim,by=c("longitude","latitude"),all.x=T)
# ,by.y=c("Group.1","Group.2"),all.x=T)
test2=Tot$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$espece=SpeciesOrder[i]
DataPFi_w0$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_"
# ,SpeciesOrder[i],".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)))
table(names(DataPFi_purge))
dim(DataPFi_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"))
}else{
if(i==1)
{
ValidCir=aggregate(DataRPPF$participation
,by=c(list(DataRPPF$site),
list(DataRPPF$date_debut)
,list(DataRPPF$expansion_direct)
,list(DataRPPF$siteloc))
,FUN=length)
fwrite(ValidCir,"ValidCir.csv",sep=";")
}
}
if(PurgeZeros)
{
PropZeros=aggregate(DataRPPF$nb_contacts_strict,by=list(DataRPPF$siteloc)
,FUN=function(x) (sum(x==0))/length(x))
PZ_threshold=mean(PropZeros$x)+(1-mean(PropZeros$x))*0.9
SL_PZ=subset(PropZeros$Group.1,PropZeros$x<PZ_threshold)
#Excl_PZ=subset(PropZeros$Group.1,PropZeros$x>=PZ_threshold)
DataRPPF=subset(DataRPPF,DataRPPF$siteloc %in% SL_PZ)
SpPZ=c(SpPZ,SpeciesOrder[i])
PZ=c(PZ,PZ_threshold)
}
test=nrow(subset(DataRPPF,DataRPPF$nb_contacts_strict>0))
if(test>20)
{
#filtering locations makes models unstable
#NdataPerSite=aggregate(DataRPPF$nb_contacts,by=list(DataRPPF$siteloc)
# ,FUN=sum)
#SitePresence=subset(NdataPerSite$Group.1,NdataPerSite$x>0)
#DataRPPF=subset(DataRPPF,DataRPPF$siteloc %in% SitePresence)
fwrite(DataRPPF,paste0("./VigieChiro/Raw/forGLM/DataRPPF_",SpeciesOrder[i],".csv"))
if(GLM)
{
main.glm(id=paste0(Sys.Date(),"_",SpeciesOrder[i],"_",TagData)
,
donneesAll=list(DataRPPF)
,
donneesName=TagData
,
method="glmmTMB"
,
family="nbinom2"
,
#only_direct=""
only_direct=
,
only_exp=""
,
seuilOccu=2
,
col_sp="espece"
,
col_date_julien="julian"
,
col_site="site"
,
col_nbcontact="nb_contacts"
,
assessIC= TRUE
,
listSp=NULL
,
tabsp="SpeciesList.csv"
,
first_year=NULL
,
last_year=NULL
,
figure=TRUE
,
description=c("Abondances brutes","Occurrences","Proportion","Nombre de sites")
,
tendanceSurFigure=TRUE
,
tendanceGroupSpe = FALSE
,
seuilSignif=0.05
,
seuilAbond=NA
,
ecritureStepByStep=TRUE
,
doBeep=F
,
VarEffect=VarEffectI
,
RandomEffect=RandomEffectI
)
}
}
}
#beep()
}
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