misc/Valid/ShiftScoresSpeciesValid.R
In cesco-lab/Vigie-Chiro_scripts: Predict Distribution Of Chiropter
library(data.table)
library(raster)
library(sf)
library(lubridate)
SpeciesList=fread("C:/Users/yvesb/Documents/Tadarida/Tadarida-C/tadaridaC_src/other_inputs/SpeciesList.csv")
ValidData=fread("C:/Users/yvesb/Downloads/export_validtot220305.txt")
ListPartWavArchiv=fread("C:/Users/yvesb/Documents/www/wavarchivees2.txt")
Particip=fread("C:/Users/yvesb/Documents/www/p_export_forLinux.csv",encoding="UTF-8")
SiteLocF="C:/Users/yvesb/Documents/www/sites_localites.csv"
Zone="C:/Users/yvesb/Documents/SIG/Limite_administrative/France_dep_L93.shp"
SLpred="C:/Users/yvesb/Documents/VigieChiro/gbifData/SL"
DateSp="C:/Users/yvesb/Documents/VigieChiro/gbifData/DateSp/"
UseDate=F
Nsel=90 #per species, compter un ratio de 0.7 pour obtenir n fichiers
SpIdTot=fread("C:/Users/yvesb/Documents/www/SpNuit2Valid_DI_0_DataLP_PF_exportTot.csv")
#SpIdTot=fread("DataRP_SpSecteur_0.csv")
RP=F
SelSp=c("Tetvir"
,"Leppun"
,"Phogri"
,"Phanan"
,"Testes"
,"Rusnit"
,"Plaint"
,"Plaalb"
,"Yerray"
,"Urosp"
,"Cyrscu"
,"Epheph"
,"Isopyr"
,"Barfis"
,"Antsp"
,"Rhasp"
,"Plaaff"
,"Confus"
,"Roeroe"
,"Plasab"
,"Eupsp"
,"Sepsep"
,"Tyllil"
,"Phofem"
,"Metbra"
,"Decalb"
,"Plafal"
,"Phafal"
,"Ptepon"
,"Antped"
,"Condor"
,"Pteger"
,"Tetcan"
,"Bicbic"
,"Antius"
,"Thycor"
,"Urorug"
,"Antsor"
,"Yerbey"
,"Lepbos"
,"Lepalb")
SelSp=c("Barbar"
,"Hypsav"
,"Eptser"
,"Nyclei"
,"Nycnoc"
,"Vesmur"
,"Eptnil"
,"Nyclas"
,"Tadten"
,"Pipkuh"
,"Pipnat"
,"Pippip"
,"Pippyg"
,"Minsch"
,"Rhifer"
,"Rhihip"
,"Rhieur"
,"Pleaur"
,"Plemac"
,"Pleaus"
,"Myodau"
,"Myonat"
,"Myomys"
,"Myoalc"
,"Myoema"
,"MyoGT")
SelSp=c("Myodau"
,"Myonat"
,"Myomys"
,"Myoalc"
,"Myoema"
,"MyoGT","Myocap","Myobec","Pipnat","Eptser","Eptnil","Vesmur","Nyclei","Nycnoc","Nyclas","Rhihip","Rhieur"
,"Minsch")
SelSp=c("MyoGT","Eptser","Eptnil","Vesmur","Nyclei","Nycnoc","Nyclas","Tadten"
,"Pleaus","Plemac","Pleaur")
Id=aggregate(SpIdTot$score_max,by=c(list(SpIdTot$participation)
,list(SpIdTot$espece)),max)
#test=match("5f4a3e232baea1000ff00a70",Id$Group.1)
#test=match("5f4a3e232baea1000ff00a70",SpIdTot$participation)
Particip$ProperDate= dmy_hm(Particip$date_debut)
Particip$yday=yday(Particip$ProperDate)
Particip=subset(Particip
,Particip$participation %in% ListPartWavArchiv$V1)
SiteLoc=fread(SiteLocF)
DateF=list.files(DateSp,full.names=T)
DateL=list()
for (h in 1:length(DateF))
{
DateL[[h]]=fread(DateF[h])
}
DateAll=rbindlist(DateL)
SLfiles=list.files(SLpred,full.names=T)
FranceD= shapefile(Zone)
p=st_as_sf(FranceD)
pbuf = st_buffer(p, 1000)
FranceD=as(pbuf,'Spatial')
proj4string(FranceD)=CRS("+init=epsg:2154")
coordinates(SiteLoc)=c("longitude","latitude")
proj4string(SiteLoc)=CRS("+init=epsg:4326")
SiteLoc=spTransform(SiteLoc,CRS("+init=epsg:2154"))
Tri_FR=over(SiteLoc,FranceD)
SiteLoc=fread(SiteLocF)
SL_FR=subset(SiteLoc,!is.na(Tri_FR$CHEF_LIE0))
if(RP)
{
Part_FRPF=subset(Particip,!substr(Particip$site,1,19)=="Vigiechiro - Point ")
}else{
Part_FRPF=subset(Particip,paste(Particip$site,Particip$point)
%in% paste(SL_FR$site,SL_FR$nom))
Part_FRPF=subset(Part_FRPF
,substr(Part_FRPF$site,1,19)=="Vigiechiro - Point ")
#Part_RP=subset(Particip,!substr(Particip$site,1,19)=="Vigiechiro - Point ")
#PartFR=c(Part_FRPF$participation,Part_RP$participation)
#test=subset(Part_RP,Part_RP$participation=="5a2aa7ac552423000d77e090")
}
SpeciesSel=subset(SpeciesList,SpeciesList$Group %in% c("bat","bush-cricket"))
SpeciesSel=subset(SpeciesSel,!grepl("sp.",SpeciesSel$`Scientific name`))
SpeciesSel=subset(SpeciesSel,SpeciesSel$France=="x")
SpeciesSel=subset(SpeciesSel,SpeciesSel$Esp %in% SelSp)
#points fixes
ValidFR=subset(ValidData,ValidData$participation %in% Part_FRPF$participation)
SpValidN=aggregate(ValidFR$participation,by=list(ValidFR$valid.espece)
,length)
test=subset(ValidFR,ValidFR$validateur_taxon=="Eptisa")
SpeciesSel2=unique(SpeciesSel,by="Nesp2")
SpeciesSelN=merge(SpeciesSel2,SpValidN,by.x="Nesp2",by.y="Group.1"
,all.x=T)
SpeciesSelN$x[is.na(SpeciesSelN$x)]=0
SpeciesSelN=SpeciesSelN[order(SpeciesSelN$x)]
ValidV=subset(ValidData,ValidData$validateur_taxon!="")
Partdispo=subset(Part_FRPF,!(Part_FRPF$participation %in% ValidV$participation))
#positive shifts
ParSel=vector()
Esp=vector()
icount=0
while(icount<Nsel)
{
Spi=SpeciesSel[sample(nrow(SpeciesSel),1),]
print(paste(icount,Spi$Nesp2))
#Datei=subset(DateAll
# ,DateAll$ListSpValide==Spi$`Scientific name`[1])
#if(nrow(Datei)==0){
# Datei$ListSpValide[1]=Spi$`Scientific name`[1]
#Datei$PicSp[1]=sample(c(16:374),1)
#}
#Parti=subset(Partdispo,(Partdispo$yday>Datei$PicSp[1]-30)
# &(Partdispo$yday<Datei$PicSp[1]+30))
Parti=Partdispo
if(RP){
SL_u=unique(SL_FR,by="site")
PartSLi=merge(Parti,SL_u,by=c("site"))
}else{
PartSLi=merge(Parti,SL_FR,by.x=c("site","point"),by.y=c("site","nom"))
}
Idi=subset(Id,Id$Group.2==Spi$Nesp2)
SLi=subset(SLfiles,grepl(Spi$`Scientific name`[1]
,basename(SLfiles)))
if(length(SLi)>0)
{
SLpredi=fread(SLi[1])
PartSLpredi=merge(PartSLi,SLpredi,by.x=c("longitude","latitude")
,by.y=c("Group.1","Group.2"))
PartSLpredis=merge(PartSLpredi,Idi,by.x="participation"
,by.y="Group.1")
PartSLpredis=subset(PartSLpredis,!(PartSLpredis$participation
%in% ParSel))
if(nrow(PartSLpredis)>0)
{
#more than expected
PartSLpredis$PS=PartSLpredis$x-PartSLpredis$pred
PartSLpredis=PartSLpredis[sample(nrow(PartSLpredis)),]
PartSLpredis=PartSLpredis[order(PartSLpredis$PS,decreasing=T),]
Q75=quantile(PartSLpredis$PS,0.75)
Max=max(PartSLpredis$PS)
PartSLpredis$Weights=pmax(0,(PartSLpredis$PS-Q75)/(Max-Q75))
#PartSLpredis=subset(PartSLpredis,PartSLpredis$Weights>0)
PartSLpredis1=PartSLpredis[sample(nrow(PartSLpredis),1,prob=PartSLpredis$Weights),]
ParSeli=PartSLpredis1$participation[1]
ParSel=c(ParSel,ParSeli)
Esp=c(Esp,Spi$Nesp2)
icount=icount+1
}
}
}
ParSelFPSpecies=data.frame(cbind(ParSel,Esp))
ParSelFPSpecies$type="FP"
#false negatives tracking
#part 1: missing sp
ParSel=vector()
Esp=vector()
for (i in 1:round(nrow(ParSelFPSpecies)/2))
{
Spi=subset(SpeciesList,SpeciesList$Esp==ParSelFPSpecies$Esp[i])
print(paste(i,Spi$Nesp2[1]))
if(nchar(as.character(ParSelFPSpecies$Esp[i]))<6)
{
Spg=subset(SpeciesList,SpeciesList$Nesp2==ParSelFPSpecies$Esp[i])
Spg=subset(Spg,nchar(Spg$Esp)==6)
}else{
Spg=Spi
}
Sps=Spg[sample(nrow(Spg),1),]
Datei=subset(DateAll
,DateAll$ListSpValide==Sps$`Scientific name`[1])
if(nrow(Datei)==0){
Datei=DateAll[1,]
Datei$ListSpValide[1]=Spi$`Scientific name`[1]
Datei$PicSp[1]=sample(c(16:374),1)
}
if(UseDate){
Parti=subset(Partdispo,(Partdispo$yday>Datei$PicSp[1]-30)
&(Partdispo$yday<Datei$PicSp[1]+30))
}else{
Parti=Partdispo
}
#Parti=Partdispo
if(RP){
SL_u=unique(SL_FR,by="site")
PartSLi=merge(Parti,SL_u,by=c("site"))
}else{
PartSLi=merge(Parti,SL_FR,by.x=c("site","point"),by.y=c("site","nom"))
}
Idi=subset(Id,Id$Group.2==Spi$Nesp2)
PartSLi=subset(PartSLi,!(PartSLi$participation %in% Idi$Group.1))
SLi=subset(SLfiles,grepl(Sps$`Scientific name`[1]
,basename(SLfiles)))
if(length(SLi)>0)
{
SLpredi=fread(SLi[1])
PartSLpredi=merge(PartSLi,SLpredi,by.x=c("longitude","latitude")
,by.y=c("Group.1","Group.2"))
PartSLpredi=PartSLpredi[sample(nrow(PartSLpredi)),]
PartSLpredi=PartSLpredi[order(PartSLpredi$pred,decreasing=T),]
PartSLpredi=subset(PartSLpredi
,!(PartSLpredi$participation %in% ParSel))
#test=match("5f4a3e232baea1000ff00a70",PartSLpredi$participation)
PartSLpredi=subset(PartSLpredi
,(PartSLpredi$participation %in% Id$Group.1))
#test=match("5f4a3e232baea1000ff00a70",PartSLpredi$participation)
#test=match("5f4a3e232baea1000ff00a70",Idi$Group.1)
if(nrow(PartSLpredi)>0)
{
Q75=quantile(PartSLpredi$pred,0.75)
Max=max(PartSLpredi$pred)
PartSLpredi$Weights=pmax(0,(PartSLpredi$pred-Q75)/(Max-Q75))
#PartSLpredis=subset(PartSLpredis,PartSLpredis$Weights>0)
PartSLpredis1=PartSLpredi[sample(nrow(PartSLpredi),1,prob=PartSLpredi$Weights),]
ParSeli=PartSLpredi1$participation[1]
ParSel=c(ParSel,ParSeli)
Esp=c(Esp,Spi$Nesp2)
}
}
}
ParSelFNmSpecies=data.frame(cbind(ParSel,Esp))
ParSelFNmSpecies$type="FNm"
#fn part 2: low scores
ParSel=vector()
Esp=vector()
for (i in (round(nrow(ParSelFPSpecies)/2)+1):nrow(ParSelFPSpecies))
{
Spi=subset(SpeciesList,SpeciesList$Esp==ParSelFPSpecies$Esp[i])
print(paste(i,Spi$Nesp2[1]))
if(nchar(as.character(ParSelFPSpecies$Esp[i]))<6)
{
Spg=subset(SpeciesList,SpeciesList$Nesp2==ParSelFPSpecies$Esp[i])
Spg=subset(Spg,nchar(Spg$Esp)==6)
}else{
Spg=Spi
}
Sps=Spg[sample(nrow(Spg),1),]
Datei=subset(DateAll
,DateAll$ListSpValide==Sps$`Scientific name`[1])
if(nrow(Datei)==0){
Datei=DateAll[1,]
Datei$ListSpValide[1]=Spi$`Scientific name`[1]
Datei$PicSp[1]=sample(c(16:374),1)
}
if(UseDate){
Parti=subset(Partdispo,(Partdispo$yday>Datei$PicSp[1]-30)
&(Partdispo$yday<Datei$PicSp[1]+30))
}else{
Parti=Partdispo
}
if(RP){
SL_u=unique(SL_FR,by="site")
PartSLi=merge(Parti,SL_u,by=c("site"))
}else{
PartSLi=merge(Parti,SL_FR,by.x=c("site","point"),by.y=c("site","nom"))
}
Idi=subset(Id,Id$Group.2==Spi$Nesp2)
SLi=subset(SLfiles,grepl(Sps$`Scientific name`[1]
,basename(SLfiles)))
if(length(SLi)>0)
{
SLpredi=fread(SLi[1])
PartSLpredi=merge(PartSLi,SLpredi,by.x=c("longitude","latitude")
,by.y=c("Group.1","Group.2"))
PartSLpredis=merge(PartSLpredi,Idi,by.x="participation"
,by.y="Group.1")
PartSLpredis=subset(PartSLpredis,!(PartSLpredis$participation
%in% ParSel))
if(nrow(PartSLpredis)>0)
{
#more than expected
PartSLpredis$PS=PartSLpredis$pred-PartSLpredis$x
PartSLpredis=PartSLpredis[sample(nrow(PartSLpredis)),]
PartSLpredis=PartSLpredis[order(PartSLpredis$PS,decreasing=T),]
Q75=quantile(PartSLpredis$PS,0.75)
Max=max(PartSLpredis$PS)
PartSLpredis$Weights=pmax(0,(PartSLpredis$PS-Q75)/(Max-Q75))
#PartSLpredis=subset(PartSLpredis,PartSLpredis$Weights>0)
PartSLpredis1=PartSLpredis[sample(nrow(PartSLpredis),1,prob=PartSLpredis$Weights),]
ParSeli=PartSLpredis1$participation[1]
ParSel=c(ParSel,ParSeli)
Esp=c(Esp,Spi$Nesp2)
}else{
PartSLpredi=subset(PartSLpredi,!(PartSLpredi$participation
%in% ParSel))
PartSLpredi=PartSLpredi[sample(nrow(PartSLpredi)),]
PartSLpredi=PartSLpredi[order(PartSLpredi$pred,decreasing=T),]
PartSLpredi=subset(PartSLpredi
,!(PartSLpredi$participation %in% ParSel))
PartSLpredi=subset(PartSLpredi
,(PartSLpredi$participation %in% Id$Group.1))
if(nrow(PartSLpredi)>0)
{
ParSeli=PartSLpredi$participation[1]
ParSel=c(ParSel,ParSeli)
Esp=c(Esp,Spi$Nesp2)
}
}
}
}
ParSelFNlSpecies=data.frame(cbind(ParSel,Esp))
ParSelFNlSpecies$type="FNl"
ParSelShifts=rbind(ParSelFPSpecies,ParSelFNmSpecies)
ParSelShifts=rbind(ParSelShifts,ParSelFNlSpecies)
fwrite(ParSelShifts,paste0("ParSelShifts",Sys.Date(),".csv")
,sep=";")
cesco-lab/Vigie-Chiro_scripts documentation built on April 4, 2024, 4:27 a.m.
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library(data.table)
library(raster)
library(sf)
library(lubridate)
SpeciesList=fread("C:/Users/yvesb/Documents/Tadarida/Tadarida-C/tadaridaC_src/other_inputs/SpeciesList.csv")
ValidData=fread("C:/Users/yvesb/Downloads/export_validtot220305.txt")
ListPartWavArchiv=fread("C:/Users/yvesb/Documents/www/wavarchivees2.txt")
Particip=fread("C:/Users/yvesb/Documents/www/p_export_forLinux.csv",encoding="UTF-8")
SiteLocF="C:/Users/yvesb/Documents/www/sites_localites.csv"
Zone="C:/Users/yvesb/Documents/SIG/Limite_administrative/France_dep_L93.shp"
SLpred="C:/Users/yvesb/Documents/VigieChiro/gbifData/SL"
DateSp="C:/Users/yvesb/Documents/VigieChiro/gbifData/DateSp/"
UseDate=F
Nsel=90 #per species, compter un ratio de 0.7 pour obtenir n fichiers
SpIdTot=fread("C:/Users/yvesb/Documents/www/SpNuit2Valid_DI_0_DataLP_PF_exportTot.csv")
#SpIdTot=fread("DataRP_SpSecteur_0.csv")
RP=F
SelSp=c("Tetvir"
,"Leppun"
,"Phogri"
,"Phanan"
,"Testes"
,"Rusnit"
,"Plaint"
,"Plaalb"
,"Yerray"
,"Urosp"
,"Cyrscu"
,"Epheph"
,"Isopyr"
,"Barfis"
,"Antsp"
,"Rhasp"
,"Plaaff"
,"Confus"
,"Roeroe"
,"Plasab"
,"Eupsp"
,"Sepsep"
,"Tyllil"
,"Phofem"
,"Metbra"
,"Decalb"
,"Plafal"
,"Phafal"
,"Ptepon"
,"Antped"
,"Condor"
,"Pteger"
,"Tetcan"
,"Bicbic"
,"Antius"
,"Thycor"
,"Urorug"
,"Antsor"
,"Yerbey"
,"Lepbos"
,"Lepalb")
SelSp=c("Barbar"
,"Hypsav"
,"Eptser"
,"Nyclei"
,"Nycnoc"
,"Vesmur"
,"Eptnil"
,"Nyclas"
,"Tadten"
,"Pipkuh"
,"Pipnat"
,"Pippip"
,"Pippyg"
,"Minsch"
,"Rhifer"
,"Rhihip"
,"Rhieur"
,"Pleaur"
,"Plemac"
,"Pleaus"
,"Myodau"
,"Myonat"
,"Myomys"
,"Myoalc"
,"Myoema"
,"MyoGT")
SelSp=c("Myodau"
,"Myonat"
,"Myomys"
,"Myoalc"
,"Myoema"
,"MyoGT","Myocap","Myobec","Pipnat","Eptser","Eptnil","Vesmur","Nyclei","Nycnoc","Nyclas","Rhihip","Rhieur"
,"Minsch")
SelSp=c("MyoGT","Eptser","Eptnil","Vesmur","Nyclei","Nycnoc","Nyclas","Tadten"
,"Pleaus","Plemac","Pleaur")
Id=aggregate(SpIdTot$score_max,by=c(list(SpIdTot$participation)
,list(SpIdTot$espece)),max)
#test=match("5f4a3e232baea1000ff00a70",Id$Group.1)
#test=match("5f4a3e232baea1000ff00a70",SpIdTot$participation)
Particip$ProperDate= dmy_hm(Particip$date_debut)
Particip$yday=yday(Particip$ProperDate)
Particip=subset(Particip
,Particip$participation %in% ListPartWavArchiv$V1)
SiteLoc=fread(SiteLocF)
DateF=list.files(DateSp,full.names=T)
DateL=list()
for (h in 1:length(DateF))
{
DateL[[h]]=fread(DateF[h])
}
DateAll=rbindlist(DateL)
SLfiles=list.files(SLpred,full.names=T)
FranceD= shapefile(Zone)
p=st_as_sf(FranceD)
pbuf = st_buffer(p, 1000)
FranceD=as(pbuf,'Spatial')
proj4string(FranceD)=CRS("+init=epsg:2154")
coordinates(SiteLoc)=c("longitude","latitude")
proj4string(SiteLoc)=CRS("+init=epsg:4326")
SiteLoc=spTransform(SiteLoc,CRS("+init=epsg:2154"))
Tri_FR=over(SiteLoc,FranceD)
SiteLoc=fread(SiteLocF)
SL_FR=subset(SiteLoc,!is.na(Tri_FR$CHEF_LIE0))
if(RP)
{
Part_FRPF=subset(Particip,!substr(Particip$site,1,19)=="Vigiechiro - Point ")
}else{
Part_FRPF=subset(Particip,paste(Particip$site,Particip$point)
%in% paste(SL_FR$site,SL_FR$nom))
Part_FRPF=subset(Part_FRPF
,substr(Part_FRPF$site,1,19)=="Vigiechiro - Point ")
#Part_RP=subset(Particip,!substr(Particip$site,1,19)=="Vigiechiro - Point ")
#PartFR=c(Part_FRPF$participation,Part_RP$participation)
#test=subset(Part_RP,Part_RP$participation=="5a2aa7ac552423000d77e090")
}
SpeciesSel=subset(SpeciesList,SpeciesList$Group %in% c("bat","bush-cricket"))
SpeciesSel=subset(SpeciesSel,!grepl("sp.",SpeciesSel$`Scientific name`))
SpeciesSel=subset(SpeciesSel,SpeciesSel$France=="x")
SpeciesSel=subset(SpeciesSel,SpeciesSel$Esp %in% SelSp)
#points fixes
ValidFR=subset(ValidData,ValidData$participation %in% Part_FRPF$participation)
SpValidN=aggregate(ValidFR$participation,by=list(ValidFR$valid.espece)
,length)
test=subset(ValidFR,ValidFR$validateur_taxon=="Eptisa")
SpeciesSel2=unique(SpeciesSel,by="Nesp2")
SpeciesSelN=merge(SpeciesSel2,SpValidN,by.x="Nesp2",by.y="Group.1"
,all.x=T)
SpeciesSelN$x[is.na(SpeciesSelN$x)]=0
SpeciesSelN=SpeciesSelN[order(SpeciesSelN$x)]
ValidV=subset(ValidData,ValidData$validateur_taxon!="")
Partdispo=subset(Part_FRPF,!(Part_FRPF$participation %in% ValidV$participation))
#positive shifts
ParSel=vector()
Esp=vector()
icount=0
while(icount<Nsel)
{
Spi=SpeciesSel[sample(nrow(SpeciesSel),1),]
print(paste(icount,Spi$Nesp2))
#Datei=subset(DateAll
# ,DateAll$ListSpValide==Spi$`Scientific name`[1])
#if(nrow(Datei)==0){
# Datei$ListSpValide[1]=Spi$`Scientific name`[1]
#Datei$PicSp[1]=sample(c(16:374),1)
#}
#Parti=subset(Partdispo,(Partdispo$yday>Datei$PicSp[1]-30)
# &(Partdispo$yday<Datei$PicSp[1]+30))
Parti=Partdispo
if(RP){
SL_u=unique(SL_FR,by="site")
PartSLi=merge(Parti,SL_u,by=c("site"))
}else{
PartSLi=merge(Parti,SL_FR,by.x=c("site","point"),by.y=c("site","nom"))
}
Idi=subset(Id,Id$Group.2==Spi$Nesp2)
SLi=subset(SLfiles,grepl(Spi$`Scientific name`[1]
,basename(SLfiles)))
if(length(SLi)>0)
{
SLpredi=fread(SLi[1])
PartSLpredi=merge(PartSLi,SLpredi,by.x=c("longitude","latitude")
,by.y=c("Group.1","Group.2"))
PartSLpredis=merge(PartSLpredi,Idi,by.x="participation"
,by.y="Group.1")
PartSLpredis=subset(PartSLpredis,!(PartSLpredis$participation
%in% ParSel))
if(nrow(PartSLpredis)>0)
{
#more than expected
PartSLpredis$PS=PartSLpredis$x-PartSLpredis$pred
PartSLpredis=PartSLpredis[sample(nrow(PartSLpredis)),]
PartSLpredis=PartSLpredis[order(PartSLpredis$PS,decreasing=T),]
Q75=quantile(PartSLpredis$PS,0.75)
Max=max(PartSLpredis$PS)
PartSLpredis$Weights=pmax(0,(PartSLpredis$PS-Q75)/(Max-Q75))
#PartSLpredis=subset(PartSLpredis,PartSLpredis$Weights>0)
PartSLpredis1=PartSLpredis[sample(nrow(PartSLpredis),1,prob=PartSLpredis$Weights),]
ParSeli=PartSLpredis1$participation[1]
ParSel=c(ParSel,ParSeli)
Esp=c(Esp,Spi$Nesp2)
icount=icount+1
}
}
}
ParSelFPSpecies=data.frame(cbind(ParSel,Esp))
ParSelFPSpecies$type="FP"
#false negatives tracking
#part 1: missing sp
ParSel=vector()
Esp=vector()
for (i in 1:round(nrow(ParSelFPSpecies)/2))
{
Spi=subset(SpeciesList,SpeciesList$Esp==ParSelFPSpecies$Esp[i])
print(paste(i,Spi$Nesp2[1]))
if(nchar(as.character(ParSelFPSpecies$Esp[i]))<6)
{
Spg=subset(SpeciesList,SpeciesList$Nesp2==ParSelFPSpecies$Esp[i])
Spg=subset(Spg,nchar(Spg$Esp)==6)
}else{
Spg=Spi
}
Sps=Spg[sample(nrow(Spg),1),]
Datei=subset(DateAll
,DateAll$ListSpValide==Sps$`Scientific name`[1])
if(nrow(Datei)==0){
Datei=DateAll[1,]
Datei$ListSpValide[1]=Spi$`Scientific name`[1]
Datei$PicSp[1]=sample(c(16:374),1)
}
if(UseDate){
Parti=subset(Partdispo,(Partdispo$yday>Datei$PicSp[1]-30)
&(Partdispo$yday<Datei$PicSp[1]+30))
}else{
Parti=Partdispo
}
#Parti=Partdispo
if(RP){
SL_u=unique(SL_FR,by="site")
PartSLi=merge(Parti,SL_u,by=c("site"))
}else{
PartSLi=merge(Parti,SL_FR,by.x=c("site","point"),by.y=c("site","nom"))
}
Idi=subset(Id,Id$Group.2==Spi$Nesp2)
PartSLi=subset(PartSLi,!(PartSLi$participation %in% Idi$Group.1))
SLi=subset(SLfiles,grepl(Sps$`Scientific name`[1]
,basename(SLfiles)))
if(length(SLi)>0)
{
SLpredi=fread(SLi[1])
PartSLpredi=merge(PartSLi,SLpredi,by.x=c("longitude","latitude")
,by.y=c("Group.1","Group.2"))
PartSLpredi=PartSLpredi[sample(nrow(PartSLpredi)),]
PartSLpredi=PartSLpredi[order(PartSLpredi$pred,decreasing=T),]
PartSLpredi=subset(PartSLpredi
,!(PartSLpredi$participation %in% ParSel))
#test=match("5f4a3e232baea1000ff00a70",PartSLpredi$participation)
PartSLpredi=subset(PartSLpredi
,(PartSLpredi$participation %in% Id$Group.1))
#test=match("5f4a3e232baea1000ff00a70",PartSLpredi$participation)
#test=match("5f4a3e232baea1000ff00a70",Idi$Group.1)
if(nrow(PartSLpredi)>0)
{
Q75=quantile(PartSLpredi$pred,0.75)
Max=max(PartSLpredi$pred)
PartSLpredi$Weights=pmax(0,(PartSLpredi$pred-Q75)/(Max-Q75))
#PartSLpredis=subset(PartSLpredis,PartSLpredis$Weights>0)
PartSLpredis1=PartSLpredi[sample(nrow(PartSLpredi),1,prob=PartSLpredi$Weights),]
ParSeli=PartSLpredi1$participation[1]
ParSel=c(ParSel,ParSeli)
Esp=c(Esp,Spi$Nesp2)
}
}
}
ParSelFNmSpecies=data.frame(cbind(ParSel,Esp))
ParSelFNmSpecies$type="FNm"
#fn part 2: low scores
ParSel=vector()
Esp=vector()
for (i in (round(nrow(ParSelFPSpecies)/2)+1):nrow(ParSelFPSpecies))
{
Spi=subset(SpeciesList,SpeciesList$Esp==ParSelFPSpecies$Esp[i])
print(paste(i,Spi$Nesp2[1]))
if(nchar(as.character(ParSelFPSpecies$Esp[i]))<6)
{
Spg=subset(SpeciesList,SpeciesList$Nesp2==ParSelFPSpecies$Esp[i])
Spg=subset(Spg,nchar(Spg$Esp)==6)
}else{
Spg=Spi
}
Sps=Spg[sample(nrow(Spg),1),]
Datei=subset(DateAll
,DateAll$ListSpValide==Sps$`Scientific name`[1])
if(nrow(Datei)==0){
Datei=DateAll[1,]
Datei$ListSpValide[1]=Spi$`Scientific name`[1]
Datei$PicSp[1]=sample(c(16:374),1)
}
if(UseDate){
Parti=subset(Partdispo,(Partdispo$yday>Datei$PicSp[1]-30)
&(Partdispo$yday<Datei$PicSp[1]+30))
}else{
Parti=Partdispo
}
if(RP){
SL_u=unique(SL_FR,by="site")
PartSLi=merge(Parti,SL_u,by=c("site"))
}else{
PartSLi=merge(Parti,SL_FR,by.x=c("site","point"),by.y=c("site","nom"))
}
Idi=subset(Id,Id$Group.2==Spi$Nesp2)
SLi=subset(SLfiles,grepl(Sps$`Scientific name`[1]
,basename(SLfiles)))
if(length(SLi)>0)
{
SLpredi=fread(SLi[1])
PartSLpredi=merge(PartSLi,SLpredi,by.x=c("longitude","latitude")
,by.y=c("Group.1","Group.2"))
PartSLpredis=merge(PartSLpredi,Idi,by.x="participation"
,by.y="Group.1")
PartSLpredis=subset(PartSLpredis,!(PartSLpredis$participation
%in% ParSel))
if(nrow(PartSLpredis)>0)
{
#more than expected
PartSLpredis$PS=PartSLpredis$pred-PartSLpredis$x
PartSLpredis=PartSLpredis[sample(nrow(PartSLpredis)),]
PartSLpredis=PartSLpredis[order(PartSLpredis$PS,decreasing=T),]
Q75=quantile(PartSLpredis$PS,0.75)
Max=max(PartSLpredis$PS)
PartSLpredis$Weights=pmax(0,(PartSLpredis$PS-Q75)/(Max-Q75))
#PartSLpredis=subset(PartSLpredis,PartSLpredis$Weights>0)
PartSLpredis1=PartSLpredis[sample(nrow(PartSLpredis),1,prob=PartSLpredis$Weights),]
ParSeli=PartSLpredis1$participation[1]
ParSel=c(ParSel,ParSeli)
Esp=c(Esp,Spi$Nesp2)
}else{
PartSLpredi=subset(PartSLpredi,!(PartSLpredi$participation
%in% ParSel))
PartSLpredi=PartSLpredi[sample(nrow(PartSLpredi)),]
PartSLpredi=PartSLpredi[order(PartSLpredi$pred,decreasing=T),]
PartSLpredi=subset(PartSLpredi
,!(PartSLpredi$participation %in% ParSel))
PartSLpredi=subset(PartSLpredi
,(PartSLpredi$participation %in% Id$Group.1))
if(nrow(PartSLpredi)>0)
{
ParSeli=PartSLpredi$participation[1]
ParSel=c(ParSel,ParSeli)
Esp=c(Esp,Spi$Nesp2)
}
}
}
}
ParSelFNlSpecies=data.frame(cbind(ParSel,Esp))
ParSelFNlSpecies$type="FNl"
ParSelShifts=rbind(ParSelFPSpecies,ParSelFNmSpecies)
ParSelShifts=rbind(ParSelShifts,ParSelFNlSpecies)
fwrite(ParSelShifts,paste0("ParSelShifts",Sys.Date(),".csv")
,sep=";")
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