Merge pull request #2 from Charlotte-Roemer/Sonotype

Sonotype

Sonotypes/AggContacts_Sonotype.R

@@ -327,7 +327,7 @@ while (nrow(ProbEsp)>0)
                ,Tstart=TDeb1$x,Tend=TFin1$x,NbCris=NbCris1$x
                ,DurMed=Dur50$x,Dur90=Dur90$x,Ampm50=Ampm50$x
                ,Ampm90=Ampm90$x,AmpSMd=AmpSMd$x,DiffME=DiffME,SR=SR
-               ,Ramp90=Ramp90$x, RAN90=RAN90$x
+               ,Ramp90=Ramp90$x
                ,Order=paste0("N",j))
 
   if(exists("IdTot")==T){IdTot=rbind(IdTot,IdTemp)}else{IdTot=IdTemp}
@@ -365,9 +365,9 @@ IdTot= IdTot[order(IdTot$Filename, IdTot$SpMaxF2), ]
 if(exists("r"))
 {
   fwrite(IdTot,paste0(PreFichPE,"IdTot.csv"))
-  fwrite(cbind(Filename=IdTot[,1],IdTot[,((ncol(IdTot)-20):ncol(IdTot))]),paste0(PreFichPE,"Idshort.csv"))
+  fwrite(cbind(Filename=IdTot[,1],IdTot[,((ncol(IdTot)-19):ncol(IdTot))]),paste0(PreFichPE,"Idshort.csv"))
 }else{
   fwrite(IdTot,paste0(tadir,"/IdTot.csv"))
-  fwrite(cbind(Filename=IdTot[,1],IdTot[,((ncol(IdTot)-20):ncol(IdTot))]),paste0(tadir,"/Idshort.csv"))
+  fwrite(cbind(Filename=IdTot[,1],IdTot[,((ncol(IdTot)-19):ncol(IdTot))]),paste0(tadir,"/Idshort.csv"))
 }
 

Sonotypes/README.txt

@@ -17,6 +17,11 @@ Release of the scripts and of the classifier (compilation date 11 December 2020)
 Tadarida-C is a set of scripts running under [R environment](https://www.r-project.org/). These scripts need the installation of two packages:
 -randomForest
 -data.table
+-plyr
+-dplyr
+-beepr
+-Hmisc
+-ggplot2
 If you use R in command line, you can run the “init.r” script provided on the Github repository (https://github.com/YvesBas/Tadarida-C) to install those two libraries.
 If asked, you should prefer to install those libraries in a “personal libraries” folder.
 

Sonotypes/VarSel_Sonotype.csv

@@ -0,0 +1,152 @@
+VarSel
+FileDur
+SampleRate
+StTime
+Dur
+PrevSt
+Fmin
+BW
+PosMP
+PrevMP1
+PrevMP2
+NextMP1
+NextMP2
+Amp1
+Amp2
+Amp3
+Amp4
+NoisePrev
+NoiseNext
+NoiseDown
+NoiseUp
+CVAmp
+CO2_FPkD
+CO2_TPk
+CM_Slope
+CS_Slope
+CN_Slope
+CO_Slope
+CO2_Slope
+CO2_ISlope
+CM_THCF
+CS_THCF
+CN_THCF
+CO_THCF
+CO2_THCF
+CM_FIF
+CS_FIF
+CN_FIF
+CM_UpSl
+CS_UpSl
+CN_UpSl
+CO_UpSl
+CO2_UpSl
+CM_LoSl
+CS_LoSl
+CN_LoSl
+CO_LoSl
+CO2_LoSl
+CM_StSl
+CS_StSl
+CN_StSl
+CO_StSl
+CO2_StSl
+CM_EnSl
+CS_EnSl
+CN_EnSl
+CO_EnSl
+CO2_EnSl
+CS_FPSl
+CN_FPSl
+CO_FPSl
+CM_FISl
+CO2_FISl
+CM_5dBBW
+CM_5dBDur
+CO2_5dBBW
+CO2_5dBDur
+Hup_RFMP
+Hup_AmpDif
+Hlo_PosEn
+Hlo_AmpDif
+Ramp_2_1
+Ramp_3_1
+Ramp_3_2
+Ramp_1_2
+Ramp_2_3
+RAN_2_1
+RAN_3_1
+RAN_3_2
+RAN_1_2
+RAN_4_3
+RAN_2_3
+HetX
+Dbl8
+Stab
+HeiET
+HeiEM
+HeiRT
+HeiRM
+HeiEMT
+HeiRTT
+HeiRMT
+Int25
+Int75
+RInt1
+SmIntDev
+LgIntDev
+VarInt
+VarSmInt
+VarLgInt
+RIntDev1
+EnStabSm
+EnStabLg
+HetYr
+HetCMC
+HetCMD
+HetCTC
+HetCTD
+HetCMfP
+HetCTfP
+HetPicsMALD
+HetPicsMABD
+HetPicsMRLBD
+HetPicsTABD
+HetPicsTRLBD
+VLDPPicsM
+VBDPPicsM
+VLDPPicsT
+VBDPPicsT
+CM_SDCR
+CS_SDCR
+CN_SDCR
+CO_SDCR
+CO2_SDCR
+CM_SDCRXY
+CS_SDCRXY
+CM_SDCL
+CM_SDCLOP
+CM_SDCLROP
+CM_SDCLRWB
+CM_SDCLRXYOPWB
+CM_SDCLR_DNP
+CS_SDCLOP
+CS_SDCLROP
+CS_SDCLRYOP
+CS_SDCLWB
+CS_SDCLR_DNP
+CS_SDCLRY_DNP
+CM_ELBPOS
+CS_ELBPOS
+CM_ELBSB
+CS_ELBSB
+CM_ELB2POS
+CS_ELB2POS
+CM_ELB2SB
+CS_ELB2SB
+CM_RAFE
+CM_RAFP3
+CM_SBMP
+CM_SAMP
+CM_SBAR
+FreqSup17