In MovingUngulate/Part: Ungulate Parturition Modeling and Predicting

title: "Neonate Status Update" output: pdf_document: dev: png html_document: null word_document: null params: tabby: tabby vhist: vhist

\pdfminorversion=5 \pdfcompresslevel=9 \pdfobjcompresslevel=2

pdf.options(useDingbats = TRUE,compress=T)
library(knitr)
library(jpeg)


tabby<-readRDS(params$tabby)
  vhist<-read.csv(params$vhist,stringsAsFactors = F)
  vhist<-vhist[complete.cases(vhist$Serial),]
  vhist<-vhist[which(vhist$Species=='FMD'),]
      if(TRUE %in% (nchar(vhist$ActBD)>0)){
    vhist$ActBD<-as.POSIXct(paste0(vhist$ActBD,' 5'),'%m/%d/%Y %H',tz='MST')
      vhist<-vhist[is.na(vhist$ActBD),]
    }

This is an automated updated for neonate capture.\vspace{5mm}

\large\textbf {Report Date: r format(Sys.time(), '%d %B, %Y %H:%M')} \vspace{10mm}

\large\textbf {Birth Freqs}

tabby$Serial<-as.character(tabby$Serial)
tabby<-tabby[tabby$Serial %in% vhist$Serial,]
tabby$`Mom Freq`<-as.character(tabby$`Mom Freq`)
tabby$`VIT Freq`<-as.character(tabby$`VIT Freq`)

tabby$CurrentVitStatus<-ifelse(tabby$CurrentVitStatus=='Birth Not yet triggered','BNYT',
                               ifelse(tabby$CurrentVitStatus=='Birth-triggered by light and temperature','B_Sensor',
                     ifelse(tabby$CurrentVitStatus=='Birth triggered by light and temperature', 'B_Sensor',
                                           ifelse(tabby$CurrentVitStatus=='Birth triggered by temperature','B_Sensor',
                                                  ifelse(tabby$CurrentVitStatus=='Birth triggered by light','Birth_Sensor',ifelse(tabby$CurrentVitStatus=='Birth triggered by lack of comm','B_Comm',
                                                                                                                                  ifelse(tabby$CurrentVitStatus == 'No Status','No Status',tabby$CurrentVitStatus)))))))

if(!('AID' %in% names(tabby))){
tabl<-tabby[,c(1,2,3,4,5,6,9,13)]
colnames(tabl)<-c('Serial','MomFreq','#Fetus','VitFreq','SC','SC3Day','VitStat','Dist')
}
if('AID' %in% names(tabby)){
tabl<-tabby[,c(14,1,2,3,4,5,6,9,13)]
colnames(tabl)<-c('AID','Serial','MomFreq','#Fetus','VitFreq','SC','SC3Day','VitStat','Dist')
}
tabl<-tabl[order(tabl$MomFreq,decreasing=F),]



tabl1<-tabl[which(!(tabl$VitStat=='BNYT')),]
tabl1<-tabl1[which(!(tabl1$VitStat=='No Status')),]


kable(tabl1,format='markdown',row.names=F,align='c',digits=2,padding=0,caption='Birth Freqs')

\vspace{1mm}

\large\textbf {Birth Data}

if(!('AID' %in% names(tabby))){
tabl3<-tabby[,c(2,7,8,11,12,10,9)]
colnames(tabl3)<-c('MomFreq','E_East','E_North','M_East','M_North','LastDate','VitStat')
tabl3<-tabl3[order(tabl3$MomFreq,decreasing=F),]
tabl3<-tabl3[which(!(tabl3$VitStat=='BNYT')),]
tabl3<-tabl3[which(!(tabl3$VitStat=='No Status')),]

tabl3<-tabl3[,-7]
}

if('AID' %in% names(tabby)){
 tabl3<-tabby[,c(14,2,7,8,11,12,10,9)]
colnames(tabl3)<-c('AID','MomFreq','E_East','E_North','M_East','M_North','LastDate','VitStat')
tabl3<-tabl3[order(tabl3$AID,decreasing=F),] 
tabl3<-tabl3[which(!(tabl3$VitStat=='BNYT')),]
tabl3<-tabl3[which(!(tabl3$VitStat=='No Status')),]

tabl3<-tabl3[,-8]
}






tabl3$E_East<-floor(tabl3$E_East)
tabl3$E_North<-floor(tabl3$E_North)
tabl3$M_East<-floor(tabl3$M_East)
tabl3$M_North<-floor(tabl3$M_North)

kable(tabl3,format='markdown',row.names=F,align='c',digits=2,padding=0,caption='Birth Data')

\vspace{1mm}

\clearpage

\large\textbf {Non-Birth Freqs}

tabl2<-tabl[which(tabl$VitStat=='BNYT'|tabl$VitStat=='No Status'),]
kable(tabl2,format='markdown',row.names=F,align='c',digits=2,padding=0,caption='Non Birth Freqs')