plottingVideo.Rmd

---
title: "Turtle Ant Video Data Analysis"
author: "Xingyao Chen"
date: "7/20/2017"
output: pdf_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
knitr::opts_chunk$set(cache  = TRUE)
```

Install/library in Packages and Load Data from GDrive
```{r}
setwd('../turtleAnt_dataAnalysis/')
library(ggplot2)
library(gsheet)
library(reshape2)
urls=c(
  #'https://docs.google.com/spreadsheets/d/1OCKoUgQ_A-do18Uc_ulIzoQ_P22nb8lim9wBlwROR4c/edit#gid=1849028624',
  'https://docs.google.com/spreadsheets/d/1OCKoUgQ_A-do18Uc_ulIzoQ_P22nb8lim9wBlwROR4c/edit#gid=0',
  'https://docs.google.com/spreadsheets/d/1OCKoUgQ_A-do18Uc_ulIzoQ_P22nb8lim9wBlwROR4c/edit#gid=433819656',
  'https://docs.google.com/spreadsheets/d/1OCKoUgQ_A-do18Uc_ulIzoQ_P22nb8lim9wBlwROR4c/edit#gid=1138436910')

colData=data.frame()
colonies=c('V1','V2','V3')
for(i in 1:length(urls)){
  coli=read.csv(text=gsheet2text(urls[i], format='csv'))[-1,1:14]
  coli$colony=colonies[i]
  print(names(coli))
  colData=rbind(colData,coli)
}
```


#Clean Up and Add Time Data
```{r}
colData=na.omit(colData)
colData$Posix=as.POSIXct(colData$Time , format = "%I:%M:%S")
colData$Enter.Box=as.numeric(as.character(colData$Enter.Box))
colData$Box=as.factor(colData$Box)
colData$colony=as.factor(colData$colony)
colData=na.omit(colData)
summary(colData)
colData$Enter.Nest=as.numeric(as.character(colData$Enter.Nest))
colData$Exit.Nest=as.numeric(as.character(colData$Exit.Nest))
```

#Plot # of Entries into Nest Over Time for Each Colony 
```{r}
#system('mkdir 7-17-17')
for(i in colonies){
  #png(paste0('7-17-17/enterNest_col',i,'png'))
p=ggplot(colData[c(colData$colony==i&colData$Nest!=colData$Nest[1]),], aes(y=Enter.Nest, x=Posix, fill=Nest, color=Nest))+
  #geom_bar(stat='identity')+
  geom_line(size=1.5)+
  labs(x='Time')+
  scale_colour_manual(values=c( 'dodgerblue2','deepskyblue1','dodgerblue4', 'firebrick3', 'firebrick1', 'firebrick4'))+
  theme(axis.title=element_text(size=14), legend.title=element_text(size=14),legend.text=element_text(size=12))+
  theme_classic()
plot(p)
#graphics.off()
}
```


#Add a Column for Which Section (R or D)
```{r}
r=c(2,3,5,6)
d=c(7,8,9,10,11,12)

for(i in 1:nrow(colData)){
  if(colData$Box[i]%in%r){
    colData$Section[i]='R'
  }
  else if(colData$Box[i]%in%d){
    colData$Section[i]='D'
  }
}
colData_sec=colData[!is.na(colData$Section),]

#Make new, shortened dataframe
colData_s=colData_sec[,c('Posix','Section','Enter.Box','Exit.Box','colony')]
#colData_s=colData_s[colData_s$Box!=colData_s$Box[1],]
colData_s$Enter.Box=as.numeric(as.character(colData_s$Enter.Box))
colData_s$Exit.Box=as.numeric(as.character(colData_s$Exit.Box))
colData_s$colony=as.factor(colData_s$colony)

colData_split=split(colData_s, colData_s$colony)
```

Add up the total number of entries and exits every 10 minutes
```{r}

cols=c('V1','V2','V3')
fullSum=data.frame()
for(i in 1:length(colData_split)){
sumdf=cbind(melt(acast(colData_split[[i]][,c(1,2,3)], Section~Posix, sum)),
            melt(acast(colData_split[[i]][,c(1,2,4)], Section~Posix, sum))$value)
sumdf$Colony=cols[i]
names(sumdf)=c('Section','Time','Exit','Enter','Colony')
fullSum=rbind(fullSum,sumdf)
}

fullSum=melt(fullSum, id.vars=c('Section','Colony','Time'))

fullSum$Time=as.POSIXct(fullSum$Time)
head(fullSum)
```

#Plot the results
```{r}
#png('finalPoster/activity_ct.png')
ggplot(fullSum,aes(y=value, x=Time, color=Section, group=Section))+
  geom_line(size=1.3)+
  geom_point()+
  facet_wrap(~Colony)+
  scale_color_manual(values=c('dodgerblue2','firebrick'),name=c('Section'))+
  theme(title=element_text(size=14, face='bold'),axis.title=element_text(size=13), 
        axis.text=element_text(size=12, angle=45, hjust=1),
        legend.title=element_text(size=13),legend.text=element_text(size=12))+
  labs(y='Ant Activity (# of entries and exits')+
  theme_classic()
#graphics.off()
##

```


#Plot Movment from O to R and O to D 
```{r}
colData=data.frame()
colonies=c(4,5,6)
for(i in 1:length(urls)){
  coli=read.csv(text=gsheet2text(urls[i], format='csv'))[-1,c(2,5,16:17)]
  coli$colony=colonies[i]
  print(names(coli))
  colData=rbind(colData,coli)
}

colDataOR=na.omit(colData[,-3])
colDataOD=na.omit(colData[,-4])

colData$Posix=as.POSIXct(colData$Time , format = "%I:%M:%S")

#colData$Enter.Box=as.numeric(as.character(colData$Enter.Box))
#colData$Box=as.factor(colData$Box)
colData$colony=as.factor(colData$colony)

dts=na.omit(melt(colData[,-c(1:2)], id.vars=c("Posix",'colony')))

ggplot(dts, aes(x=Posix,y=value, color=as.factor(variable)))+
  geom_point()+
  geom_line(size=1.3)+
  facet_wrap(~colony)+
  scale_color_manual(values=c('dodgerblue2','firebrick'),name=c('Section'))+
  theme(title=element_text(size=14, face='bold'),axis.title=element_text(size=13), legend.title=element_text(size=13),legend.text=element_text(size=12))+
  theme_classic()
```