---
title: "Instar Duration and Time to Molt"
author: "Ben Jahnes"
date: "Mar. 16, 2018"
output:
  pdf_document: default
  html_notebook: default
---

```{r}
setwd("~/GFPa2Length")
GFPA2Summ<- read.csv("GFPA2Summ.csv", header =T)
GFPA2duration<- read.csv("GFPA2InstarDuration.csv", header =T)
GFPA2InDur<- read.csv("GFPA2InDur.csv", header =T)
InDur<- read.csv("InDurformat.csv",header=T)
Data=InDur

#################
#Data$Dur4<-as.numeric(Data$Dur4)
#Data$start.I1<-as.numeric(Data$start.I1)
Data$Indur<-as.factor(Data$Indur)
Data$molt<-as.factor(Data$molt)
Data$TrtDr <- factor(Data$TrtDr, levels=unique(Data$TrtDr))
Data$TrtMlt <- factor(Data$TrtMlt, levels=unique(Data$TrtMlt))
#################

library(PMCMR)
library(nlme)
library(car)
library(MASS)
library(RColorBrewer)
library(coin)
library(FSA)
library(plyr)
```


Wilcox Test
```{r}
#GFGT Instar Duration

TrtdrMW1<-wilcox.test(durval~TrtDr, data = Data[Data$Indur=="1",])
TrtdrMW2<-wilcox.test(durval~TrtDr, data = Data[Data$Indur=="2",])
TrtdrMW3<-wilcox.test(durval~TrtDr, data = Data[Data$Indur=="3",])
TrtdrMW4<-wilcox.test(durval~TrtDr, data = Data[Data$Indur=="4",])


TrtdrMW1
TrtdrMW2
TrtdrMW3
TrtdrMW4
```

```{r}

nins1<-count(Data$Treatment[Data$molt==1])
nins2<-count(Data$Treatment[Data$molt==2])
nins3<-count(Data$Treatment[Data$molt==3])
nins4<-count(Data$Treatment[Data$molt==4])
nbw<-rbind(nins1, nins2, nins3, nins4)
nbwvec <- nbw$freq

```



```{r}
par(mfrow=c(1,1),lwd=1.5)
N<-c("n=",nbwvec)
boxplot(durval~Treatment*Indur,data=Data, varwidth=F,outpch = NA, font.lab=2, ylab="Duration (days)", main="Instar Duration",
        xaxt="n",ylim=c(4,18.5), col = c("tomato","steelblue"))
#add points
stripchart(durval~Treatment*Indur, data = Data[Data$Treatment=="GF",],  
          vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="tomato", 
           add = TRUE)             
stripchart(durval~Treatment*Indur, data = Data[Data$Treatment=="GT",],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="Steelblue", 
           add = TRUE) 
axis(1, at=seq(.5,8.5, by=2), labels = FALSE, cex=1)
text(y=3.5,x= seq(1.5,8.5, by=2), par("usr")[3] - 0.2, labels = c("First", "Second", "Third","Fourth"), srt = 0, pos = 1, xpd = TRUE, cex=1)
legend("topleft", inset=.04, c("Germ Free", "Germ Typical"), fill=c("tomato","steelblue"),horiz=F,cex=1)
#text(1.1, 16.1, paste("Mann-Whitney Test
#GF1-GT1 p=", round(TrtdrMW1$p.value, 4), sep=""), cex=.7)
#text(1.1, 15.3, paste("GF2-GT2 p=", round(TrtdrMW2$p.value, 6), sep=""), cex=.7)
#text(1.1, 14.8, paste("GF3-GT3 p=", round(TrtdrMW3$p.value, 4), sep=""), cex=.7)
#text(1.1, 14.3, paste("GF4-GT4 p=", round(TrtdrMW4$p.value, 4), sep=""), cex=.7)
text(y=0,x= seq(0,8, by=1), paste(labels=N,sep=""), srt = 0, xpd = TRUE, cex=1, font=1)
title(xlab="Instar", line=1.5, cex.lab=1)
```

```{r}

TrtMltMW1.2<-wilcox.test(moltval~TrtMlt, data = Data[Data$Indur=="1",])
TrtMltMW2.2<-wilcox.test(moltval~TrtMlt, data = Data[Data$Indur=="2",])
TrtMltMW3.2<-wilcox.test(moltval~TrtMlt, data = Data[Data$Indur=="3",])
TrtMltMW4.2<-wilcox.test(moltval~TrtMlt, data = Data[Data$Indur=="4",])

TrtMltMW1.2
TrtMltMW2.2
TrtMltMW3.2
TrtMltMW4.2
```







```{r}
par(mfrow=c(1,1),lwd=1.5)
N<-c("n=",nbwvec)

boxplot(moltval~Treatment*molt,data=Data,ylab="Time (days)",outpch=NA, font.lab=2, main="Time to Molt",
        xaxt="n",ylim=c(2,48), col = c("tomato","steelblue"))
#add points
stripchart(moltval~Treatment*molt, data = Data[Data$Treatment=="GF",],  
          vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="tomato", 
           add = TRUE)             
stripchart(moltval~Treatment*molt, data = Data[Data$Treatment=="GT",],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="Steelblue", 
           add = TRUE) 

axis(1, at=seq(.5,8.5, by=2), labels = FALSE)
text(y=0,x= seq(1.5,8.2, by=2), par("usr")[3] - 0.2, labels = c("1st - 2nd", "2nd - 3rd", "3rd - 4th","4th  - 5th"), srt = 0, pos = 1, xpd = TRUE, cex=.9)
legend("topleft", inset=.04, c("Germ Free", "Germ Typical"), fill=c("tomato","steelblue"),horiz=F,cex=1)
text(y=-13,x= seq(0,8, by=1), paste(labels=N,sep=""), srt = 0, xpd = TRUE, cex=1, font=1)
title(xlab="Molting Event (instar - instar)", line=1.5, cex.lab=1, font=2)

#text(1.1, 40.3, paste("Mann-Whitney Test
#GF1-GT1 p=", round(TrtMltMW1$p.value, 4), sep=""), cex=.7)

#text(1.1, 37.8, paste("GF2-GT2 p=", round(TrtMltMW2$p.value, 3), sep=""), cex=.7)
#text(1.1, 36.3, paste("GF3-GT3 p=", round(TrtMltMW3$p.value, 3), sep=""), cex=.7)
#text(1.1, 34.8, paste("GF4-GT4 p=", round(TrtMltMW4$p.value, 4), sep=""), cex=.7)
#text(y=3,x= seq(1,8, by=1), paste(labels=N,sep=""), srt = 0, xpd = TRUE, cex=.8)

```


```{r}
par(mfrow=c(1,1),lwd=1.5)
N<-c("n=",nbwvec)

boxplot(moltval~Treatment*molt,data=Dat,ylab="Time (days)",outpch=NA, font.lab=2, main="Time to Molt",
        xaxt="n",ylim=c(2,48), col = c("tomato","steelblue"))
```