##Statistical analysis PFOA/GenX

library(coda)
library(reshape)
library(coefplot2)
library(ggplot2)
library(dplyr)
library(data.table)
library(lme4)
library(lmtest)
library(nlme)

getwd()
setwd("C:/Users/blakebe/Documents/CD1 PFOA GenX/R CSV files")
df<-read.csv("Combined maternal and fetal data E11 and E17 with Elmore data points BEB 10192018.csv")

#Convert to lowercase col headers
names(df)<-tolower(names(df))
names(df)
#df$dam.id<-as.factor(df$dam.id)
str(df)


pf<-read.csv("Fetal placental data E11 and E17 R format BEB updated on 08262019.csv")
#pf$dam.id<-as.factor(pf$dam.id)
names(pf)
str(pf)

fet.length<-dplyr::select(pf, timepoint, block, dam.id, obs, fet.l)

mat.pf<-merge(df,fet.length, by=c("timepoint","block","dam.id","obs"))

n.obs.summary<-mat.pf%>%
  dplyr::group_by(timepoint, group)%>%
  dplyr::summarise(n.dams=length(unique(dam.id)),
            n.obs=length(fet.l),
            obs.litter=mean(n.obs/n.dams))
n.obs.summary

pf.11<-subset(mat.pf, timepoint=="E11.5")
pf.17<-subset(mat.pf, timepoint=="E17.5")



####Embryo length analysis

##E11 first
hist(pf.11$fet.wt)
hist(pf.11$pl.wt)
hist(pf.11$fp.rat)
hist(pf.11$fet.l)

##Fetal length marginally sig differ among groups at E11.5
m0<-lmer(fet.l~litter.n+(1|dam.id),data=pf.11, REML=F)
m1<-lmer(fet.l~group+litter.n+(1|dam.id),data=pf.11,REML=F)
anova(m0,m1)
## Group not significantly associated with fetal length

f.11<-coefplot2(m1, main="E11.5 Fetus Length (mm)\n")

summary(m1)
confint(m1)

##Fetal length marginally sig differ among groups at E17.5
m1<-lmer(fet.l~group+litter.n+(1|dam.id),data=pf.17,REML=F)
m0<-lmer(fet.l~litter.n+(1|dam.id),data=pf.17,REML=F)
anova(m0,m1)

##Group is significantly associated with embryo length

summary(m1)
confint(m1)


f.17<-coefplot2(m1, main="E17.5 Fetus Length (mm)\n")