#### CD1 Gestational PFOA/GenX Maternal and litter outcomes summary and statistics #### BEB 12202018 ### library(reshape) library(tidyr) library(dplyr) library(multcomp) setwd("C:/Users/blakebe/Documents/CD1 PFOA GenX/R CSV files") datapoints<-read.csv("Combined necropsy data E11.5 and E17.5_updated.csv") names(datapoints) df.preg<-datapoints%>% filter(pregnant=="Yes") names(df.preg) df.drop<-df.preg[ , -which(names(df.preg) %in% c("block","breeding.group","dam.id","chem","dose","d.wt.11","d.wt.p.11", "d.wt.17","d.wt.pt.17","pregnant"))] names(df.drop) summary.stats<-df.drop%>% group_by(timepoint,group)%>%summarise_all(funs(mean,sd),na.rm=TRUE) summary.stats df.drop %>% group_by(timepoint,group) %>% summarise(n()) na.omit(df.drop) %>% group_by(timepoint,group) %>% summarise(n()) write.csv(summary.stats, "Maternal and litter necropsy data summary statistics mean SD_updated.csv",row.names = F) e11<-subset(df.drop, timepoint=="E11.5") summary(glht(aov(liv~group, data=e11), linfct=mcp(group="Tukey"))) summary(glht(aov(liv.p.wt~group, data=e11), linfct=mcp(group="Tukey"))) summary(glht(aov(d.wt.0~group, data=e11), linfct=mcp(group="Tukey"))) summary(glht(aov(implant.n~group, data=e11), linfct=mcp(group="Tukey"))) summary(glht(aov(litter.n~group, data=e11), linfct=mcp(group="Tukey"))) summary(glht(aov(resorp.n~group, data=e11), linfct=mcp(group="Tukey"))) summary(glht(aov(nonvia~group, data=e11), linfct=mcp(group="Tukey"))) summary(glht(aov(viable~group, data=e11), linfct=mcp(group="Tukey"))) summary(glht(aov(p.resorb~group, data=e11), linfct=mcp(group="Tukey"))) summary(glht(aov(p.nonviable~group, data=e11), linfct=mcp(group="Tukey"))) summary(glht(aov(p.viable~group, data=e11), linfct=mcp(group="Tukey"))) summary(glht(aov(kid~group, data=e11), linfct=mcp(group="Tukey"))) summary(glht(aov(kid.p.wt~group, data=e11), linfct=mcp(group="Tukey"))) e17<-subset(df.drop, timepoint=="E17.5") summary(glht(aov(liv~group, data=e17), linfct=mcp(group="Tukey"))) summary(glht(aov(liv.p.wt~group, data=e17), linfct=mcp(group="Tukey"))) summary(glht(aov(d.wt.0~group, data=e17), linfct=mcp(group="Tukey"))) summary(glht(aov(implant.n~group, data=e17), linfct=mcp(group="Tukey"))) summary(glht(aov(resorp.n~group, data=e17), linfct=mcp(group="Tukey"))) summary(glht(aov(nonvia~group, data=e17), linfct=mcp(group="Tukey"))) summary(glht(aov(viable~group, data=e17), linfct=mcp(group="Tukey"))) summary(glht(aov(p.resorb~group, data=e17), linfct=mcp(group="Tukey"))) summary(glht(aov(p.nonviable~group, data=e17), linfct=mcp(group="Tukey"))) summary(glht(aov(p.viable~group, data=e17), linfct=mcp(group="Tukey"))) summary(glht(aov(kid~group, data=e17), linfct=mcp(group="Tukey"))) summary(glht(aov(kid.p.wt~group, data=e17), linfct=mcp(group="Tukey")))