Revision b7e3088e28025ac34513778ccb23368246fc532c authored by Victoria Sugrue on 18 June 2021, 08:47:24 UTC, committed by GitHub on 18 June 2021, 08:47:24 UTC
1 parent 65507f1
FigS6A_LambMass.R
library(ggplot2)
weight <- read.csv("/Users/victoriasugrue/Desktop/sheepweights.csv")
#this is a simplified version of file "YoungRamWetherInfo_DNAQuantEtc.csv" in long table format
summarySE <- function(data=NULL, measurevar, groupvars=NULL, na.rm=FALSE,
conf.interval=.95, .drop=TRUE) {
library(plyr)
# New version of length which can handle NA's: if na.rm==T, don't count them
length2 <- function (x, na.rm=FALSE) {
if (na.rm) sum(!is.na(x))
else length(x)
}
# This does the summary. For each group's data frame, return a vector with
# N, mean, and sd
datac <- ddply(data, groupvars, .drop=.drop,
.fun = function(xx, col) {
c(N = length2(xx[[col]], na.rm=na.rm),
mean = mean (xx[[col]], na.rm=na.rm),
sd = sd (xx[[col]], na.rm=na.rm)
)
},
measurevar
)
# Rename the "mean" column
datac <- rename(datac, c("mean" = measurevar))
datac$se <- datac$sd / sqrt(datac$N) # Calculate standard error of the mean
# Confidence interval multiplier for standard error
# Calculate t-statistic for confidence interval:
# e.g., if conf.interval is .95, use .975 (above/below), and use df=N-1
ciMult <- qt(conf.interval/2 + .5, datac$N-1)
datac$ci <- datac$se * ciMult
return(datac)
}
weightsummary <- summarySE(weight, measurevar="mass", groupvars="sex")
weightsummary
weightsummary2 <- weightsummary
weightsummary2$sex <- factor(weightsummary2$sex)
# Error bars represent standard error of the mean
ggplot(weightsummary2, aes(x=sex, y=mass, fill=sex)) +
geom_bar(position=position_dodge(), colour="black", stat="identity") +
geom_errorbar(aes(ymin=mass-se, ymax=mass+se),
width=.5, # Width of the error bars
position=position_dodge(.9)) +
theme_bw() +
ggtitle("Weights of young rams and wethers") +
ylab("Mass (kg)") +
xlab("Castration status") +
scale_fill_manual(values=c("#CCCCCC","#FFFFFF"))
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