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FS17 Temp Data.R
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FS17 Temp Data.R
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# setwd("~/Documents/FS Studies/FS17/FS17 Obj2 Temp Data/")
library(tidyverse) ##tidyverse contains ggplot2, dplyr, tidr, readr
Temp <- read.csv(file = "./data/FS17 Obj2 Temp Data.csv", header = T, stringsAsFactors = F)
head(Temp)
Temp %>% ## shows temperature by dpi for each trt group individually
ggplot(aes(x=dpi,y=TempC)) +
geom_boxplot(aes(group = dpi, color = Trt)) +
theme(axis.text.x=element_text(angle = -45, hjust =0)) +
facet_wrap( ~ Trt)
Temp %>% filter(Trt == "inBCG-Ch") %>% ##looks at individual pigs by treatment groups
ggplot(aes(x=dpi, y=TempC)) +
geom_line(aes(group = pig, color = pig))
## need function to calculate standard error for each treatment group by day post infection (dpi)
## something like... sem <- sd(x)/sqrt(length(x))
## and then use it in the code below and switch out sd for sem in geom_errorbar
# you were so close!
Mean <- Temp %>%
group_by(Trt, dpi) %>%
summarize(mean=mean(TempC), sd=sd(TempC), n=length(TempC)) %>%
ggplot(aes(x=dpi, y=mean)) +
geom_line(aes(group = Trt, color = Trt)) +
geom_errorbar(aes(ymin=mean-sd, ymax=mean+sd, color=Trt))
# try this
Temp %>%
group_by(Trt, dpi) %>%
summarize(mean=mean(TempC),
sd=sd(TempC),
n=n(), # n() is a shortcut to count the number of obs in your grouping
se=sd/sqrt(n)) %>%
ggplot(aes(x=dpi, y=mean)) +
geom_line(aes(group = Trt, color = Trt)) +
geom_errorbar(aes(ymin=mean-se, ymax=mean+se, color=Trt))
# to make it look a little nicer...
Temp %>%
group_by(Trt, dpi) %>%
summarize(mean=mean(TempC),
sd=sd(TempC),
n=n(),
se=sd/sqrt(n)) %>%
ggplot(aes(x=dpi, y=mean)) +
geom_line(aes(group = Trt, color = Trt)) +
geom_errorbar(aes(ymin=mean-se,ymax=mean+se,color=Trt),width=.2) +
theme_bw()
Temp %>%
group_by(Trt, dpi) %>%
summarize(mean=mean(TempC),
sd=sd(TempC),
n=n(),
se=sd/sqrt(n)) %>%
ggplot(aes(x=dpi, y=mean)) +
geom_line(aes(group = Trt, color = Trt)) +
geom_errorbar(aes(ymin=mean-se,ymax=mean+se,color=Trt),width=.2) +
theme_bw()