Boxplots for LCHF study

Repeated measures low carb high fat diet

Packages

Load the various packages.

# packages for analysis of repeated measures
library(nlme)
library(car)
# document definition and construction
library(knitr)
opts_knit$set(eval.after = "fig.cap")
library(rmarkdown)
#reading and writing files of various types (in this case, csv and text files)
library(readr)
# data manipulation
library(tidyr)
library(dplyr)
library(tibble)
# pipelining commands
library(magrittr)
# plots
library(ggplot2)

Prepare the data

obs <- read_csv("mep_observations.csv")

Parsed with column specification:
cols(
  Subject = col_integer(),
  TestNumber = col_integer(),
  MEPHR = col_double(),
  Weight = col_double(),
  MaxRelVO2 = col_double(),
  FatBIA = col_double(),
  FatSF = col_double(),
  Avgkcals = col_integer(),
  AvgFat = col_integer(),
  AvgCHO = col_integer(),
  AvgPro = col_integer()
)

#sort data by subject
obs <- obs[order(obs$Subject),]
# these models work with factors
obs$Subject <- as.factor(obs$Subject)
obs$TestNumber <- as.factor(obs$TestNumber)
obs <- as_tibble(obs)
obs$Week <- obs$TestNumber
levels(obs$Week) <- c("Baseline", "Week1", "Week2", "Week3")
obs

MEP HR

aboxplot <- ggplot(data=obs, aes(x=Week,y=MEPHR)) + 
  geom_boxplot() +
  ylim(120,200) +
  annotate(geom="text", label="*", x=2.01, y=182, size=6, family="serif") +
  labs(x="", y=expression("MEP Heart Rate"))
aboxplot

Weight

aboxplot <- ggplot(data=obs, aes(x=Week,y=Weight)) + 
  geom_boxplot() +
  ylim(115,180) + 
  annotate(geom="text", label="*", x=3, y=161, size=6, family="serif") +
  labs(x="", y=expression("Weight (lbs)"))
aboxplot

MaxRelVO2

aboxplot <- ggplot(data=obs, aes(x=Week,y=MaxRelVO2)) + 
  geom_boxplot() + 
  ylim(30,90) + 
  annotate(geom="text", label="*", x=4, y=73, size=6, family="serif") +
  labs(x="", y=bquote('Relative ' ~VO[2]~ 'Max'))
aboxplot

FatBIA

aboxplot <- ggplot(data=obs, aes(x=Week,y=FatBIA)) + 
  geom_boxplot() +
  ylim(25,70) + 
  annotate(geom="text", label="*", x=3, y=57, size=6, family="serif") +
  labs(x="", y="Fat (lbs)")
aboxplot