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teaching_reproducible_science_R

Introduction

Material and notes for teaching reproducible science in R.

Installation

Install R

https://www.r-project.org/
and R Studio

https://www.rstudio.com/products/rstudio/download/preview/

Install the following packages in R:

install.packages('rmarkdown')
install.packages('knitr')
install.packages('tinytex')
install.packages('sqldf')
install.packages('ggplot2')
install.packages('gplots')
install.packages('lme4')
install.packages('lmerTest')
install.packages('pROC')
install.packages('precrec')
install.packages('PRROC')
install.packages('boot')
install.packages('mlbench')
install.packages('caret')

Download a zip file of this repository and unzip it

or

clone it

git clone https://github.com/neelsoumya/teaching_reproducible_science_R

cd teaching_reproducible_science_R

Go to this new directory and set working directory to this directory in R.

setwd('~/teaching_reproducible_science_R')

In R studio, run the markdown

rmarkdown.rmd

https://github.com/neelsoumya/teaching_reproducible_science_R/blob/main/rmarkdown.rmd

Code and lecture notes

Your data, your model decisions, parameters and your data filtering decisions will keep on changing. How do you know 6 months later what has changed? Document your code and your output and your design decisions all in one place.
Reproducible pipeline
Know exactly what changed and when
Know how to rerun the analysis and get the (same) results
This is like your research notebook
Some experiences/case studies of using Rmarkdown notebooks and helping biologists use them to analyze their own data
A typical header of a R markdown file will look like

---

title: "Analysis and Writeup"

header-includes:

- \usepackage{placeins}

- \usepackage{float}

- \floatplacement{figure}{H}

output:

  pdf_document:

    fig_caption: yes

    keep_tex: yes

    latex_engine: xelatex

    number_sections: yes

  word_document: default

  html_document:

    df_print: paged

bibliography: Periphery_project.bib

urlcolor: blue

---

```{r include=FALSE}

knitr::opts_chunk$set(echo = TRUE)

knitr::opts_chunk$set(cache = TRUE)

knitr::opts_chunk$set(warning = FALSE)

knitr::opts_chunk$set(out.extra = '')

#knitr::opts_chunk$set(fig.pos = 'H')

\begin{centering}

\vspace{3 cm}

\Large

\normalsize

Soumya Banerjee, r format(Sys.time(), "%b %d %Y")

\vspace{3 cm}

\end{centering}

\setcounter{tocdepth}{2}

\tableofcontents

\newpage


library(knitr)

library(gridExtra)

library(rmarkdown)

# EQUATIONS in rmarkdown

$$ eGFR = eGFR_{0} + b_{before}*t_{before} $$

Italics in rmarkdown using metafor

Code can be rendered or shown in rmarkdown using


dsBaseClient::ds.summary(x='surv_object')


# Load packages and settings

library(sqldf)

library(ggplot2)

library(knitr)

library(rmarkdown)

library(gplots)

library(RColorBrewer)

library(reshape2)

library(png)

library(grid)

library(gridExtra)

library(lme4)

library(lmerTest)

library(rpart)