First Commit

.Rbuildignore

+^.*\.Rproj$
+^\.Rproj\.user$
+^README\.Rmd$

.gitignore

+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

DESCRIPTION

+Package: JoeTools
+Type: Package
+Title: Loads Frequently Used Functions
+Version: 0.1.0
+Author: Joe Jalbert <joejalbert@gmail.com>
+Maintainer: Joe Jalbert <joejalbert@gmail.com>
+Description: Loads frequently used functions for data analysis and reporting.
+License: file LICENSE
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 7.0.2
+Imports:
+    lazyeval,
+    tidyverse,
+    xlsx
+    

JoeTools.Rproj

+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX

LICENSE

+Copyright 2020 Joseph Jalbert. All rights reserved.

NAMESPACE

+# Generated by roxygen2: do not edit by hand
+
+export(report)
+export(se)
+export(wbsave)
+import(lazyeval)
+import(tidyverse)
+import(xlsx)
+importFrom(stats,sd)

R/JoeToolFunctions.R

+#' Standard Error
+#'
+#' @param data The vector or dataset over which the standard error is calculated
+#'
+#' @return The calulated Standard Error
+#' @importFrom stats sd
+#' @export
+#'
+#' @examples
+#' x=c(10, 20, 30, 40, 50)
+#' se(x)
+se=function(data){
+  return(sd(data, na.rm=T)/sqrt(sum(!is.na(data))))
+}
+
+#' Flexible Workbook Creation Function
+#'
+#' @param df The dataframe to be saved
+#' @param filename Name of the file, including the xlsx extension
+#' @param sheetBy Option to create sheets based on the values in a particular column of the dataframe
+#' @param keepNames The function automatically renames the column names with \code{\link[stringr:case]{stringr::str_to_sentence()}}. Setting this to TRUE will leave your column names unaltered
+#'
+#' @return Creates a Excel workbook from the supplied dataframe
+#' @import tidyverse
+#' @import xlsx
+#' @import lazyeval
+#' @export
+#'
+#' @examples
+#' library(datasets)
+#' library(tidyverse)
+#' library(xlsx)
+#' data(iris)
+#' wbsave(iris, "Iris report.xlsx")
+#' wbsave(iris, "Iris report - by Species.xlsx", sheetBy="Species", keepNames=TRUE)
+wbsave=function(df,filename,sheetBy=NULL,keepNames=FALSE){
+  if(keepNames==FALSE) {names(df)=str_to_sentence(names(df))}
+  if(!is.null(sheetBy)) {sheetBy=str_to_sentence(sheetBy)}
+  wb=createWorkbook()
+  TABLE_COLNAMES_STYLE <- CellStyle(wb)+ Font(wb,  heightInPoints=11, color="#44546A", isBold=TRUE)+
+    Border(color = "#8EA9DB", position = "BOTTOM", pen="BORDER_THICK")
+  sheetAll=createSheet(wb,sheetName = "All")
+  wbdata=NULL
+  wbAll=NULL
+  if(!is.null(sheetBy)) {l=levels(as.factor(df[[sheetBy]]))}
+  if(!is.null(sheetBy)) {for (i in l){
+    filter_criteria <- interp(~y == x, .values=list(y = as.name(sheetBy), x = i))
+    wbdata=df%>%
+      filter_(filter_criteria)
+    wbAll[[i]]=wbdata
+    sheet=createSheet(wb,sheetName = i)
+    addDataFrame(wbdata,sheet, colnamesStyle = TABLE_COLNAMES_STYLE)
+    autoSizeColumn(sheet, colIndex = 1:ncol(df)+1)
+  }}
+  addDataFrame(df,sheetAll, colnamesStyle = TABLE_COLNAMES_STYLE)
+  autoSizeColumn(sheetAll, colIndex = 1:ncol(df)+1)
+  saveWorkbook(wb, filename)
+}
+
+#' Creates a Report with t-tests for a Vector of Outcomes
+#'
+#' @param df Dataframe to use for the report
+#' @param Measures A vector of string names for columns to take means for. Order will be used to make the report.
+#' @param Factor A binary factor which will be used for comparisons.  Must be 1 (Treatment) or 0 (No_Treatment)
+#' @param paired Options for running t-test.  "Yes" forces paired, t-tests, "No" assumes no pairing, and "Try" will try a paired t-test, and follow up with a unpaired t-test if it fails to run.
+#'
+#' @return
+#' @import tidyverse
+#' @export
+#'
+#'
+#' @examples
+
+report=function(df, Measures, Factor, paired=c("Yes", "No", "Try")){
+  output=df%>%
+    group_by(.data[[Factor]])%>%
+    summarise_at(vars(Measures), mean,na.rm=T)%>%
+    mutate(Levels =ifelse(.data[[Factor]]==1, "Treatment", "No_Treatment"))%>%
+    select(-.data[[Factor]])%>%
+    pivot_longer(cols=Outcomes, names_to = "Measure")%>%
+    pivot_wider(names_from = "Levels", values_from = "value")%>%
+    mutate(Diff=Treatment-No_Treatment)%>%
+    mutate(Measure=factor(.data$Measure,levels=Measures))%>%
+    arrange(Measure)
+
+
+  reportpvaluecount=0
+  for(i in Measures){
+    reportpvaluecount=reportpvaluecount+1
+    form=paste0(i, "~",Factor)
+    if(paired=="Yes"){p[reportpvaluecount]=as.numeric(try(t.test(formula=as.formula(form), data=df, paired=T)$p.value))}
+    else if (paired=="No"){p[reportpvaluecount]=as.numeric(try(t.test(formula=as.formula(form), data=df)$p.value))}
+    else {p[reportpvaluecount]=tryCatch(as.numeric(t.test(formula=as.formula(form), data=df, paired=T)$p.value), error=function(err)
+      p[reportpvaluecount]=as.numeric(try(t.test(formula=as.formula(form), data=df)$p.value)), finally = NA)}
+
+  }
+
+  output$p_value=p
+
+  output=output%>%
+    mutate(Signif=ifelse(p_value<.001, "***",ifelse(p_value<.01, "**",
+                                                    ifelse(p_value<.05, "*", ifelse(p_value<.1, ".", "")))))
+}

README.Rmd

+---
+output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "man/figures/README-",
+  out.width = "100%"
+)
+```
+
+# JoeTools
+
+Loads frequently used functions for data analysis and reporting.
+
+## Installation
+
+You can install the released version of JoeTools from [CRAN](https://CRAN.R-project.org) with:
+
+``` r
+install.packages("JoeTools")
+```
+
+## Example
+
+This is a basic example which shows you how to solve a common problem:
+
+```{r example}
+library(JoeTools)
+## basic example code
+```
+
+What is special about using `README.Rmd` instead of just `README.md`? You can include R chunks like so:
+
+```{r cars}
+summary(cars)
+```
+
+You'll still need to render `README.Rmd` regularly, to keep `README.md` up-to-date.
+
+You can also embed plots, for example:
+
+```{r pressure, echo = FALSE}
+plot(pressure)
+```
+
+In that case, don't forget to commit and push the resulting figure files, so they display on GitHub!

man/report.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/JoeToolFunctions.R
+\name{report}
+\alias{report}
+\title{Creates a Report with t-tests for a Vector of Outcomes}
+\usage{
+report(df, Measures, Factor, paired = c("Yes", "No", "Try"))
+}
+\arguments{
+\item{df}{Dataframe to use for the report}
+
+\item{Measures}{A vector of string names for columns to take means for. Order will be used to make the report.}
+
+\item{Factor}{A binary factor which will be used for comparisons.  Must be 1 (Treatment) or 0 (No_Treatment)}
+
+\item{paired}{Options for running t-test.  "Yes" forces paired, t-tests, "No" assumes no pairing, and "Try" will try a paired t-test, and follow up with a unpaired t-test if it fails to run.}
+}
+\value{
+
+}
+\description{
+Creates a Report with t-tests for a Vector of Outcomes
+}

man/se.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/JoeToolFunctions.R
+\name{se}
+\alias{se}
+\title{Standard Error}
+\usage{
+se(data)
+}
+\arguments{
+\item{data}{The vector or dataset over which the standard error is calculated}
+}
+\value{
+The calulated Standard Error
+}
+\description{
+Standard Error
+}
+\examples{
+x=c(10, 20, 30, 40, 50)
+se(x)
+}

man/wbsave.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/JoeToolFunctions.R
+\name{wbsave}
+\alias{wbsave}
+\title{Flexible Workbook Creation Function}
+\usage{
+wbsave(df, filename, sheetBy = NULL, keepNames = FALSE)
+}
+\arguments{
+\item{df}{The dataframe to be saved}
+
+\item{filename}{Name of the file, including the xlsx extension}
+
+\item{sheetBy}{Option to create sheets based on the values in a particular column of the dataframe}
+
+\item{keepNames}{The function automatically renames the column names with \code{\link[stringr:case]{stringr::str_to_sentence()}}. Setting this to TRUE will leave your column names unaltered}
+}
+\value{
+Creates a Excel workbook from the supplied dataframe
+}
+\description{
+Flexible Workbook Creation Function
+}
+\examples{
+library(datasets)
+library(tidyverse)
+library(xlsx)
+data(iris)
+wbsave(iris, "Iris report.xlsx")
+wbsave(iris, "Iris report - by Species.xlsx", sheetBy="Species", keepNames=TRUE)
+}