making stats-tools a "real" R package

.gitignore

@@ -0,0 +1,3 @@
+*.swo
+*.swp
+docs

.scripts/build_documentation.R

@@ -0,0 +1,3 @@
+library("devtools")
+
+devtools::document()

.scripts/build_documentation_html.R

@@ -0,0 +1,4 @@
+library(pkgdown)
+
+pkgdown::build_site()
+

.scripts/build_package.R

@@ -0,0 +1,3 @@
+library(devtools)
+
+devtools::build()

.scripts/check_package.R

@@ -0,0 +1,2 @@
+library(devtools)
+devtools::check()

.scripts/install_package.R

@@ -0,0 +1,2 @@
+library(devtools)
+devtools::install(upgrade=FALSE)

.scripts/test_package.R

@@ -0,0 +1,2 @@
+library(devtools)
+devtools::test()

.scripts/test_package_cov.R

@@ -0,0 +1,2 @@
+library(covr)
+report()

DESCRIPTION

@@ -0,0 +1,24 @@
+Package: statstool
+Title: An awesome R package with stats tolos
+Version: 0.0.0
+Author: Alex Paxton <alex.paxton@uconn.edu>
+Maintainer: Alex Paxton <alex.paxton@uconn.edu>
+Description: What the package does.
+Depends: R (>= 3.5)
+Imports: dplyr,
+	 pander,
+	 xtable,
+	 plyr
+Suggests: testthat (>= 1.0.0),
+	  knitr,
+	  rmarkdown,
+	  covr,
+	  shiny,
+	  DT,
+	  roxygen2,
+	  kableExtra
+VignetteBuilder: knitr
+License: MIT License + file LICENSE
+Encoding: UTF-8
+LazyData: false
+RoxygenNote: 6.1.1

Makefile

@@ -0,0 +1,25 @@
+RSCRIPT ?= Rscript
+
+
+all: doc-doxygen check build install test
+
+build:
+	$(RSCRIPT) .scripts/build_package.R
+
+install: doc-doxygen
+	$(RSCRIPT) .scripts/install_package.R
+
+
+check:
+	$(RSCRIPT) .scripts/check_package.R
+
+doc-doxygen:
+	$(RSCRIPT) .scripts/build_documentation.R
+
+doc-html: install
+	$(RSCRIPT) .scripts/build_documentation_html.R
+
+doc: doc-html
+
+test:
+	$(RSCRIPT) .scripts/test_package.R

NAMESPACE

@@ -0,0 +1,6 @@
+# Generated by roxygen2: do not edit by hand
+
+export(pander_anova)
+export(pander_lm)
+export(pander_lme_to_latex)
+export(xtable_lme)

pander_anova.r → R/pander_anova.R

@@ -1,21 +1,13 @@
+library(pander)
+library(plyr)
+
+#' Create a cleaner ANOVA model output with pander.
+#'
+#' @param anova_model_name ANOVA model. Model whose output will be cleaned.
+#' @return neat_output	pander table. Cleaned ANOVA model output.
+#' @export
 pander_anova = function(anova_model_name){
 
-  #'  Create a cleaner ANOVA model output with pander.
-  #'
-  #'  Parameters
-  #'  ----------
-  #'  anova_model_name : ANOVA model
-  #'     Model whose output will be cleaned.
-  #'
-  #'  Output
-  #'  ------
-  #'  neat_output : pander table
-  #'     Cleaned ANOVA model output.
-
-  # load in pander
-  require(pander)
-  require(plyr)
-
   # disable scientific notation
   options(scipen = 999)
 

pander_lm.R → R/pander_lm.R

@@ -1,20 +1,21 @@
+#'  Create a cleaner lm model output with pander.
+#'
+#'  Parameters
+#'  ----------
+#'  lm_model_name : lm model
+#'     Model whose output will be cleaned.
+#'
+#'  stats.caption : boolean, optional (default: FALSE)
+#'     Specify whether or not to provide the adjusted
+#'     R-squared and F-statistics in the table caption.
+#'
+#'  Output
+#'  ------
+#'  neat_output : table
+#'     Cleaned lm model output.
+#' @export
 pander_lm = function(lm_model_name, stats.caption=FALSE){
 
-  #'  Create a cleaner lm model output with pander.
-  #'
-  #'  Parameters
-  #'  ----------
-  #'  lm_model_name : lm model
-  #'     Model whose output will be cleaned.
-  #'
-  #'  stats.caption : boolean, optional (default: FALSE)
-  #'     Specify whether or not to provide the adjusted
-  #'     R-squared and F-statistics in the table caption.
-  #'
-  #'  Output
-  #'  ------
-  #'  neat_output : table
-  #'     Cleaned lm model output.
 
   # load in pander
   require(pander)

pander_lme.R → R/pander_lme.R

@@ -1,23 +1,23 @@
+#'  Create a cleaner lme4 model output with pander.
+#'
+#'  Parameters
+#'  ----------
+#'  lme_model_name : lme4 model
+#'     Model whose output will be cleaned.
+#'
+#'  stats.caption : boolean, optional (default: FALSE)
+#'     Specify whether or not to provide the marginal
+#'     (i.e., fixed effects only) and conditional (i.e.,
+#'     fixed and random effects) R-squared values in the
+#'     table's caption.
+#'
+#'  Output
+#'  ------
+#'  neat_output : pander table
+#'     Cleaned lme4 model output.
+#' export
 pander_lme = function(lme_model_name, stats.caption=FALSE){
 
-  #'  Create a cleaner lme4 model output with pander.
-  #'
-  #'  Parameters
-  #'  ----------
-  #'  lme_model_name : lme4 model
-  #'     Model whose output will be cleaned.
-  #'
-  #'  stats.caption : boolean, optional (default: FALSE)
-  #'     Specify whether or not to provide the marginal
-  #'     (i.e., fixed effects only) and conditional (i.e.,
-  #'     fixed and random effects) R-squared values in the
-  #'     table's caption.
-  #'
-  #'  Output
-  #'  ------
-  #'  neat_output : pander table
-  #'     Cleaned lme4 model output.
-
   # load in pander
   require(pander)
 

pander_lme_to_latex.r → R/pander_lme_to_latex.R

@@ -1,25 +1,25 @@
+#'  Export an LMER summary table to a LaTex file.
+#'
+#'  Note that this will retain the row index column,
+#'  which will be given a name`neat" in the table.
+#'  This will be need to be manually removed in the
+#'  final `.tex` file.
+#'
+#'  Parameters
+#'  ----------
+#'  lme_model_name : lme4 model
+#'     Model whose output will be cleaned.
+#'
+#'  save_filename : str
+#'     File name for saved LaTex model.
+#'
+#'  Output
+#'  ------
+#'  neat_output : pander table
+#'     Cleaned lme4 model output.
+#' @export
 pander_lme_to_latex = function(lme_model_name, save_filename){
 
-  #'  Export an LMER summary table to a LaTex file.
-  #'
-  #'  Note that this will retain the row index column,
-  #'  which will be given a name`neat" in the table.
-  #'  This will be need to be manually removed in the
-  #'  final `.tex` file.
-  #'
-  #'  Parameters
-  #'  ----------
-  #'  lme_model_name : lme4 model
-  #'     Model whose output will be cleaned.
-  #'
-  #'  save_filename : str
-  #'     File name for saved LaTex model.
-  #'
-  #'  Output
-  #'  ------
-  #'  neat_output : pander table
-  #'     Cleaned lme4 model output.
-
   # load in pander
   require(pander)
   require(Hmisc)

xtable_lme.r → R/xtable_lme.R

@@ -1,18 +1,17 @@
+#'  Create a cleaner lme4 model output for printing with xtable.
+#'
+#'  Parameters
+#'  ----------
+#'  lme_model_name : lme4 model
+#'     Model whose output will be cleaned.
+#'
+#'  Output
+#'  ------
+#'  neat_output : table
+#'     Cleaned lme4 model output.
+#' @export
 xtable_lme = function(lme_model_name){
 
-  #'  Create a cleaner lme4 model output for
-  #'  printing with xtable.
-  #'
-  #'  Parameters
-  #'  ----------
-  #'  lme_model_name : lme4 model
-  #'     Model whose output will be cleaned.
-  #'
-  #'  Output
-  #'  ------
-  #'  neat_output : table
-  #'     Cleaned lme4 model output.
-
   # load in pander
   library(pander)
   library(dplyr)

man/README

@@ -0,0 +1 @@
+This folder is automatically generated. DO NOT EDIT MANUALLY.