Added Beers Law lab and chem_scatter

.Rbuildignore

@@ -0,0 +1,2 @@
+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

@@ -0,0 +1,3 @@
+.Rproj.user
+.Rhistory
+.RData

DESCRIPTION

@@ -0,0 +1,21 @@
+Package: chemistr
+Title: Facilitates use of R functions and R Markdown files for Chemistry lab
+    reports
+Version: 0.0.0.9000
+Authors@R: person("Chester", "Ismay", email = "chester.ismay@gmail.com", role = c("aut", "cre"))
+Description: This package is designed to assist students with little to no
+    programming experience create reproducible analyses using R and R Markdown.
+    One goal is to reduce the sometimes large amount of arguments pass into
+    functions, while also allowing students to be able to customize as they
+    wish.  Another goal is to add error messages into R when, say, a percent
+    sign is used in a LaTeX table title to assist with debugging.
+Depends:
+    R (>= 3.2.0)
+Imports:
+    dplyr,
+    xtable,
+    ggplot2
+License: GPL-3
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 5.0.1

NAMESPACE

@@ -0,0 +1,4 @@
+# Generated by roxygen2: do not edit by hand
+
+export(Beers_Law)
+export(chem_scatter)

R/chem_lab.R

@@ -0,0 +1,25 @@
+#' Creates an R Markdown PDF document for the Beers Law Lab
+#'
+#' This is a function called in output in the YAML of the driver Rmd file to
+#' specify using a tweaked version of the default LaTeX pandoc template.
+#'
+#' @export
+#' @param fig_height A positive numeric giving the default height of images
+#' @param fig_width A positive numeric giving the default width of images
+#' @return A modified \code{pdf_document} based on slightly modified knitr
+#' LaTeX default file
+#' @examples
+#' \dontrun{
+#'  output:
+#'    chemistr::Beers_Law
+#' }
+Beers_Law <- function(fig_height = 2.5, fig_width = 5){
+  template <- find_resource("Beers_Law", "template.tex")
+
+    base <- rmarkdown::pdf_document(template = template,
+                                    fig_caption = TRUE,
+                                    fig_height = fig_height,
+                                    fig_width = fig_width,
+                                    keep_tex = TRUE)
+    base
+}

R/chem_scatter.R

@@ -0,0 +1,57 @@
+#' Creates a scatterplot with regression line
+#'
+#'
+#' @export
+#' @param data A data frame containing variables to be plotted
+#' @param xvar The name of the x-variable
+#' @param yvar The name of the y-variable
+#' @param xlab A string containing the x-axis label
+#' @param ylab A string containing the y-axis label
+#' @return A plot
+#' @examples
+#' \dontrun{
+#'  chem_scatter(iris, Sepal.Width, Sepal.Length)
+#' }
+
+chem_scatter <- function(data, xvar, yvar,
+  xlab = "Insert X-axis label",
+  ylab = "Insert Y-axis label",
+  gg = TRUE, intercept = FALSE){
+  data_gd <- NULL
+  data_gd$xvar <- tryCatch(
+    expr = lazyeval::lazy_eval(substitute(xvar), data = data),
+    error = function(e) eval(envir = data, expr = parse(text = xvar))
+  )
+  data_gd$yvar <- tryCatch(
+    expr = lazyeval::lazy_eval(substitute(yvar), data = data),
+    error = function(e) eval(envir = data, expr = parse(text = yvar))
+  )
+  if(gg == TRUE){
+ #   if(intercept == FALSE){
+      ggplot(data = as.data.frame(data_gd), mapping = aes(x = xvar, y = yvar)) +
+        geom_point() +
+        theme_bw() +
+        geom_smooth(method = "lm", se = FALSE, color = "black", size = 0.3,
+          formula = if(intercept == FALSE){y ~ x + 0} else{y ~ x}) +
+        labs(x = xlab, y = ylab)
+    #}
+  #   else{
+  #     ggplot(data = as.data.frame(data_gd), mapping = aes(x = xvar, y = yvar)) +
+  #       geom_point() +
+  #       theme_bw() +
+  #       geom_smooth(method = "lm", se = FALSE, color = "black", size = 0.3,
+  #         formula = y ~ x) +
+  #       labs(x = xlab, y = ylab)}
+   }
+  else{
+      plot(yvar ~ xvar + 0, data = data,
+        xlab = "Insert X-axis label",
+        ylab = "Insert Y-axis label",
+        pch = 20)
+      if(intercept == FALSE)
+        abline(lm(yvar ~ xvar + 0))
+      else
+        abline(lm(yvar ~ xvar))
+
+   }
+}

R/utils.R

@@ -0,0 +1,78 @@
+find_file <- function(template, file) {
+  template <- system.file("rmarkdown", "templates", template, "skeleton",
+    file,
+                          package = "chemistr")
+  if (template == "") {
+    stop("Couldn't find template file ", template, "/", file, call. = FALSE)
+  }
+
+  template
+}
+
+find_resource <- function(template, file) {
+  find_file(template, file.path("../resources", file))
+}
+
+knitr_fun <- function(name) utils::getFromNamespace(name, 'knitr')
+
+output_asis <- knitr_fun('output_asis')
+
+#' Render a pandoc template.
+#'
+#' This is a hacky way to access the pandoc templating engine.
+#'
+#' @param metadata A named list containing metadata to pass to template.
+#' @param template Path to a pandoc template.
+#' @param output Path to save output.
+#' @return (Invisibly) The path of the generate file.
+#' @examples
+#' x <- rticles:::template_pandoc(
+#'   list(preamble = "%abc", filename = "wickham"),
+#'   rticles:::find_resource("rjournal_article", "RJwrapper.tex"),
+#'   tempfile()
+#' )
+#' if (interactive()) file.show(x)
+#' @noRd
+template_pandoc <- function(metadata, template, output, verbose = FALSE) {
+  tmp <- tempfile(fileext = ".md")
+  on.exit(unlink(tmp))
+
+  cat("---\n", file = tmp)
+  cat(yaml::as.yaml(metadata), file = tmp, append = TRUE)
+  cat("---\n", file = tmp, append = TRUE)
+  cat("\n", file = tmp, append = TRUE)
+
+  rmarkdown::pandoc_convert(tmp, "markdown", output = output,
+                            options = paste0("--template=", template), verbose = verbose)
+
+  invisible(output)
+}
+
+
+# Call rmarkdown::pdf_document and mark the return value as inheriting pdf_document
+inherit_pdf_document <- function(...) {
+  fmt <- rmarkdown::pdf_document(...)
+  fmt$inherits <- "pdf_document"
+  fmt
+}
+
+# Helper function to create a custom format derived from pdf_document
+# that includes a custom LaTeX template and custom CSL definition
+pdf_document_format <- function(..., format, template, csl) {
+
+  # base format
+  fmt <- inherit_pdf_document(..., template = find_resource(format, template))
+
+  # add csl to pandoc_args
+  fmt$pandoc$args <- c(fmt$pandoc$args,
+                       "--csl",
+                       rmarkdown::pandoc_path_arg(find_resource(format, csl)))
+
+
+  # return format
+  fmt
+}
+
+
+
+

chemistr.Rproj

@@ -0,0 +1,21 @@
+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace