second try at RProject structure

.gitignore

@@ -4,34 +4,25 @@
 
 # Session Data files
 .RData
-
 # Example code in package build process
 *-Ex.R
-
 # Output files from R CMD build
 /*.tar.gz
-
 # Output files from R CMD check
 /*.Rcheck/
-
 # RStudio files
 .Rproj.user/
-
 # produced vignettes
 vignettes/*.html
 vignettes/*.pdf
-
 # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
 .httr-oauth
-
 # knitr and R markdown default cache directories
 /*_cache/
 /cache/
-
 # Temporary files created by R markdown
 *.utf8.md
 *.knit.md
-
 # personal files to ignore
 setupScript.R
 .Rproj.user

RProject/.Rbuildignore

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

RProject/DESCRIPTION

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+Package: DSTools
+Title: What the Package Does (one line, title case)
+Version: 0.0.0.9000
+Authors@R: person("First", "Last", email = "[email protected]", role = c("aut", "cre"))
+Description: What the package does (one paragraph).
+Depends:
+    R (>= 3.2.5)
+License: What license is it under?
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 5.0.1

RProject/NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(ds.plot)

RProject/R/ds_plot.R

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+library(ggplot2)
+
+#' A Smooth Plot DataShop Learning Curves
+#'
+#' Creates a loess smoothed ggplot from a student step roll up output from Datashop.
+#'
+#' @param stu.step   A data.frame of a direct load of a student-step rollup file.
+#' @param model      The name of a KC model to use as it appears in DataShop
+#' @param kc         The name of a particular Kc to get individual kc curves or its number in the list of kcs
+#' @param title      A title for the plot
+#' @param axis.scale A scaling factor for the y axis of the plot.
+#' @keywords ds.plot
+#' @export
+ds.plot <- function(stu.step, model, kc="all", title=NULL,axis.scale=1){
+
+  mod.name <- paste0("KC (",model,")")
+  opp.name <- paste0("Opportunity (",model,")")
+  pred.name <- paste0("Predicted Error Rate (",model,")")
+
+  ds <- stu.step
+  ds$knowledge_component <- as.factor(ds[[mod.name]])
+  ds$opportunity <- ds[[opp.name]]
+  ds$afm.predict <- ds[[pred.name]]
+  ds$actual <- 1
+  ds$actual[ds[["First Attempt"]] == "correct"] <- 0
+
+  if (kc == "all" || kc < 1) {
+    opp <- ds$opportunity
+    y <- ds$actual
+    afm.std <- ds$afm.predict
+    kc.name = "all"
+  }
+  else {
+    kcs <- unique(unlist(Map(function(x) strsplit(toString(x), "~~"), ds$knowledge_component)))
+    if (class(kc) == "character"){
+      kc.name <- kc
+      kc <- match(kc,kcs)
+    }
+    else {
+      kc.name <- kcs[kc]
+    }
+    ds$kcid <- match(ds$knowledge_component, kcs)
+    opp <- ds$opportunity[ds$kcid == kc]
+    y <- ds$actual[ds$kcid == kc]
+    afm.std <- ds$afm.predict[ds$kcid == kc]
+  }
+  error <- c(y, afm.std)
+  label <- as.factor(c(rep("Actual", length(y)), rep("AFM", length(afm.std))))
+  plotData = data.frame(opp, error, label)
+
+  if(is.null(title)) {
+    if(kc.name == "all") {
+      title = model
+    }
+    else {
+      title = kc.name
+    }
+  }
+
+  plot <- ggplot() +
+    geom_smooth(data=plotData, aes(x=opp, y=error, group=label, color=label, fill=label)) +
+    coord_cartesian(ylim=c(0, 1)) +
+    labs(title=title) +
+    ylab("Error Rate") +
+    xlab("Opportunities") +
+    ggtitle(title) +
+    theme(
+      plot.title = element_text(size=rel(axis.scale)),
+      axis.text = element_text(size=rel(axis.scale)),
+      axis.title = element_text(size=rel(axis.scale)),
+      legend.position = "none"
+    )
+
+  return(plot)
+}
+
+
+#' Read in a DataShop Student-Step rollup file
+#'
+#' @param file.name The name of the file to read in.
+ds.read <- function(file.name) {
+  return(read.csv(file = file.name,sep="\t",check.names=F))
+}
+
+
+#' Save a ds.plot in a commonly useful png format.
+#'
+#' @param plot   The plot data
+#' @param name   The desired filename
+#' @param width  The width in inches (defaults to 3, which is recommended width for AcM/EDM format)
+#' @param height The height in inches (which I default to 2.5)
+#' @param dpi    The dpi to output at (defaults to 300)
+ds.save <- function(plot, name, width=3, height=2.5, dpi=300) {
+  ggsave(plot,name,width=width,height=height,dpi=300,units="in")
+}
+
+
+
+#' Return a list of the available KC models in a Student-Step file.
+#'
+#' @param stu.step A Student-Step export from datashop
+ds.models <- function(stu.step) {
+  x <- names(test.data)
+  m <- regexpr("KC (.*)",x,perl=TRUE)
+  mods <- regmatches(x,m)
+  return(unlist(lapply(mods, function(s) (substr(s,5,nchar(s)-1)))))
+}
+
+#' Return a list of the kcs within a partiuclar model.
+#' 
+#' @param stu.step A DataShop Student-Step export data.frame
+#' @param model    The name of a KC model within the dataset
+ds.kcs <- function(stu.step, model) {
+  mod.name <- paste0("KC (",model,")")
+  if(mod.name %in% names(stu.step)) {
+    ds <- stu.step
+    ds$knowledge_component <- as.factor(ds[[mod.name]])
+    return(unique(unlist(Map(function(x) strsplit(toString(x), "~~"), ds$knowledge_component))))
+  }
+  else {
+    warning(paste0('KC model "',model,'" not found in stu.step'))
+    return(list())
+  }
+}

RProject/RProject.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source