Dev - fit stats extraction

.Rbuildignore

@@ -9,5 +9,6 @@
 
 documentation_peek.pdf
 documentation_for_developers/
+libs/
 playgrounds/
 utility_scripts/

.gitignore

@@ -1,12 +1,17 @@
-# History files
+# History and RStudio files
 .Rhistory
 .Rapp.history
 .RData
-
-# RStudio files
 .Rproj.user
 .Rproj.user/
+
 # produced vignettes
 vignettes/*.html
 vignettes/*.pdf
 inst/doc
+
+# README htmls in any folder
+README.html
+
+# The devtools zip is downloaded when the package is updating itself.  If it's not deleted, there's no reason to commit it to the repository.
+devtools.zip

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: IalsaSynthesis
 Title: Synthesizing Information Across Collaborating Research
-Version: 0.0-1
-Date: 2015-04-29
+Version: 0.0-3
+Date: 2015-04-30
 Authors@R: c(person("Will", "Beasley", email="wibeasley@hotmail.com", role=c("aut", "cre")),
     person("Andrey", "Koval", email="andkov@uvic.ca", role = c("aut")),
     person(given="Integrative Analysis of Longitudinal Studies of Aging (IALSA)", role = c("cph")))
@@ -16,6 +16,7 @@ Depends:
     R(>= 3.0.0),
     stats
 Imports:
+    readr,
     testit
 Suggests:
     devtools,

NAMESPACE

@@ -1,3 +1,10 @@
 # Generated by roxygen2 (4.1.1): do not edit by hand
 
+export(extract_aic)
+export(extract_bic)
+export(extract_bic_adjusted)
+export(extract_free_parameter_count)
+export(extract_loglikelihood)
+export(extract_output_filename)
+export(extract_scaling_correction)
 export(validate_filename_output)

R/extract.R

@@ -0,0 +1,89 @@
+#' @name extract
+#' @aliases extract_output_filename extract_free_parameter_count extract_loglikelihood extract_scaling_correction extract_aic extract_bic extract_bic_adjusted
+#' @export extract_output_filename extract_free_parameter_count extract_loglikelihood extract_scaling_correction extract_aic extract_bic extract_bic_adjusted
+#' 
+#' @title Extract the values within model output files.
+#'  
+#' @description Functions that extract the values within model output files.
+#' 
+#' @param mplus_output Text containing model output.
+#' 
+#' @return A \code{numeric} value corresponding to the desired quantity.
+#' 
+#' @author Will Beasley
+#' 
+#' @examples
+#' library(IalsaSynthesis) #Load the package into the current R session.
+
+extract_output_filename <- function( mplus_output ) {
+  # gsub(pattern="DATA:  File = (.+);", replacement="\\1", mplus_output, perl=T)
+
+  matches <- regexpr(".+DATA:  File = (.+);.*", mplus_output, perl=TRUE);
+  result <- attr(matches, "capture.start")[,1]
+  attr(result, "match.length") <- attr(matches, "capture.length")[,1]
+  observed_snippet <- regmatches(mplus_output, result)
+
+  return( observed_snippet )
+}
+
+extract_free_parameter_count <- function( mplus_output ) {
+  matches <- regexpr("Number of Free Parameters\\s+(\\d{1,})\\s+", mplus_output, perl=TRUE);
+  result <- attr(matches, "capture.start")[,1]
+  attr(result, "match.length") <- attr(matches, "capture.length")[,1]
+  matched_string <- regmatches(mplus_output, result)
+  matched_float <- as.numeric(matched_string)
+
+  return( matched_float )
+}
+
+extract_loglikelihood <- function( mplus_output ) {
+  matches <- regexpr("Loglikelihood\\s+H0 Value\\s+([-\\d\\.]+)\\s+", mplus_output, perl=TRUE);
+  result <- attr(matches, "capture.start")[,1]
+  attr(result, "match.length") <- attr(matches, "capture.length")[,1]
+  matched_string <- regmatches(mplus_output, result)
+  matched_float <- as.numeric(matched_string)
+
+  return( matched_float )
+}
+
+extract_scaling_correction <- function( mplus_output ) {
+  matches <- regexpr("\\s+H0 Scaling Correction Factor\\s+([-\\d\\.]+)\\s+for MLR\\s+", mplus_output, perl=TRUE);
+  result <- attr(matches, "capture.start")[,1]
+  attr(result, "match.length") <- attr(matches, "capture.length")[,1]
+  matched_string <- regmatches(mplus_output, result)
+  matched_float <- ifelse(length(matched_string>0), as.numeric(matched_string), NA_real_)
+
+  return( matched_float )
+}
+
+extract_aic <- function( mplus_output ) {
+  matches <- regexpr("Akaike \\(AIC\\)\\s+([-\\d\\.]+)\\s+", mplus_output, perl=TRUE);
+  result <- attr(matches, "capture.start")[,1]
+  attr(result, "match.length") <- attr(matches, "capture.length")[,1]
+  matched_string <- regmatches(mplus_output, result)
+  matched_float <- as.numeric(matched_string)
+
+  return( matched_float )
+}
+
+extract_bic <- function( mplus_output ) {
+  matches <- regexpr("Bayesian \\(BIC\\)\\s+([-\\d\\.]+)\\s+", mplus_output, perl=TRUE);
+  result <- attr(matches, "capture.start")[,1]
+  attr(result, "match.length") <- attr(matches, "capture.length")[,1]
+  matched_string <- regmatches(mplus_output, result)
+  matched_float <- as.numeric(matched_string)
+
+  return( matched_float )
+}
+
+extract_bic_adjusted <- function( mplus_output ) {
+  # matches <- regexpr("\\s+Sample-Size Adjusted BIC\\s+(\\d+(\\.\\d+)?)\\s+", mplus_output, perl=TRUE);
+  # matches <- regexpr("\\s+Sample-Size Adjusted BIC\\s+(.+)\\s+", mplus_output, perl=TRUE);
+  matches <- regexpr("\\s+Sample-Size Adjusted BIC\\s+([-\\d\\.]+)\\s+", mplus_output, perl=TRUE);
+  result <- attr(matches, "capture.start")[,1]
+  attr(result, "match.length") <- attr(matches, "capture.length")[,1]
+  matched_string <- regmatches(mplus_output, result)
+  matched_float <- as.numeric(matched_string)
+
+  return( matched_float )
+}