Version 1.0.5

.Rd2pdf860/Rd2.tex

@@ -0,0 +1,13 @@
+\nonstopmode{}
+\documentclass[a4paper]{book}
+\usepackage[times,inconsolata,hyper]{Rd}
+\usepackage{makeidx}
+\usepackage[utf8]{inputenc} % @SET ENCODING@
+% \usepackage{graphicx} % @USE GRAPHICX@
+\makeindex{}
+\begin{document}
+\chapter*{}
+\begin{center}
+{\textbf{\huge \R{} documentation}} \par\bigskip{{\Large of \file{C:/Users/Usuario/OneDrive - Universidad Pontificia Comillas/Programación/GitHub/cdmTools} etc.}}
+\par\bigskip{\large \today}
+\end{center}

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 1.0.3
-Date: 2023-03-30 13:39:41 UTC
-SHA: b91779562fc4a44ee56fa282d810ecd52b095e5a
+Version: 1.0.4
+Date: 2023-11-14 14:30:10 UTC
+SHA: ce3c3f87fc179f26bec0810d9a5ada0b58fec136

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: cdmTools
 Type: Package
 Title: Useful Tools for Cognitive Diagnosis Modeling
-Version: 1.0.4
-Date: 2023-11-14
+Version: 1.0.5
+Date: 2024-01-03
 Authors@R: c(person(given = "Pablo", family = "Nájera", role = c("aut", "cre", "cph"), email = "[email protected]"), person(given = "Miguel A.", family = "Sorrel", role = c("aut", "cph"), email = "[email protected]"), person(given = "Francisco J.", family = "Abad", role = c("aut", "cph")), person(given = "Rodrigo S.", family = "Kreitchmann", role = c("ctb")), person(given = "Kevin", family = "Santos", role = c("ctb")))
 Description: Provides useful tools for cognitive diagnosis modeling (CDM). The package includes functions for empirical Q-matrix estimation and validation, such as the Hull method (Nájera, Sorrel, de la Torre, & Abad, 2021, <doi:10.1111/bmsp.12228>) and the discrete factor loading method (Wang, Song, & Ding, 2018, <doi:10.1007/978-3-319-77249-3_29>). It also contains dimensionality assessment procedures for CDM, including parallel analysis and automated fit comparison as explored in Nájera, Abad, and Sorrel (2021, <doi:10.3389/fpsyg.2021.614470>). Other relevant methods and features for CDM applications, such as the restricted DINA model (Nájera et al., 2023; <doi:10.3102/10769986231158829>), the general nonparametric classification method (Chiu et al., 2018; <doi:10.1007/s11336-017-9595-4>), and corrected estimation of the classification accuracy via multiple imputation (Kreitchmann et al., 2022; <doi:10.3758/s13428-022-01967-5>) are also available. Lastly, the package provides some useful functions for CDM simulation studies, such as random Q-matrix generation and detection of complete/identified Q-matrices.
 License: GPL-3

NAMESPACE

@@ -13,6 +13,7 @@ S3method(print,valQ)
 export(CA.MI)
 export(GNPC)
 export(RDINA)
+export(RDINA2GDINA)
 export(estQ)
 export(genQ)
 export(is.Qid)

NEWS.md

@@ -1,3 +1,8 @@
+# cdmTools 1.0.5
+* Added - `RDINA2GDINA` function to increase compatibility with the `GDINA` package
+* Changed - `CA.MI` and `personFit` have been updated to be compatible with `RDINA` objects
+* Kevin Santos is included as a contributor
+
 # cdmTools 1.0.4
 * Changed - `is.Qid` has been updated to include new identifiability criteria
 * Added - `personfit` function to identify aberrant response patterns
@@ -8,7 +13,7 @@
 
 # cdmTools 1.0.2
 * Added - `CA.MI` function to calculate corrected classification accuracy with multiple imputation
-* Added - Rodrigo S. Kreitchmann as a contributor
+* Rodrigo S. Kreitchmann is included as a contributor
 
 # cdmTools 1.0.1
 * Added - `GNPC` function to estimate attribute profiles

R/CA.MI.R

@@ -4,7 +4,7 @@
 #' The classification accuracy indices are the ones developed by Iaconangelo (2017) and Wang et al. (2015).
 #' It is only applicable to dichotomous attributes. The function is built upon the \code{CA} function from the \code{GDINA} package (Ma & de la Torre, 2020).
 #'
-#' @param fit A G-DINA model fit object from the \code{GDINA} package (Ma & de la Torre, 2020).
+#' @param fit An object of class \code{RDINA} or \code{GDINA} (Ma & de la Torre, 2020).
 #' @param what What attribute estimates are used? The default is \code{"EAP"}.
 #' @param R Number of bootstrap samples and imputations. The default is 500.
 #' @param n.cores Number of processors to use to speed up multiple imputation. The default is 2.
@@ -19,7 +19,7 @@
 #' \item{\code{CCM}}{Conditional classification matrix, see Iaconangelo (2017, p. 13) (\code{matrix}).}
 #' }
 #'
-#' @author {Rodrigo S. Kreitchmann, Universidad Pontificia Comillas}
+#' @author {Rodrigo S. Kreitchmann, Universidad Nacional de Educación a Distancia}
 #'
 #' @references
 #' Iaconangelo, C.(2017). \emph{Uses of classification error probabilities in the three-step approach to estimating cognitive diagnosis models}. (Unpublished doctoral dissertation). New Brunswick, NJ: Rutgers University.
@@ -43,10 +43,10 @@
 #' ca.mi <- CA.MI(fit)
 #' ca.mi
 #' }
-
 CA.MI <- function(fit, what = "EAP", R = 500, n.cores = 1, verbose = TRUE, seed = NULL){
 
-  if(!inherits(fit, "GDINA")){stop("Error in CA.MI: fit must be of class 'GDINA'.")}
+  if(inherits(fit, "RDINA")){fit <- RDINA2GDINA(fit)}
+  if(!inherits(fit, "GDINA")){stop("Error in CA.MI: fit must be of class 'RDINA' or 'GDINA'.")}
   if(!what %in% c("EAP", "MAP", "MLE")){stop("Error in CA.MI: what must be either 'EAP', 'MAP', or 'MLE'.")}
   if(any(apply(fit$options$dat, 2, stats::sd, na.rm = TRUE) == 0)){stop("Error in CA.MI: The data must not contain constant responses for an item.")}
   if((!is.numeric(R) & !is.double(R)) | length(R) > 1){stop("Error in CA.MI: R must be a unique numeric value.")}

R/RDINA2GDINA.R

@@ -0,0 +1,53 @@
+#' Translate RDINA object into GDINA object
+#'
+#' @description This function translates an object of class \code{RDINA} to an object of class \code{GDINA}, so that the estimated R-DINA object is compatible with most of the functions in the \code{GDINA} package (Ma & de la Torre, 2020), including model fit, item fit, and Q-matrix validation.
+#'
+#' @param fit An object of class \code{RDINA}.
+#'
+#' @return \code{RDINA2GDINA} returns an object of class \code{GDINA}. See the \code{GDINA} package for more information.
+#'
+#' @author {Pablo Nájera, Universidad Pontificia Comillas}
+#'
+#' @references
+#' Ma, W., & de la Torre, J. (2020). GDINA: An R package for cognitive diagnosis modeling. \emph{Journal of Statistical Software}, \emph{93}(14). https://doi.org/10.18637/jss.v093.i14
+#'
+#' @export
+#'
+#' @examples
+#' \donttest{
+#' library(GDINA)
+#' dat <- sim30DINA$simdat
+#' Q <- sim30DINA$simQ
+#' fit1 <- RDINA(dat, Q)
+#' fit2 <- RDINA2GDINA(fit1)
+#' modelfit(fit2) # Model fit evaluation
+#' itemfit(fit2) # Item fit evaluation
+#' }
+RDINA2GDINA <- function(fit){
+  if(!inherits(fit, "RDINA")){stop("Error in RDINA2GDINA: fit must be of class 'RDINA'.")}
+  dat <- fit$specifications$dat
+  Q <- fit$specifications$Q
+  N <- nrow(dat)
+  J <- nrow(Q)
+  K <- ncol(Q)
+  L <- 2^K
+  phi <- fit$phi
+  catprob.parm <- list()
+  for(j in 1:J){
+    lj <- 2^sum(Q[j,])
+    if(fit$specifications$gate == "AND"){
+      catprob.parm[[j]] <- c(rep(phi, lj - 1), 1 - phi)
+    } else {
+      catprob.parm[[j]] <- c(phi, rep(1 - phi, lj - 1))
+    }
+  }
+  model <- ifelse(fit$specifications$gate == "AND", "DINA", "DINO")
+  res <- GDINA::GDINA(dat, Q, model = model, catprob.parm = catprob.parm, control = list(maxitr = 0), verbose = 0)
+  res$struc.parm <- as.numeric(fit$post.probs$lp)
+  res$testfit[3] <- 1
+  res$testfit[-3] <- fit$test.fit
+  res$technicals$free.item.npar <- 1
+  res$technicals$total.npar <- L
+  res$extra$call <- "RDINA"
+  return(res)
+}

R/personFit.R

@@ -2,7 +2,7 @@
 #'
 #' @description This function calculates the standardized log-likelihood statistic (lZ; Cui & Li, 2015; Drasgow et al. 1985) and the proposals for correcting its distribution discussed in Santos et al. (2019).
 #'
-#' @param fit A G-DINA model fit object from the \code{GDINA} package (Ma & de la Torre, 2020).
+#' @param fit An object of class \code{RDINA} or \code{GDINA} (Ma & de la Torre, 2020).
 #' @param att.est What attribute estimates are used? The default is \code{"MLE"}.
 #' @param sig.level Scalar numeric. Alpha level for decision. Default is 0.05.
 #' @param p.adjust.method Scalar character. Correction method for p-values. Possible values include "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", and "none". See p.adjust function from the stats R package for additional details. Default is BH.
@@ -36,8 +36,9 @@
 #' res.personFit <- personFit(fit)
 #' res.personFit
 #' }
-
 personFit <- function(fit, att.est = "MLE", sig.level = 0.05, p.adjust.method = "BH"){
+  if(inherits(fit, "RDINA")){fit <- RDINA2GDINA(fit)}
+  if(!inherits(fit, "GDINA")){stop("Error in personFit: fit must be of class 'RDINA' or 'GDINA'.")}
   dat <- fit$options$dat
   Q <- fit$options$Q
   N <- nrow(dat)

README.md

@@ -5,7 +5,7 @@
 [![](http://cranlogs.r-pkg.org/badges/grand-total/cdmTools?color=blue)](https://cran.r-project.org/package=cdmTools)
 
 ## How to cite this package
-Nájera, P., Sorrel, M. A., & Abad, F. J. (2023). *cdmTools: Useful Tools for Cognitive Diagnosis Modeling*. R package version 1.0.4. https://cran.r-project.org/web/packages/cdmTools/.
+Nájera, P., Sorrel, M. A., & Abad, F. J. (2024). *cdmTools: Useful Tools for Cognitive Diagnosis Modeling*. R package version 1.0.5. https://cran.r-project.org/web/packages/cdmTools/.
 ## Features of the package
 * Empirical Q-matrix estimation and validation
 * Empirical dimensionality assessment of CDM data

cran-comments.md

@@ -1,3 +1,28 @@
+## cdmTools_1.0.5 (January 03, 2024)
+
+#### News & Comments
+* We have added the RDINA2GDINA function
+* We have slightly modified the CA.MI and personFit functions
+* We have listed Kevin Santos as a contributor
+
+#### Test envirnoments
+* Local Windows 10 x64, R 4.1.2
+* Ubuntu Linux 16.04 LTS, R-release, GCC (check_rhub)
+* Windows Server 2008 R2 SP1, R-devel, 32/64 bit (check_rhub)
+* Fedora Linux, R-devel, clang, gfortran (check_rhub)
+* (check_win_devel)
+
+#### R CMD check results
+
+* There were no ERRORs or WARNINGs.
+* There was 1 NOTE:
+```
+Maintainer: 'Pablo Nájera <[email protected]>'
+   
+Uses the superseded package: 'doSNOW'
+```
+The `doSNOW` package is required to show a progress bar inside a `foreach` loop.
+
 ## cdmTools_1.0.4 (November 10, 2023)
 
 #### News & Comments