3.6-29

alexanderrobitzsch · Jan 24, 2021 · e5c6d26 · e5c6d26
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: TAM
 Type: Package
 Title: Test Analysis Modules
-Version: 3.6-28
-Date: 2021-01-19 15:04:01
+Version: 3.6-29
+Date: 2021-01-24 15:14:26
 Author:
     Alexander Robitzsch [aut,cre] (<https://orcid.org/0000-0002-8226-3132>),
     Thomas Kiefer [aut], 

diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -1,5 +1,5 @@
 ## File Name: RcppExports.R
-## File Version: 3.006028
+## File Version: 3.006029
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 

diff --git a/R/designMatrices.R b/R/designMatrices.R
@@ -1,5 +1,5 @@
 ## File Name: designMatrices.R
-## File Version: 9.194
+## File Version: 9.195
 
 designMatrices <- function( modeltype=c( "PCM", "RSM" ),
             maxKi=NULL, resp=resp, ndim=1, A=NULL, B=NULL, Q=NULL, R=NULL,
@@ -122,8 +122,8 @@ designMatrices <- function( modeltype=c( "PCM", "RSM" ),
     #*****************************
     # constraint="items"
     unidim <- is.null(Q)
-    
-    if ( constraint=="items"){        
+
+    if ( constraint=="items"){
         if ( ! is.null(Q) ){
             unidim <- ncol(Q)==1
         }
@@ -174,13 +174,13 @@ designMatrices <- function( modeltype=c( "PCM", "RSM" ),
         vars <- colnames(resp)
         vars <- c(vars, paste0( "Cat", 1:(maxK-1) ) )
         dimnames(A)[[3]] <- vars
-        
+
         if ( (constraint=="items") & unidim ){
             v1 <- A[I,,I]
             A[I,,1:(I-1)] <- -v1
             A <- A[,,-c(I)]
         }
-        
+
         A.draft <- A
     }
     if ( ! is.null(A0)){

diff --git a/R/tam.jml.R b/R/tam.jml.R
@@ -1,5 +1,5 @@
 ## File Name: tam.jml.R
-## File Version: 9.361
+## File Version: 9.363
 
 
 tam.jml <- function( resp, group=NULL, adj=.3, disattenuate=FALSE,
@@ -42,7 +42,8 @@ tam.jml <- function( resp, group=NULL, adj=.3, disattenuate=FALSE,
     #- process item parameters
     res$AXsi <- tam_jml_compute_Axsi(A=res$A, xsi=res$xsi, resp=resp)
     #- item parameter table
-    res$item1 <- tam_jml_itempartable( resp=resp, maxK=res$maxK, AXsi=res$AXsi,
+    res$item1 <- res$item
+    res$item <- tam_jml_itempartable( resp=resp, maxK=res$maxK, AXsi=res$AXsi,
                     B=res$B, resp.ind=res$resp.ind)
     #- theta summary
     res$theta_summary <- tam_jml_proc_abilities(theta=res$theta,

diff --git a/R/tam.jml.fit.R b/R/tam.jml.fit.R
@@ -1,8 +1,8 @@
 ## File Name: tam.jml.fit.R
-## File Version: 9.201
+## File Version: 9.204
 
 
-tam.jml.fit <- function( tamobj )
+tam.jml.fit <- function( tamobj, trim_val=10 )
 {
     s1 <- Sys.time()
     resp <- tamobj$resp
@@ -28,7 +28,7 @@ tam.jml.fit <- function( tamobj )
     B.0[ is.na(B.0) ] <- 0
     B1 <- B.0[,,1]
     BB <- B1^2
-    theta.unique <- unique( theta )
+    theta.unique <- unique(theta)
     NU <- length(theta.unique)
     B_bari <- array(0,dim=c(NU, nitems))
     BB_bari <- array(0, dim=c(NU, nitems))
@@ -43,15 +43,15 @@ tam.jml.fit <- function( tamobj )
         BB_bari <- BB_bari + t( BB[,kk] * rprobs[, kk, ] )
     }
     ind.theta <- match( theta, theta.unique)
-    rprobs <- rprobs[,,  ind.theta ]
+    rprobs <- rprobs[,, ind.theta ]
     B_bari <- B_bari[ ind.theta, ]
     BB_bari <- BB_bari[ ind.theta, ]
     B_bari <- B_bari * resp.ind
     BB_bari <- BB_bari  * resp.ind
     B_var <- BB_bari - (B_bari^2)
     z_sq <- (resp - B_bari)^2/B_var
-    zsd <- sd(as.matrix(z_sq),na.rm=TRUE)
-    z_sq[z_sq > 10*zsd] <-  10*zsd   #Trim extreme values
+    zsd <- stats::sd(as.matrix(z_sq),na.rm=TRUE)
+    z_sq[z_sq > trim_val*zsd] <-  trim_val*zsd   #Trim extreme values
     B_bariM <- aperm(outer(B_bari,rep(1,maxK)),c(2,3,1))
     B1M <- outer(B1,rep(1,nstud))
     for (kk in 1:maxK){
@@ -82,11 +82,11 @@ tam.jml.fit <- function( tamobj )
     fit.item <- data.frame(item=colnames(tamobj$resp), outfitItem=outfitItem,
                     outfitItem_t=outfitItem_t, infitItem=infitItem,
                     infitItem_t=infitItem_t)
-
     fit.person <- data.frame(outfitPerson=outfitPerson,
                     outfitPerson_t=outfitPerson_t, infitPerson=infitPerson,
                     infitPerson_t=infitPerson_t)
 
+    #-- output
     s2 <- Sys.time()
     v1 <- c(s1, s2)
     res <- list(fit.item=fit.item, fit.person=fit.person, time=v1)

diff --git a/R/tam_thurstonian_threshold.R → R/tam.threshold.R b/R/tam_thurstonian_threshold.R → R/tam.threshold.R
@@ -1,16 +1,19 @@
-## File Name: tam_thurstonian_threshold.R
-## File Version: 9.11
+## File Name: tam.threshold.R
+## File Version: 9.15
+
+
+#**** Thurstonian thresholds (gammas)
 
-####################################################################
-# Thurstonian thresholds (gammas)
-#...................................................................
 tam.threshold <- function (tamobj, prob.lvl=0.5)
 {
     resp <- tamobj$resp
     nitems <- tamobj$nitems
     maxK <- tamobj$maxK
     AXsi <- tamobj$AXsi
-    xsi <- ( tamobj$xsi )[,1]
+    xsi <- tamobj$xsi
+    if (class(tamobj)!="tam.jml"){
+        xsi <- xsi[,1]
+    }
     A <- tamobj$A
     B <- tamobj$B
     maxKi <- apply( resp, 2, max, na.rm=TRUE )

diff --git a/R/tam_jml_version2.R b/R/tam_jml_version2.R
@@ -1,5 +1,5 @@
 ## File Name: tam_jml_version2.R
-## File Version: 9.525
+## File Version: 9.526
 
 tam_jml_version2 <- function( resp, group=NULL, adj=.3, disattenuate=FALSE,
             bias=TRUE, xsi.fixed=NULL,  xsi.inits=NULL, A=NULL, B=NULL, Q=NULL,
@@ -153,7 +153,7 @@ tam_jml_version2 <- function( resp, group=NULL, adj=.3, disattenuate=FALSE,
 
     # center theta?
     center_theta <- is.null(xsi.fixed) & (constraint=="cases")
-    
+
     deviance <- 0
     deviance.history <- matrix( 0, nrow=maxiter, ncol=2)
     colnames(deviance.history) <- c("iter", "deviance")

diff --git a/README.md b/README.md
@@ -22,9 +22,9 @@ The CRAN version can be installed from within R using:
 utils::install.packages("TAM")
 ```
 
-#### GitHub version `TAM` 3.6-28 (2021-01-19)
+#### GitHub version `TAM` 3.6-29 (2021-01-24)
 
-[![](https://img.shields.io/badge/github%20version-3.6--28-orange.svg)](https://github.com/alexanderrobitzsch/TAM)&#160;&#160;
+[![](https://img.shields.io/badge/github%20version-3.6--29-orange.svg)](https://github.com/alexanderrobitzsch/TAM)&#160;&#160;
 
 The version hosted [here](https://github.com/alexanderrobitzsch/TAM) is the development version of `TAM`. 
 The GitHub version can be installed using `devtools` as:

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 1.13.1
 pkgdown: 1.5.1
 pkgdown_sha: ~
 articles: []
-last_built: 2021-01-19T14:20Z
+last_built: 2021-01-24T14:29Z
 
diff --git a/docs/reference/tam.fit.html b/docs/reference/tam.fit.html
diff --git a/docs/reference/tam.jml.html b/docs/reference/tam.jml.html
diff --git a/inst/NEWS b/inst/NEWS
@@ -42,7 +42,7 @@ http://www.edmeasurementsurveys.com/TAM/Tutorials/
 
 
 -------------------------------------------------------------
-VERSIONS TAM 3.6  |  2021-01-19  |  Last: TAM 3.6-28
+VERSIONS TAM 3.6  |  2021-01-24  |  Last: TAM 3.6-29
 -------------------------------------------------------------
 
 FIXED * fixed an issue in tam.linking() if number of maximum
@@ -60,6 +60,11 @@ FIXED * handling of person weights in multi faceted models
 NOTE  * added constraints option in designMatrices() function
         for rating scale models (modeltype='RSM')
         (thanks to Stefanie Wind)
+NOTE  * switched labeling of output values 'item' and 'item1'
+        in models of class 'tam.jml'
+NOTE  * included argument 'trim_val' in tam.jml.fit()
+FIXED * tam.threshold() now works for objects of class 'tam.jml'
+        (requested by Angel Zegarra)
 
 
 DATA  * included/modified datasets: ---

diff --git a/man/tam.fit.Rd b/man/tam.fit.Rd
@@ -1,5 +1,5 @@
 %% File Name: tam.fit.Rd
-%% File Version: 2.561
+%% File Version: 2.562
 
 \name{tam.fit}
 
@@ -24,7 +24,7 @@ tam.fit(tamobj, ...)
 tam.mml.fit(tamobj, FitMatrix=NULL, Nsimul=NULL,progress=TRUE,
    useRcpp=TRUE, seed=NA, fit.facets=TRUE)
 
-tam.jml.fit(tamobj)
+tam.jml.fit(tamobj, trim_val=10)
 
 \method{summary}{tam.fit}(object, file=NULL, \dots)
 }
@@ -54,6 +54,8 @@ The latter is consistent with \pkg{TAM} (<=1.1).}
 \item{seed}{Fixed simulation seed.}
 \item{fit.facets}{An optional logical indicating whether
 fit for all facet parameters should be computed.}
+\item{trim_val}{Optional trimming value. Squared standardized reaisuals
+larger than \code{trim_val} are set to \code{trim_val}.}
 \item{object}{Object of class \code{tam.fit}}
 \item{file}{Optional file name for summary output}
 \item{\dots}{Further arguments to be passed}

diff --git a/man/tam.jml.Rd b/man/tam.jml.Rd
@@ -1,5 +1,5 @@
 %% File Name: tam.jml.Rd
-%% File Version: 2.401
+%% File Version: 2.402
 
 \name{tam.jml}
 
@@ -125,7 +125,7 @@ A file name in which the summary output will be written
 
 \value{
 A list with following entries
-\item{item}{Data frame with item parameters}
+\item{item1}{Data frame with item parameters}
 \item{xsi}{Vector of item parameters \eqn{\xi}}
 \item{errorP}{Standard error of item parameters \eqn{\xi}}
 \item{theta}{MLE in final step}
@@ -150,7 +150,7 @@ A list with following entries
 \item{resp.ind.list}{Like \code{resp.ind}, only in the format of a list}
 \item{xsi.fixed}{Fixed \eqn{\xi} item parameters}
 \item{control}{Control list}
-\item{item1}{Extended data frame of item parameters}
+\item{item}{Extended data frame of item parameters}
 \item{theta_summary}{Summary of person parameters}
 \item{\dots}{}
 }

diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
@@ -1,5 +1,5 @@
 //// File Name: RcppExports.cpp
-//// File Version: 3.006028
+//// File Version: 3.006029
 // Generated by using Rcpp::compileAttributes() -> do not edit by hand
 // Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 

diff --git a/src/init.c b/src/init.c
@@ -1,5 +1,5 @@
 //// File Name: init.c
-//// File Version: 3.006028
+//// File Version: 3.006029
 #include <R.h>
 #include <Rinternals.h>
 #include <stdlib.h> // for NULL