diff --git a/DESCRIPTION b/DESCRIPTION index e02ba87..dba7661 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: TAM Type: Package Title: Test Analysis Modules -Version: 4.0-1 -Date: 2021-06-25 14:15:15 +Version: 4.1-1 +Date: 2022-05-15 09:03:38 Author: Alexander Robitzsch [aut,cre] (), Thomas Kiefer [aut], @@ -27,7 +27,7 @@ Imports: graphics, methods, Rcpp, stats, utils Suggests: coda, GPArotation, grDevices, lattice, lavaan, MASS, - miceadds, mvtnorm, plyr, psych, sfsmisc, sirt, splines, + miceadds, mvtnorm, plyr, psych, sfsmisc, splines, WrightMap LinkingTo: Rcpp, RcppArmadillo diff --git a/R/IRT.informationCurve.R b/R/IRT.informationCurve.R index d54db20..5d516d9 100644 --- a/R/IRT.informationCurve.R +++ b/R/IRT.informationCurve.R @@ -1,5 +1,5 @@ ## File Name: IRT.informationCurve.R -## File Version: 9.19 +## File Version: 9.212 @@ -47,25 +47,19 @@ informationCurves_mml <- function( object, h=.0001, B=B, xsi=xsi, theta=theta, nnodes=nnodes, maxK=maxK, recalc=TRUE) - #**** - # calculate probabilities - if ( class(object) %in% c("tam.mml","tam.mml.2pl", "tam.mml.mfr") ){ + #--- calculate probabilities + if ( inherits(object, c("tam.mml","tam.mml.2pl", "tam.mml.mfr") ) ){ fct <- "tam_calc_prob" - p0 <- do.call( what=fct, args=calc_args )$rprobs - p1 <- do.call( what=fct, args=tam_args_replace_value( args=calc_args, - variable="theta", value=theta+h ) )$rprobs - p2 <- do.call( what=fct, args=tam_args_replace_value( args=calc_args, - variable="theta", value=theta-h ) )$rprobs } - if ( class(object) %in% c("tam.mml.3pl" ) ){ + if ( inherits(object, c("tam.mml.3pl") ) ){ calc_args$guess <- guess fct <- "tam_mml_3pl_calc_prob" - p0 <- do.call( what=fct, args=calc_args )$rprobs - p1 <- do.call( what=fct, args=tam_args_replace_value( args=calc_args, - variable="theta", value=theta+h ) )$rprobs - p2 <- do.call( what=fct, args=tam_args_replace_value( args=calc_args, - variable="theta", value=theta-h ) )$rprobs } + p0 <- do.call( what=fct, args=calc_args )$rprobs + args1 <- tam_args_replace_value( args=calc_args, variable="theta", value=theta+h ) + p1 <- do.call( what=fct, args=args1 )$rprobs + args2 <- tam_args_replace_value( args=calc_args, variable="theta", value=theta-h ) + p2 <- do.call( what=fct, args=args2 )$rprobs p0a <- p0 p0[ is.na(p0) ] <- 0 p1[ is.na(p1) ] <- 0 diff --git a/R/IRT.residuals.R b/R/IRT.residuals.R index 08da4e2..f878fa6 100644 --- a/R/IRT.residuals.R +++ b/R/IRT.residuals.R @@ -1,5 +1,5 @@ ## File Name: IRT.residuals.R -## File Version: 9.15 +## File Version: 9.161 ##################################################### @@ -15,7 +15,7 @@ IRT.residuals <- function (object, ...) tam.residuals <- function( object, ... ) { tamobj <- object - if (class(tamobj)!="tam.jml"){ + if (! inherits(tamobj,"tam.jml")){ res <- tam.wle( tamobj, progress=FALSE, output.prob=TRUE, ... ) probs <- res$probs probs[ is.na(probs) ] <- 0 diff --git a/R/IRTLikelihood.cfa.R b/R/IRTLikelihood.cfa.R index dffe579..4e75da7 100644 --- a/R/IRTLikelihood.cfa.R +++ b/R/IRTLikelihood.cfa.R @@ -1,5 +1,5 @@ ## File Name: IRTLikelihood.cfa.R -## File Version: 9.19 +## File Version: 9.201 #---- IRTLikelihood for fitted CFA model IRTLikelihood.cfa <- function( data, cfaobj=NULL, @@ -25,7 +25,7 @@ IRTLikelihood.cfa <- function( data, cfaobj=NULL, } theta0 <- snodes.adj * seq(-3,3,len=21) if (D>2){ - r1 <- sirt_import_sfsmisc_QUnif(n=snodes, min=0, max=1, n.min=1, p=D, leap=409) + r1 <- tam_import_sfsmisc_QUnif(n=snodes, min=0, max=1, n.min=1, p=D, leap=409) theta <- stats::qnorm( r1 ) for ( dd in 1:D){ theta[,dd] <- snodes.adj*theta[,dd] diff --git a/R/RcppExports.R b/R/RcppExports.R index 6bc7268..6a4cb9e 100644 --- a/R/RcppExports.R +++ b/R/RcppExports.R @@ -1,5 +1,5 @@ ## File Name: RcppExports.R -## File Version: 4.000001 +## File Version: 4.001001 # Generated by using Rcpp::compileAttributes() -> do not edit by hand # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393 diff --git a/R/designMatrices_aux.R b/R/designMatrices_aux.R index dc84c43..064018c 100644 --- a/R/designMatrices_aux.R +++ b/R/designMatrices_aux.R @@ -1,5 +1,5 @@ ## File Name: designMatrices_aux.R -## File Version: 9.103 +## File Version: 9.104 ############################################################# print.designMatrices <- @@ -215,8 +215,6 @@ if (FALSE){ ind.mm <- grep(sg, rownames(mm)) mm.sg.temp <- rbind( 0, apply( mm[ ind.mm,], 2, cumsum ) ) # mm.sg.temp <- rbind( 0, colCumsums.sirt( mm[ ind.mm,] ) ) - # substitute the following line later if the sirt function - # colCumsums.sirt is available at CRAN # mm.sg.temp <- rbind( 0, colCumsums.sirt( mm[ grep(sg, rownames(mm)),] ) ) rownames(mm.sg.temp)[1] <- gsub("step([[:digit:]])*", "step0", sg, fixed=T) A <- rbind(A, mm.sg.temp) diff --git a/R/plotDevianceTAM.R b/R/plotDevianceTAM.R index 48e09fa..ede7590 100644 --- a/R/plotDevianceTAM.R +++ b/R/plotDevianceTAM.R @@ -1,10 +1,11 @@ ## File Name: plotDevianceTAM.R -## File Version: 9.10 -############################################################################### -plotDevianceTAM <- function ( tam.obj, omitUntil=1, reverse=TRUE, +## File Version: 9.111 + + +plotDevianceTAM <- function ( tam.obj, omitUntil=1, reverse=TRUE, change=TRUE) { - stopifnot(class(tam.obj) %in% c("tam.mml","tam.mml.2pl","tam.mml.mfr","tam.mml.3pl","tamaan") ) + stopifnot(inherits(tam.obj, c("tam.mml","tam.mml.2pl","tam.mml.mfr","tam.mml.3pl","tamaan")) ) devhistory <- tam.obj$deviance.history if(omitUntil>0) { @@ -20,7 +21,7 @@ plotDevianceTAM <- function ( tam.obj, omitUntil=1, reverse=TRUE, } if(reverse){ - devChange <- -1 * devChange + devChange <- -devChange } devChange <- data.frame ( nr=omitUntil + 1:length(devChange), devChange) xm <- ceiling( max(devChange[,1])/10 )*10 @@ -41,4 +42,3 @@ plotDevianceTAM <- function ( tam.obj, omitUntil=1, reverse=TRUE, dcr <- devChange[devChange[,2]<0,] graphics::points( dcr[,1], dcr[,2], pch=20, cex=cex, col="red") } -############################################################################### diff --git a/R/summary.tam.R b/R/summary.tam.R index a98d7e6..ef657e5 100644 --- a/R/summary.tam.R +++ b/R/summary.tam.R @@ -1,5 +1,5 @@ ## File Name: summary.tam.R -## File Version: 9.586 +## File Version: 9.587 #****** summary for tam object summary.tam <- function( object, file=NULL, ...) @@ -7,7 +7,7 @@ summary.tam <- function( object, file=NULL, ...) tam_osink(file=file) latreg <- FALSE - if ( class(object)=="tam.latreg" ){ + if ( inherits(object,"tam.latreg") ){ latreg <- TRUE object$irtmodel <- "tam.latreg" } diff --git a/R/tam.fit.R b/R/tam.fit.R index f0011f9..c2714b4 100644 --- a/R/tam.fit.R +++ b/R/tam.fit.R @@ -1,12 +1,12 @@ ## File Name: tam.fit.R -## File Version: 9.16 +## File Version: 9.171 tam.fit <- function( tamobj, ... ) { CALL <- match.call() - if(class(tamobj)=="tam.mml"){ + if(inherits(tamobj,"tam.mml")){ res <- tam.mml.fit( tamobj, ...) } - if(class(tamobj)=="tam.jml"){ + if(inherits(tamobj,"tam.jml")){ res <- tam.jml.fit( tamobj, ...) } res$CALL <- CALL diff --git a/R/tam.mml.3pl.R b/R/tam.mml.3pl.R index 9229a56..485fe44 100644 --- a/R/tam.mml.3pl.R +++ b/R/tam.mml.3pl.R @@ -1,5 +1,5 @@ ## File Name: tam.mml.3pl.R -## File Version: 9.881 +## File Version: 9.882 tam.mml.3pl <- function( resp, Y=NULL, group=NULL, formulaY=NULL, dataY=NULL, @@ -718,7 +718,7 @@ tam.mml.3pl <- function( resp, Y=NULL, group=NULL, se.xsi.min -> se.xsi se.B.min -> se.B - #*** include NAs in AXsi + #*** include NAs in AXsi AXsi <- tam_mml_include_NA_AXsi(AXsi=AXsi, maxcat=maxK, A=A, xsi=xsi) #**** standard errors AXsi diff --git a/R/tam.modelfit.IRT.R b/R/tam.modelfit.IRT.R index 5c09a83..0cac707 100644 --- a/R/tam.modelfit.IRT.R +++ b/R/tam.modelfit.IRT.R @@ -1,15 +1,14 @@ ## File Name: tam.modelfit.IRT.R -## File Version: 0.03 +## File Version: 0.06 -############################################################### tam.modelfit.IRT <- function( object, progress=TRUE ) { resp <- IRT.data(object) probs <- IRT.irfprob(object) theta <- attr( probs, "theta" ) post <- IRT.posterior( object ) - res <- tam.modelfit.args( resp, probs, theta, post, progress) + res <- tam.modelfit.args( resp=resp, probs=probs, theta=theta, + post=post, progress=progress) return(res) } -############################################################# diff --git a/R/tam.modelfit.R b/R/tam.modelfit.R index c0ff53c..1819d36 100644 --- a/R/tam.modelfit.R +++ b/R/tam.modelfit.R @@ -1,5 +1,5 @@ ## File Name: tam.modelfit.R -## File Version: 9.38 +## File Version: 9.406 # Q3 statistic and model fit statistics for objects of class tam @@ -127,12 +127,11 @@ tam.modelfit <- function( tamobj, progress=TRUE ) chisquare.itemfit$p[ii] <- min( stats::p.adjust( h1$p, method="holm") ) } chisquare.itemfit$p.holm <- stats::p.adjust( chisquare.itemfit$p, method="holm") + # maximum chi square - modelfit.test <- data.frame( - "maxX2"=max( chi2.stat$chi2), - "Npairs"=nrow(chi2.stat), - "p.holm"=min( chi2.stat$p.holm[pair_exists] ) - ) + modelfit.test <- data.frame( maxX2=max( chi2.stat$chi2), + Npairs=nrow(chi2.stat), + p.holm=min( chi2.stat$p.holm[pair_exists] ) ) #** modelfit.stat modelfit.stat <- fitstat diff --git a/R/tam.modelfit.args.R b/R/tam.modelfit.args.R index cfc5118..7a7ca12 100644 --- a/R/tam.modelfit.args.R +++ b/R/tam.modelfit.args.R @@ -1,16 +1,14 @@ ## File Name: tam.modelfit.args.R -## File Version: 0.06 +## File Version: 0.08 -######################################################## -# tam.modelfit with user defined input +#-- tam.modelfit with user defined input tam.modelfit.args <- function( resp, probs, theta, post, progress=TRUE ) { resp.ind <- as.matrix( 1- is.na(resp) ) - tamobj <- list( resp=resp, rprobs=probs, - theta=theta, hwt=post, + tamobj <- list( resp=resp, rprobs=probs, theta=theta, hwt=post, resp.ind=resp.ind ) res <- tam.modelfit( tamobj=tamobj, progress=progress) return(res) } -######################################################## + diff --git a/R/tam.personfit.R b/R/tam.personfit.R index 8b1e6bc..d60ba2a 100644 --- a/R/tam.personfit.R +++ b/R/tam.personfit.R @@ -1,10 +1,10 @@ ## File Name: tam.personfit.R -## File Version: 0.06 +## File Version: 0.07 tam.personfit <- function(tamobj) { #** WLE estimation in case of MML estimation - if ( class(tamobj) !="tam.jml" ){ + if ( ! inherits(tamobj,"tam.jml") ){ res <- tam.wle(tamobj, progress=FALSE) tamobj$theta <- res$theta tamobj$xsi <- tamobj$xsi$xsi diff --git a/R/tam.pv.R b/R/tam.pv.R index 8175249..99257af 100644 --- a/R/tam.pv.R +++ b/R/tam.pv.R @@ -1,5 +1,5 @@ ## File Name: tam.pv.R -## File Version: 9.466 +## File Version: 9.468 tam.pv <- function( tamobj, nplausible=10, ntheta=2000, normal.approx=FALSE, samp.regr=FALSE, theta.model=FALSE, np.adj=8, na.grid=5, verbose=TRUE) @@ -26,13 +26,13 @@ tam.pv <- function( tamobj, nplausible=10, #-- check for recommendation of tam.pv.mcmc res <- tam_pv_recommend_tam_pv_mcmc(tamobj=tamobj) - if ( class(tamobj)=="tam.latreg" ){ + if ( inherits(tamobj,"tam.latreg") ){ theta.model <- TRUE latreg <- TRUE like <- tamobj$like } if ( ! latreg ){ - if (class(tamobj)!="tam.mml.3pl"){ + if ( ! inherits(tamobj,"tam.mml.3pl") ){ guess <- rep( 0, dim(tamobj$B)[1] ) } else { guess <- tamobj$guess diff --git a/R/tam.se.R b/R/tam.se.R index 1bd4665..035c33e 100644 --- a/R/tam.se.R +++ b/R/tam.se.R @@ -1,19 +1,20 @@ ## File Name: tam.se.R -## File Version: 9.15 +## File Version: 9.161 + tam.se <- function( tamobj, item_pars=TRUE, ...) { SE.quick <- TRUE #------------------------------- ## "quick" standard errors if(SE.quick){ - if(class(tamobj) %in% c("tam.mml") ){ + if(inherits(tamobj,"tam.mml") ){ res <- tam_mml_se_quick( tamobj=tamobj, item_pars=item_pars, ...) } - if(class(tamobj) %in% c("tam.latreg") ){ + if(inherits(tamobj,"tam.latreg") ){ res <- tam_latreg_se_quick( tamobj=tamobj, ...) } - if(class(tamobj)=="tam.jml"){ + if(inherits(tamobj,"tam.jml")){ # res <- tam.jml.se( tamobj, ...) ## include standard errors here!! } diff --git a/R/tam.threshold.R b/R/tam.threshold.R index 7896f77..0bbcabc 100644 --- a/R/tam.threshold.R +++ b/R/tam.threshold.R @@ -1,5 +1,5 @@ ## File Name: tam.threshold.R -## File Version: 9.15 +## File Version: 9.161 #**** Thurstonian thresholds (gammas) @@ -11,7 +11,7 @@ tam.threshold <- function (tamobj, prob.lvl=0.5) maxK <- tamobj$maxK AXsi <- tamobj$AXsi xsi <- tamobj$xsi - if (class(tamobj)!="tam.jml"){ + if (! inherits(tamobj,"tam.jml")){ xsi <- xsi[,1] } A <- tamobj$A diff --git a/R/tam.wle.R b/R/tam.wle.R index f75ea7d..1ff5e23 100644 --- a/R/tam.wle.R +++ b/R/tam.wle.R @@ -1,16 +1,16 @@ ## File Name: tam.wle.R -## File Version: 9.16 +## File Version: 9.171 tam.wle <- function( tamobj, ... ) { CALL <- match.call() - if(class(tamobj)=="tam.mml"){ + if(inherits(tamobj,"tam.mml")){ res <- tam.mml.wle2( tamobj, ...) } - if(class(tamobj)=="tamaan"){ + if(inherits(tamobj,"tamaan")){ res <- tam.mml.wle2( tamobj, ...) } - if(class(tamobj)=="tam.jml"){ + if(inherits(tamobj,"tam.jml")){ res <- tam_jml_wle( tamobj, ...) } attr(res,"call") <- CALL diff --git a/R/sirt_import_sfsmisc_QUnif.R b/R/tam_import_sfsmisc_QUnif.R similarity index 58% rename from R/sirt_import_sfsmisc_QUnif.R rename to R/tam_import_sfsmisc_QUnif.R index 5ee2619..464f753 100644 --- a/R/sirt_import_sfsmisc_QUnif.R +++ b/R/tam_import_sfsmisc_QUnif.R @@ -1,7 +1,7 @@ -## File Name: sirt_import_sfsmisc_QUnif.R -## File Version: 0.05 +## File Name: tam_import_sfsmisc_QUnif.R +## File Version: 0.061 -sirt_import_sfsmisc_QUnif <- function(n, min=0, max=1, n.min=1, p, +tam_import_sfsmisc_QUnif <- function(n, min=0, max=1, n.min=1, p, leap=409, ...) { require_namespace_msg("sfsmisc") diff --git a/R/tam_mml_create_nodes.R b/R/tam_mml_create_nodes.R index fba9ad7..b0d44c9 100644 --- a/R/tam_mml_create_nodes.R +++ b/R/tam_mml_create_nodes.R @@ -1,5 +1,5 @@ ## File Name: tam_mml_create_nodes.R -## File Version: 0.31 +## File Version: 0.331 tam_mml_create_nodes <- function(snodes, nodes, ndim, QMC, skillspace="normal", theta.k=NULL) @@ -48,7 +48,8 @@ tam_mml_create_nodes <- function(snodes, nodes, ndim, QMC, # sampled theta values if (QMC){ fac <- 1 - r1 <- sirt_import_sfsmisc_QUnif(n=snodes, min=0, max=1, n.min=1, p=ndim, leap=409) + r1 <- tam_import_sfsmisc_QUnif(n=snodes, min=0, max=1, n.min=1, + p=ndim, leap=409) theta0.samp <- fac * stats::qnorm(r1) if (ndim==1){ theta0.samp <- theta0.samp[ order(theta0.samp[,1]), ] diff --git a/R/tam_osink.R b/R/tam_osink.R index 84c050a..2bb8994 100644 --- a/R/tam_osink.R +++ b/R/tam_osink.R @@ -1,7 +1,7 @@ ## File Name: tam_osink.R -## File Version: 0.04 +## File Version: 0.05 -tam_osink <- function(file, suffix="__SUMMARY.Rout") +tam_osink <- function(file, suffix=".Rout") { CDM::osink( file=file, suffix=suffix ) } diff --git a/R/tamaan.R b/R/tamaan.R index 5aff263..11e4d9b 100644 --- a/R/tamaan.R +++ b/R/tamaan.R @@ -1,5 +1,5 @@ ## File Name: tamaan.R -## File Version: 9.215 +## File Version: 9.219 #--- tamaan function diff --git a/R/tamaanify.R b/R/tamaanify.R index 8507ccf..6fcf18a 100644 --- a/R/tamaanify.R +++ b/R/tamaanify.R @@ -1,5 +1,5 @@ ## File Name: tamaanify.R -## File Version: 9.216 +## File Version: 9.233 #--- tamaanify function @@ -40,35 +40,31 @@ tamaanify <- function( tammodel, resp, tam.method=NULL, doparse=TRUE ) res$gammaslope.fixed <- NULL #*** process analysis - res <- tamaanify.proc.analysis( res ) + res <- tamaanify_proc_analysis(res=res) #*** extract lavaan model res <- tamaanify_proc_lavaanmodel(res=res, resp=resp) #*** item characteristics - res <- tamaanify.proc.items( res, resp) + res <- tamaanify_proc_items(res=res, resp=resp) #*** item type - res <- tamaanify.proc.itemtype( res ) + res <- tamaanify_proc_itemtype(res=res) #*** include model constraints - res <- tamaanify.proc.modelconstraint( res ) + res <- tamaanify_proc_modelconstraint(res=res) - #****** - # add response dataset - cols <- paste(res$items$item) - resp <- resp[, cols] - res$resp <- resp + #*** add response dataset + res <- tamaanify_proc_resp(res=res, resp=resp) - #********** - # define design matrices and model for TAM + #*** define design matrices and model for TAM res$method <- "tam.mml.2pl" if ( ! is.null(tam.method) ){ res$method <- tam.method } #*** A matrix - res <- tamaanify.create.A(res=res) + res <- tamaanify_create_A(res=res) #*** Q matrix res <- tamaanify_create_Q(res=res) @@ -83,13 +79,13 @@ tamaanify <- function( tammodel, resp, tam.method=NULL, doparse=TRUE ) res <- tamaanify_variance_fixed(res=res) #*** define design matrices for tam.mml.3pl method - res <- tamaanify.tam.mml.3pl.designMatrices(res=res) + res <- tamaanify_tam_mml_3pl_designMatrices(res=res) #*** delta design matrix res <- tamaanify.tam.mml.3pl.deltadesign(res=res) #**** model prior - res <- tamaanify.modelprior(res=res) + res <- tamaanify_modelprior(res=res) #*** define method res <- tamaanify.define.method(res=res, tam.method=tam.method) diff --git a/R/tamaanify.tam.mml.3pl.designMatrices.R b/R/tamaanify.tam.mml.3pl.designMatrices.R deleted file mode 100644 index e8d9c9e..0000000 --- a/R/tamaanify.tam.mml.3pl.designMatrices.R +++ /dev/null @@ -1,18 +0,0 @@ -## File Name: tamaanify.tam.mml.3pl.designMatrices.R -## File Version: 9.11 - - -#***** design matrices for estimation with tam.mml.3pl method -tamaanify.tam.mml.3pl.designMatrices <- function(res) -{ - anlist <- res$ANALYSIS.list - res <- switch( anlist$type, - "LCA"=tamaanify.tam.mml.3pl.designMatrices.LCA(res), - "LOCLCA"=tamaanify.tam.mml.3pl.designMatrices.LOCLCA(res), - "OLCA"=tamaanify.tam.mml.3pl.designMatrices.OLCA(res), - "TRAIT"=tamaanify.tam.mml.3pl.designMatrices.TRAIT(res), - "MIXTURE"=tamaanify.tam.mml.3pl.designMatrices.MIXTURE(res) - ) - # output - return(res) -} diff --git a/R/tamaanify.create.A.R b/R/tamaanify_create_A.R similarity index 91% rename from R/tamaanify.create.A.R rename to R/tamaanify_create_A.R index a207ec0..c6339f9 100644 --- a/R/tamaanify.create.A.R +++ b/R/tamaanify_create_A.R @@ -1,14 +1,15 @@ -## File Name: tamaanify.create.A.R -## File Version: 9.11 +## File Name: tamaanify_create_A.R +## File Version: 9.211 -#-- create A matrix -tamaanify.create.A <- function(res) +### create A matrix + +tamaanify_create_A <- function(res) { resp <- res$resp lavpartable <- res$lavpartable - #*********************************** - # create A matrix + + #*** create A matrix A <- designMatrices( resp=resp ) A <- A$A items0 <- dimnames(A)[[1]] <- res$items$item @@ -18,8 +19,7 @@ tamaanify.create.A <- function(res) dimnames(A)[[3]] <- paste0( dimnames(A)[[3]], "_Cat1") } - #********************************************* - # loop over items for smoothed nominal response models + #*** loop over items for smoothed nominal response models smooth.nrm <- FALSE itemtable <- res$items items.ind <- grep( ",", paste(itemtable$itemtype), fixed=TRUE ) @@ -58,8 +58,7 @@ tamaanify.create.A <- function(res) } } - #********************************************* - #****** xsi parameter fixings + #*** xsi parameter fixings xsi.fixed <- NULL maxK <- max( res$items$ncat )-1 lavpartable <- lavpartable[ lavpartable$user !=-99, ] @@ -120,8 +119,7 @@ tamaanify.create.A <- function(res) dimnames(A)[[3]] <- paste(lavpartable0[ ind, "label" ]) } - #*********************** - # model constraint thresholds + #*** model constraint thresholds mdfr <- res$MODELCONSTRAINT.dfr if ( ! is.null(mdfr) ){ mdfr <- mdfr[ grep( "|t", mdfr$fullsyn, fixed=TRUE), ] @@ -167,10 +165,9 @@ tamaanify.create.A <- function(res) } } } - #************************************** - #*** OUTPUT + + #--- OUTPUT res$A <- A res$xsi.fixed <- xsi.fixed return(res) } -######################################################### diff --git a/R/tamaanify.modelprior.R b/R/tamaanify_modelprior.R similarity index 93% rename from R/tamaanify.modelprior.R rename to R/tamaanify_modelprior.R index 7622279..7789f05 100644 --- a/R/tamaanify.modelprior.R +++ b/R/tamaanify_modelprior.R @@ -1,9 +1,9 @@ -## File Name: tamaanify.modelprior.R -## File Version: 9.09 +## File Name: tamaanify_modelprior.R +## File Version: 9.114 -############################################ -# model prior parsing -tamaanify.modelprior <- function(res) +### model prior parsing + +tamaanify_modelprior <- function(res) { t1 <- res$tammodel.dfr gammaslope.prior <- NULL @@ -42,8 +42,7 @@ tamaanify.modelprior <- function(res) if ( length(uu) >=5 ){ gg <- uu[5] } else {gg <- NA} return(gg) } ) )) - #******** - # type of prior parameter + #*** type of prior parameter E <- res$E Epars <- dimnames(E)[[4]] dfr$gammaslope_index <- match( paste(dfr$parm), Epars ) @@ -73,6 +72,7 @@ tamaanify.modelprior <- function(res) xsi.prior[ dfr0$A_index, ] <- as.matrix( dfr0[, c("par1","par2") ] ) } + } #**** index priors guessing parameters @@ -100,9 +100,10 @@ tamaanify.modelprior <- function(res) } } if ( is.null( res$gammaslope.prior) ){ - res$gammaslope.prior <- gammaslope.prior + res$gammaslope.prior <- gammaslope.prior } res$xsi.prior <- xsi.prior res$guess.prior <- guess.prior + return(res) } diff --git a/R/tamaanify.proc.analysis.R b/R/tamaanify_proc_analysis.R similarity index 75% rename from R/tamaanify.proc.analysis.R rename to R/tamaanify_proc_analysis.R index 2d6f90c..060cc99 100644 --- a/R/tamaanify.proc.analysis.R +++ b/R/tamaanify_proc_analysis.R @@ -1,12 +1,11 @@ -## File Name: tamaanify.proc.analysis.R -## File Version: 9.06 +## File Name: tamaanify_proc_analysis.R +## File Version: 9.072 +### process analysis - -######################################################### -# process analysis -tamaanify.proc.analysis <- function( res ){ +tamaanify_proc_analysis <- function( res ) +{ tam1 <- res$tammodel.dfr ind1 <- which( paste(tam1$syn)=="ANALYSIS:" ) res$ANALYSIS <- "" @@ -17,42 +16,39 @@ tamaanify.proc.analysis <- function( res ){ ANALYSIS.list <- list() if( length( grep("TYPE=LCA",dfr) ) > 0 ){ ANALYSIS.list$type <- "LCA" - } + } if( length( grep("TYPE=MIXTURE",dfr) ) > 0 ){ ANALYSIS.list$type <- "MIXTURE" - } + } # located latent class analysis if( length( grep("TYPE=LOCLCA",dfr) ) > 0 ){ ANALYSIS.list$type <- "LOCLCA" - } + } # trait if( length( grep("TYPE=TRAIT",dfr) ) > 0 ){ ANALYSIS.list$type <- "TRAIT" - } + } # ordered latent class analysis if( length( grep("TYPE=OLCA",dfr) ) > 0 ){ ANALYSIS.list$type <- "OLCA" - } + } ind <- grep("NCLASSES", dfr ) if ( length(ind) > 0 ){ m1 <- gsub( "NCLASSES(", "", dfr[ind], fixed=TRUE ) m1 <- as.numeric( gsub(")", "", m1, fixed=TRUE ) ) ANALYSIS.list$NCLASSES <- m1 - } + } ind <- grep("NSTARTS", dfr, fixed=TRUE) if ( length(ind) > 0 ){ m1 <- gsub( "NSTARTS(", "", dfr[ind], fixed=TRUE ) m1 <- gsub(")", "", m1, fixed=TRUE ) m1 <- as.numeric( unlist( strsplit( m1, split=",", fixed=TRUE) ) ) ANALYSIS.list$NSTARTS <- m1 - } - + } res$ANALYSIS.list <- ANALYSIS.list - } else { - + } else { res$ANALYSIS.list$type <- "TRAIT" - } - res$skillspace <- "normal" - return(res) - } -########################################################## + } + res$skillspace <- "normal" + return(res) +} diff --git a/R/tamaanify.proc.items.R b/R/tamaanify_proc_items.R similarity index 90% rename from R/tamaanify.proc.items.R rename to R/tamaanify_proc_items.R index 3186487..cfc527e 100644 --- a/R/tamaanify.proc.items.R +++ b/R/tamaanify_proc_items.R @@ -1,11 +1,10 @@ -## File Name: tamaanify.proc.items.R -## File Version: 9.09 +## File Name: tamaanify_proc_items.R +## File Version: 9.104 +### process item characteristics -############################################################ -# process item characteristics -tamaanify.proc.items <- function( res, resp) +tamaanify_proc_items <- function( res, resp) { lavpartable <- res$lavpartable ind <- which( lavpartable$op=="=~" ) @@ -75,8 +74,9 @@ tamaanify.proc.items <- function( res, resp) } #*** thresholds for (hh in 1:( max(maxK) ) ){ - ind <- which( ( paste(lavpartable2$rhs)==paste0("t", hh) ) & ( paste( lavpartable2$label )=="" ) & - ( paste(lavpartable2$op)=="|" ) ) + ind <- which( ( paste(lavpartable2$rhs)==paste0("t", hh) ) & + ( paste( lavpartable2$label )=="" ) & + ( paste(lavpartable2$op)=="|" ) ) if ( length(ind) > 0 ){ lavpartable2[ ind, "label" ] <- paste0( lavpartable2$lhs[ind], "_", "Cat", hh ) } diff --git a/R/tamaanify.proc.itemtype.R b/R/tamaanify_proc_itemtype.R similarity index 84% rename from R/tamaanify.proc.itemtype.R rename to R/tamaanify_proc_itemtype.R index 699f218..32f0142 100644 --- a/R/tamaanify.proc.itemtype.R +++ b/R/tamaanify_proc_itemtype.R @@ -1,10 +1,10 @@ -## File Name: tamaanify.proc.itemtype.R -## File Version: 9.08 +## File Name: tamaanify_proc_itemtype.R +## File Version: 9.091 -############################################################ -# process item type -tamaanify.proc.itemtype <- function( res ) +### process item type + +tamaanify_proc_itemtype <- function( res ) { tam1 <- res$tammodel.dfr ind1 <- which( paste(tam1$syn)=="ITEMTYPE:" ) @@ -40,4 +40,3 @@ tamaanify.proc.itemtype <- function( res ) } return(res) } -############################################################ diff --git a/R/tamaanify.proc.modelconstraint.R b/R/tamaanify_proc_modelconstraint.R similarity index 92% rename from R/tamaanify.proc.modelconstraint.R rename to R/tamaanify_proc_modelconstraint.R index 645010a..193a1bf 100644 --- a/R/tamaanify.proc.modelconstraint.R +++ b/R/tamaanify_proc_modelconstraint.R @@ -1,11 +1,9 @@ -## File Name: tamaanify.proc.modelconstraint.R -## File Version: 9.09 +## File Name: tamaanify_proc_modelconstraint.R +## File Version: 9.102 +### process model constraint - -######################################################### -# process model constraint -tamaanify.proc.modelconstraint <- function( res ) +tamaanify_proc_modelconstraint <- function( res ) { tam1 <- res$tammodel.dfr ind1 <- which( paste(tam1$syn)=="MODELCONSTRAINT:" ) @@ -89,4 +87,4 @@ tamaanify.proc.modelconstraint <- function( res ) res$MODELCONSTRAINT.dfr <- dfr.syncon return(res) } -###################################################################### + diff --git a/R/tamaanify_proc_resp.R b/R/tamaanify_proc_resp.R new file mode 100644 index 0000000..b90181e --- /dev/null +++ b/R/tamaanify_proc_resp.R @@ -0,0 +1,11 @@ +## File Name: tamaanify_proc_resp.R +## File Version: 0.01 + + +tamaanify_proc_resp <- function(res, resp) +{ + cols <- paste(res$items$item) + resp <- resp[, cols] + res$resp <- resp + return(res) +} diff --git a/R/tamaanify_tam_mml_3pl_designMatrices.R b/R/tamaanify_tam_mml_3pl_designMatrices.R new file mode 100644 index 0000000..4ab8b77 --- /dev/null +++ b/R/tamaanify_tam_mml_3pl_designMatrices.R @@ -0,0 +1,17 @@ +## File Name: tamaanify_tam_mml_3pl_designMatrices.R +## File Version: 9.215 + +### design matrices for estimation with tam.mml.3pl method + +tamaanify_tam_mml_3pl_designMatrices <- function(res) +{ + res <- switch( res$ANALYSIS.list$type, + "LCA"=tamaanify.tam.mml.3pl.designMatrices.LCA(res=res), + "LOCLCA"=tamaanify.tam.mml.3pl.designMatrices.LOCLCA(res=res), + "OLCA"=tamaanify.tam.mml.3pl.designMatrices.OLCA(res=res), + "TRAIT"=tamaanify.tam.mml.3pl.designMatrices.TRAIT(res=res), + "MIXTURE"=tamaanify.tam.mml.3pl.designMatrices.MIXTURE(res=res) + ) + # output + return(res) +} diff --git a/README.md b/README.md index 6ffbbbe..7e6299e 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,7 @@ If you use `TAM` and have suggestions for improvement or have found bugs, please The manual may be found here [https://alexanderrobitzsch.github.io/TAM/](https://alexanderrobitzsch.github.io/TAM/) -#### CRAN version `TAM` 3.7-16 (2021-06-24) +#### CRAN version `TAM` 4.0-16 (2022-05-13) [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version-last-release/TAM)](https://cran.r-project.org/package=TAM) @@ -22,9 +22,9 @@ The CRAN version can be installed from within R using: utils::install.packages("TAM") ``` -#### GitHub version `TAM` 4.0-1 (2021-06-25) +#### GitHub version `TAM` 4.1-1 (2022-05-15) -[![](https://img.shields.io/badge/github%20version-4.0--1-orange.svg)](https://github.com/alexanderrobitzsch/TAM)   +[![](https://img.shields.io/badge/github%20version-4.1--1-orange.svg)](https://github.com/alexanderrobitzsch/TAM)   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 index 894a6ca..e040c9a 100644 --- a/docs/404.html +++ b/docs/404.html @@ -71,7 +71,7 @@ TAM - 4.0-1 + 4.1-1 diff --git a/docs/authors.html b/docs/authors.html index 5e42c48..d84dca4 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -71,7 +71,7 @@ TAM - 4.0-1 + 4.1-1 @@ -111,12 +111,12 @@

Citation

Source: inst/CITATION -

Robitzsch, A., Kiefer, T., & Wu, M. (2021). TAM: Test Analysis Modules. R package version 4.0-1. https://CRAN.R-project.org/package=TAM

- 
@Manual{TAM_4.0-1,
+    
Robitzsch, A., Kiefer, T., & Wu, M. (2022). TAM: Test Analysis Modules. R package version 4.1-1. https://CRAN.R-project.org/package=TAM

+    
@Manual{TAM_4.1-1,
   title = {TAM: Test Analysis Modules},
   author = {Alexander Robitzsch and Thomas Kiefer and Margaret Wu},
-  year = {2021},
-  note = {R package version 4.0-1},
+  year = {2022},
+  note = {R package version 4.1-1},
   url = {https://CRAN.R-project.org/package=TAM},
 }

 
diff --git a/docs/index.html b/docs/index.html
index 62d3e17..14abc1e 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -43,7 +43,7 @@
       
       
         TAM
-        4.0-1
+        4.1-1
       
     
 
@@ -111,7 +111,7 @@ 

 

 GitHub version

 
The version hosted here is the development version of TAM. The GitHub version can be installed using devtools as:

-
devtools::install_github("alexanderrobitzsch/TAM")

+
devtools::install_github("alexanderrobitzsch/TAM")

 
 
   
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index d7c4019..e57c35c 100644
--- 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: 2021-06-25T12:33Z
+last_built: 2022-05-15T07:23Z
 
diff --git a/docs/reference/DescribeBy.html b/docs/reference/DescribeBy.html
index 13eb753..120c36a 100644
--- a/docs/reference/DescribeBy.html
+++ b/docs/reference/DescribeBy.html
@@ -72,7 +72,7 @@
       
       
         TAM
-        4.0-vv
+        4.1-vv
       
     
 
diff --git a/docs/reference/IRT.WrightMap.html b/docs/reference/IRT.WrightMap.html
index 4879af2..16c598f 100644
--- a/docs/reference/IRT.WrightMap.html
+++ b/docs/reference/IRT.WrightMap.html
@@ -76,7 +76,7 @@
       
       
         TAM
-        4.0-vv
+        4.1-vv
       
     
 
diff --git a/docs/reference/IRT.cv.html b/docs/reference/IRT.cv.html
index 6b699c8..08821c1 100644
--- a/docs/reference/IRT.cv.html
+++ b/docs/reference/IRT.cv.html
@@ -72,7 +72,7 @@
       
       
         TAM
-        4.0-vv
+        4.1-vv
       
     
 
diff --git a/docs/reference/IRT.data.tam.html b/docs/reference/IRT.data.tam.html
index fd9307f..db676b4 100644
--- a/docs/reference/IRT.data.tam.html
+++ b/docs/reference/IRT.data.tam.html
@@ -74,7 +74,7 @@
       
       
         TAM
-        4.0-vv
+        4.1-vv
       
     
 
diff --git a/docs/reference/IRT.drawPV.html b/docs/reference/IRT.drawPV.html
index 82abee7..99f71de 100644
--- a/docs/reference/IRT.drawPV.html
+++ b/docs/reference/IRT.drawPV.html
@@ -75,7 +75,7 @@
       
       
         TAM
-        4.0-vv
+        4.1-vv
       
     
 
@@ -150,11 +150,11 @@ 
Examp
 #############################################################################
 
 library(sirt)
-data(data.read,package="sirt")
+data(data.read, package="sirt")
 dat <- data.read
 
 # fit Rasch model
-mod <- rasch.mml2(dat)
+mod <- rasch.mml2(dat)
 # draw 10 plausible values
 pv1 <- TAM::IRT.drawPV(mod, NPV=10)
 }
diff --git a/docs/reference/IRT.expectedCounts.tam.html b/docs/reference/IRT.expectedCounts.tam.html index cfe3f77..abf2875 100644 --- a/docs/reference/IRT.expectedCounts.tam.html +++ b/docs/reference/IRT.expectedCounts.tam.html @@ -74,7 +74,7 @@ TAM - 4.0-vv + 4.1-vv diff --git a/docs/reference/IRT.factor.scores.tam.html b/docs/reference/IRT.factor.scores.tam.html index 5abe8b8..5056dea 100644 --- a/docs/reference/IRT.factor.scores.tam.html +++ b/docs/reference/IRT.factor.scores.tam.html @@ -74,7 +74,7 @@ TAM - 4.0-vv + 4.1-vv diff --git a/docs/reference/IRT.frequencies.tam.html b/docs/reference/IRT.frequencies.tam.html index d66dfd6..9b0e40a 100644 --- a/docs/reference/IRT.frequencies.tam.html +++ b/docs/reference/IRT.frequencies.tam.html @@ -74,7 +74,7 @@ TAM - 4.0-vv + 4.1-vv diff --git a/docs/reference/IRT.informationCurves.html b/docs/reference/IRT.informationCurves.html index a808c0d..5c28bf7 100644 --- a/docs/reference/IRT.informationCurves.html +++ b/docs/reference/IRT.informationCurves.html @@ -72,7 +72,7 @@ TAM - 4.0-vv + 4.1-vv diff --git a/docs/reference/IRT.irfprob.tam.html b/docs/reference/IRT.irfprob.tam.html index 5331e31..bc34187 100644 --- a/docs/reference/IRT.irfprob.tam.html +++ b/docs/reference/IRT.irfprob.tam.html @@ -74,7 +74,7 @@ TAM - 4.0-vv + 4.1-vv diff --git a/docs/reference/IRT.itemfit.html b/docs/reference/IRT.itemfit.html index b5a8a86..8df5af5 100644 --- a/docs/reference/IRT.itemfit.html +++ b/docs/reference/IRT.itemfit.html @@ -76,7 +76,7 @@ TAM - 4.0-vv + 4.1-vv @@ -205,7 +205,7 @@

Examp a <- rep(1,I) a[c(3,8)] <- c( 1.7, .4 ) # simulate 2PL data -dat <- sirt::sim.raschtype( theta=rnorm(N), b=b, fixed.a=a) +dat <- sirt::sim.raschtype( theta=rnorm(N), b=b, fixed.a=a) # fit 1PL model mod <- TAM::tam.mml( dat ) diff --git a/docs/reference/IRT.likelihood.tam.html b/docs/reference/IRT.likelihood.tam.html index 08ea952..615847a 100644 --- a/docs/reference/IRT.likelihood.tam.html +++ b/docs/reference/IRT.likelihood.tam.html @@ -74,7 +74,7 @@ TAM - 4.0-vv + 4.1-vv diff --git a/docs/reference/IRT.linearCFA.html b/docs/reference/IRT.linearCFA.html index 8a632ad..3437e18 100644 --- a/docs/reference/IRT.linearCFA.html +++ b/docs/reference/IRT.linearCFA.html @@ -76,7 +76,7 @@ TAM - 4.0-vv + 4.1-vv diff --git a/docs/reference/IRT.residuals.html b/docs/reference/IRT.residuals.html index 4d2d16f..05731ea 100644 --- a/docs/reference/IRT.residuals.html +++ b/docs/reference/IRT.residuals.html @@ -76,7 +76,7 @@ TAM - 4.0-vv + 4.1-vv @@ -183,19 +183,21 @@

See a

See also predict.tam.mml.

Examples

- 
#############################################################################
+    
if (FALSE) {
+#############################################################################
 # EXAMPLE 1: Residuals data.read
 #############################################################################
 
 library(sirt)
-data(data.read,package="sirt")
+data(data.read, package="sirt")
 dat <- data.read
 
 # for Rasch model
 mod <- TAM::tam.mml( dat )
 # extract residuals
 res <- TAM::IRT.residuals( mod )
-str(res)

+str(res)
+}
diff --git a/docs/reference/IRT.threshold.html b/docs/reference/IRT.threshold.html index 23bffd6..5cac63e 100644 --- a/docs/reference/IRT.threshold.html +++ b/docs/reference/IRT.threshold.html @@ -78,7 +78,7 @@ TAM - 4.0-vv + 4.1-vv diff --git a/docs/reference/IRT.truescore.html b/docs/reference/IRT.truescore.html index 10b7146..d4c271c 100644 --- a/docs/reference/IRT.truescore.html +++ b/docs/reference/IRT.truescore.html @@ -77,7 +77,7 @@ TAM - 4.0-vv + 4.1-vv @@ -157,7 +157,7 @@

Value

true scores \(\tau( \theta ) \).

See also

-

See also sirt::truescore.irt +

See also sirt::truescore.irt for a conversion function for generalized partial credit models.

Examples

diff --git a/docs/reference/IRTLikelihood.cfa.html b/docs/reference/IRTLikelihood.cfa.html index 51a07a7..f09ae94 100644 --- a/docs/reference/IRTLikelihood.cfa.html +++ b/docs/reference/IRTLikelihood.cfa.html @@ -79,7 +79,7 @@ TAM - 4.0-vv + 4.1-vv
diff --git a/docs/reference/IRTLikelihood.ctt.html b/docs/reference/IRTLikelihood.ctt.html index e8ac07a..9888c02 100644 --- a/docs/reference/IRTLikelihood.ctt.html +++ b/docs/reference/IRTLikelihood.ctt.html @@ -73,7 +73,7 @@ TAM - 4.0-vv + 4.1-vv diff --git a/docs/reference/Scale.html b/docs/reference/Scale.html index ebdffe9..94d35a4 100644 --- a/docs/reference/Scale.html +++ b/docs/reference/Scale.html @@ -72,7 +72,7 @@ TAM - 4.0-vv + 4.1-vv diff --git a/docs/reference/TAM-defunct.html b/docs/reference/TAM-defunct.html index 468e929..6f3b45b 100644 --- a/docs/reference/TAM-defunct.html +++ b/docs/reference/TAM-defunct.html @@ -73,7 +73,7 @@ TAM - 4.0-vv + 4.1-vv diff --git a/docs/reference/TAM-package.html b/docs/reference/TAM-package.html index d8dc327..468609b 100644 --- a/docs/reference/TAM-package.html +++ b/docs/reference/TAM-package.html @@ -83,7 +83,7 @@ TAM - 4.0-vv + 4.1-vv diff --git a/docs/reference/TAM-utilities.html b/docs/reference/TAM-utilities.html index 4b979a5..d571936 100644 --- a/docs/reference/TAM-utilities.html +++ b/docs/reference/TAM-utilities.html @@ -72,7 +72,7 @@ TAM - 4.0-vv + 4.1-vv @@ -139,7 +139,7 @@

Utility Functions in TAM

## round some columns in a data frame and print this data frame tam_round_data_frame_print(obji, from=1, to=ncol(obji), digits=3, rownames_null=FALSE) ## copy of CDM::osink -tam_osink(file, suffix="__SUMMARY.Rout") +tam_osink(file, suffix=".Rout") ## copy of CDM::csink tam_csink(file) diff --git a/docs/reference/WLErel.html b/docs/reference/WLErel.html index c782616..6a60330 100644 --- a/docs/reference/WLErel.html +++ b/docs/reference/WLErel.html @@ -72,7 +72,7 @@ TAM - 4.0-vv + 4.1-vv diff --git a/docs/reference/anova.tam.html b/docs/reference/anova.tam.html index 1834235..ba3b3a7 100644 --- a/docs/reference/anova.tam.html +++ b/docs/reference/anova.tam.html @@ -77,7 +77,7 @@ TAM - 4.0-vv + 4.1-vv @@ -201,7 +201,7 @@

Examp # EXAMPLE 2: Dataset reading (sirt package): 1- vs. 2-dimensional model ############################################################################# -data(data.read,package="sirt") +data(data.read, package="sirt") # 1-dimensional model mod1 <- TAM::tam.mml.2pl(resp=data.read ) diff --git a/docs/reference/cfa.extract.itempars.html b/docs/reference/cfa.extract.itempars.html index 2e6ee5b..de72ca1 100644 --- a/docs/reference/cfa.extract.itempars.html +++ b/docs/reference/cfa.extract.itempars.html @@ -76,7 +76,7 @@ TAM - 4.0-vv + 4.1-vv diff --git a/docs/reference/data.cqc.html b/docs/reference/data.cqc.html index 571b567..1f3634b 100644 --- a/docs/reference/data.cqc.html +++ b/docs/reference/data.cqc.html @@ -73,7 +73,7 @@ TAM - 4.0-vv + 4.1-vv @@ -180,7 +180,7 @@

FormatSee also

-

See the sirt::R2conquest function +

See the sirt::R2conquest function for running ConQuest software from within R.

See the WrightMap package for functions connected to reading ConQuest files and creating Wright maps. @@ -219,16 +219,16 @@

Examp #------- ConQuest # estimate model -cmod01 <- sirt::R2conquest( dat, name="mod01", path.conquest=path.conquest) +cmod01 <- sirt::R2conquest( dat, name="mod01", path.conquest=path.conquest) summary(cmod01) # summary output # read shw file with some terms -shw01a <- sirt::read.show( "mod01.shw" ) +shw01a <- sirt::read.show( "mod01.shw" ) cmod01$shw.itemparameter # read person item maps -pi01a <- sirt::read.pimap( "mod01.shw" ) +pi01a <- sirt::read.pimap( "mod01.shw" ) cmod01$shw.pimap # read plausible values (npv=10 plausible values) -pv01a <- sirt::read.pv(pvfile="mod01.pv", npv=10) +pv01a <- sirt::read.pv(pvfile="mod01.pv", npv=10) cmod01$person # read ConQuest model @@ -256,7 +256,7 @@

Examp #--- ConQuest # estimate model maxK <- max( dat, na.rm=TRUE ) -cmod02a <- sirt::R2conquest( dat, itemcodes=0:maxK, model="item+item*step", +cmod02a <- sirt::R2conquest( dat, itemcodes=0:maxK, model="item+item*step", name="mod02a", path.conquest=path.conquest) summary(cmod02a) # summary output @@ -290,7 +290,7 @@

Examp X <- data.cqc03[,"rater",drop=FALSE] X$rater <- as.numeric(substring( X$rater, 2 )) # convert 'rater' in numeric format maxK <- max( resp, na.rm=TRUE) -cmod03a <- sirt::R2conquest( resp, X=X, regression="", model="item+step+rater", +cmod03a <- sirt::R2conquest( resp, X=X, regression="", model="item+step+rater", name="mod03a", path.conquest=path.conquest, set.constraints="cases" ) summary(cmod03a) # summary output diff --git a/docs/reference/data.ctest.html b/docs/reference/data.ctest.html index cab1246..a958632 100644 --- a/docs/reference/data.ctest.html +++ b/docs/reference/data.ctest.html @@ -72,7 +72,7 @@ TAM - 4.0-vv + 4.1-vv

diff --git a/docs/reference/data.examples.html b/docs/reference/data.examples.html index 7b36037..235213d 100644 --- a/docs/reference/data.examples.html +++ b/docs/reference/data.examples.html @@ -72,7 +72,7 @@ TAM - 4.0-vv + 4.1-vv
diff --git a/docs/reference/data.fims.Aus.Jpn.html b/docs/reference/data.fims.Aus.Jpn.html index 3c85d12..30ea196 100644 --- a/docs/reference/data.fims.Aus.Jpn.html +++ b/docs/reference/data.fims.Aus.Jpn.html @@ -74,7 +74,7 @@ TAM - 4.0-vv + 4.1-vv diff --git a/docs/reference/data.geiser.html b/docs/reference/data.geiser.html index 33c1f56..2ceac3d 100644 --- a/docs/reference/data.geiser.html +++ b/docs/reference/data.geiser.html @@ -73,7 +73,7 @@ TAM - 4.0-vv + 4.1-vv diff --git a/docs/reference/data.gpcm.html b/docs/reference/data.gpcm.html index 3fe2e92..f9f997e 100644 --- a/docs/reference/data.gpcm.html +++ b/docs/reference/data.gpcm.html @@ -72,7 +72,7 @@ TAM - 4.0-vv + 4.1-vv diff --git a/docs/reference/data.janssen.html b/docs/reference/data.janssen.html index 7267e3a..94a9ee4 100644 --- a/docs/reference/data.janssen.html +++ b/docs/reference/data.janssen.html @@ -72,7 +72,7 @@ TAM - 4.0-vv + 4.1-vv diff --git a/docs/reference/data.mc.html b/docs/reference/data.mc.html index 3e069c7..eb0abc7 100644 --- a/docs/reference/data.mc.html +++ b/docs/reference/data.mc.html @@ -73,7 +73,7 @@ TAM - 4.0-vv + 4.1-vv diff --git a/docs/reference/data.numeracy.html b/docs/reference/data.numeracy.html index 54d0e35..8779c23 100644 --- a/docs/reference/data.numeracy.html +++ b/docs/reference/data.numeracy.html @@ -73,7 +73,7 @@ TAM - 4.0-vv + 4.1-vv diff --git a/docs/reference/data.sim.mfr.html b/docs/reference/data.sim.mfr.html index 39521f1..ba5364f 100644 --- a/docs/reference/data.sim.mfr.html +++ b/docs/reference/data.sim.mfr.html @@ -72,7 +72,7 @@ TAM - 4.0-vv + 4.1-vv diff --git a/docs/reference/data.sim.rasch.html b/docs/reference/data.sim.rasch.html index 8c81da7..67a4deb 100644 --- a/docs/reference/data.sim.rasch.html +++ b/docs/reference/data.sim.rasch.html @@ -72,7 +72,7 @@ TAM - 4.0-vv + 4.1-vv diff --git a/docs/reference/data.timssAusTwn.html b/docs/reference/data.timssAusTwn.html index b7adc49..025fe36 100644 --- a/docs/reference/data.timssAusTwn.html +++ b/docs/reference/data.timssAusTwn.html @@ -75,7 +75,7 @@ TAM - 4.0-vv + 4.1-vv diff --git a/docs/reference/designMatrices.html b/docs/reference/designMatrices.html index 9839b8a..9f3d452 100644 --- a/docs/reference/designMatrices.html +++ b/docs/reference/designMatrices.html @@ -72,7 +72,7 @@ TAM - 4.0-vv + 4.1-vv diff --git a/docs/reference/doparse.html b/docs/reference/doparse.html index e99990b..47aa94f 100644 --- a/docs/reference/doparse.html +++ b/docs/reference/doparse.html @@ -83,7 +83,7 @@ TAM - 4.0-vv + 4.1-vv diff --git a/docs/reference/index.html b/docs/reference/index.html index 2dff57c..413e628 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -71,7 +71,7 @@ TAM - 4.0-vv + 4.1-vv diff --git a/docs/reference/lavaanify.IRT.html b/docs/reference/lavaanify.IRT.html index 50511f3..876c4b6 100644 --- a/docs/reference/lavaanify.IRT.html +++ b/docs/reference/lavaanify.IRT.html @@ -89,7 +89,7 @@ TAM - 4.0-vv + 4.1-vv @@ -197,10 +197,10 @@

See a

lavaan::lavaanify

-

See sirt::tam2mirt for +

See sirt::tam2mirt for converting objects of class tam into mirt objects.

-

See sirt::lavaan2mirt +

See sirt::lavaan2mirt for estimating models in the mirt package using lavaan syntax.

See doparse for the DO and DO2 statements.

diff --git a/docs/reference/msq.itemfit.html b/docs/reference/msq.itemfit.html index 1b2bc51..7f7e67f 100644 --- a/docs/reference/msq.itemfit.html +++ b/docs/reference/msq.itemfit.html @@ -78,7 +78,7 @@ TAM - 4.0-vv + 4.1-vv @@ -180,7 +180,9 @@

See a

See also eRm::itemfit or mirt::itemfit.

Examples

- 
#############################################################################
+    
if (FALSE) {
+
+#############################################################################
 # EXAMPLE 1: Simulated data Rasch model
 #############################################################################
 
@@ -194,7 +196,7 @@ 
Examp
 # create some misfitting items
 a[c(1,3)] <- c(.5, 1.5 )
 # simulate data
-dat <- sirt::sim.raschtype( rnorm(N), b=b, fixed.a=a )
+dat <- sirt::sim.raschtype( rnorm(N), b=b, fixed.a=a )
 #*** estimate Rasch model
 mod1 <- TAM::tam.mml(resp=dat)
 # compute WLEs
@@ -204,7 +206,6 @@ 
Examp
 fit1 <- TAM::msq.itemfit(mod1)
 summary( fit1 )
 
-if (FALSE) {
 #--- item fit using simulation in "tam.fit"
 fit0 <- TAM::tam.fit( mod1 )
 summary(fit0)
@@ -217,7 +218,7 @@ 
Examp
 library(mirt)
 mod1b <- mirt::mirt( dat, model=1, itemtype="Rasch", verbose=TRUE )
 print(mod1b)
-sirt::mirt.wrapper.coef(mod1b)
+sirt::mirt.wrapper.coef(mod1b)
 fmod1b <- mirt::itemfit(mod1b, Theta=as.matrix(wmod1,ncol=1),
                  Zh=TRUE, X2=FALSE, S_X2=FALSE )
 cbind( fit2a$fit_data, fmod1b )
@@ -242,7 +243,6 @@ 
Examp
 # using WLEs
 fit2b <- TAM::msq.itemfitWLE( mod1, fitindices )
 summary(fit2b)
-}
 
 #############################################################################
 # EXAMPLE 2: data.read | fit statistics assessed for testlets
@@ -273,7 +273,6 @@ 
Examp
 res2 <- TAM::msq.itemfitWLE( mod, fitindices )
 summary(res2)
 
-if (FALSE) {
 #############################################################################
 # EXAMPLE 3: Fit statistics for rater models
 #############################################################################
diff --git a/docs/reference/plot.tam.html b/docs/reference/plot.tam.html
index 601d59c..f749019 100644
--- a/docs/reference/plot.tam.html
+++ b/docs/reference/plot.tam.html
@@ -73,7 +73,7 @@
       
       
         TAM
-        4.0-vv
+        4.1-vv
       
     
 
diff --git a/docs/reference/plotDevianceTAM.html b/docs/reference/plotDevianceTAM.html
index 96e585b..19ad667 100644
--- a/docs/reference/plotDevianceTAM.html
+++ b/docs/reference/plotDevianceTAM.html
@@ -72,7 +72,7 @@
       
       
         TAM
-        4.0-vv
+        4.1-vv
       
     
 
diff --git a/docs/reference/predict.html b/docs/reference/predict.html
index ab76cd1..1a2df9b 100644
--- a/docs/reference/predict.html
+++ b/docs/reference/predict.html
@@ -75,7 +75,7 @@
       
       
         TAM
-        4.0-vv
+        4.1-vv
       
     
 
diff --git a/docs/reference/tam.ctt.html b/docs/reference/tam.ctt.html
index 67f0784..8e77972 100644
--- a/docs/reference/tam.ctt.html
+++ b/docs/reference/tam.ctt.html
@@ -73,7 +73,7 @@
       
       
         TAM
-        4.0-vv
+        4.1-vv
       
     
 
diff --git a/docs/reference/tam.fa.html b/docs/reference/tam.fa.html
index 61bc60f..3404b67 100644
--- a/docs/reference/tam.fa.html
+++ b/docs/reference/tam.fa.html
@@ -75,7 +75,7 @@
       
       
         TAM
-        4.0-vv
+        4.1-vv
       
     
 
diff --git a/docs/reference/tam.fit.html b/docs/reference/tam.fit.html
index 1ccab65..f52c4c7 100644
--- a/docs/reference/tam.fit.html
+++ b/docs/reference/tam.fit.html
@@ -74,7 +74,7 @@
       
       
         TAM
-        4.0-vv
+        4.1-vv
       
     
 
@@ -219,8 +219,8 @@ 
See a
 for models fitted with JML.

 
See tam.personfit for computing person fit statistics.

 
Item fit and person fit based on estimated person parameters can also be
-calculated using the sirt::pcm.fit function
-in the sirt package (see Example 1 and Example 2).

+calculated using the sirt::pcm.fit function
+in the sirt package (see Example 1 and Example 2).

 
     
Examples

     
#############################################################################
@@ -240,6 +240,8 @@ 
Examp
   ##   3         I3  1.022    0.330    0.185 1.012   0.366   0.179
   ##   4         I4  1.047    0.720    0.118 1.054   1.650   0.025
 
+if (FALSE) {
+
 #--------
 # infit and oufit based on estimated WLEs
 library(sirt)
@@ -249,11 +251,10 @@ 
Examp
 # extract item parameters
 b1 <- - mod1$AXsi[, -1 ]
 # assess item fit and person fit
-fit1a <- sirt::pcm.fit(b=b1, theta=wle$theta, data.sim.rasch )
+fit1a <- sirt::pcm.fit(b=b1, theta=wle$theta, data.sim.rasch )
 fit1a$item       # item fit statistic
 fit1a$person     # person fit statistic
 
-if (FALSE) {
 #############################################################################
 # EXAMPLE 2: Partial credit model data.gpcm
 #############################################################################
@@ -278,7 +279,7 @@ 
Examp
 # extract item parameters
 b1 <- - mod2$AXsi[, -1 ]
 # assess fit
-fit1a <- sirt::pcm.fit(b=b1, theta=wle$theta, dat)
+fit1a <- sirt::pcm.fit(b=b1, theta=wle$theta, dat)
 fit1a$item
 
 #############################################################################
@@ -334,7 +335,7 @@ 
Examp
 # create some misfitting items
 a[c(1,3)] <- c(.5, 1.5 )
 # simulate data
-dat <- sirt::sim.raschtype( rnorm(N), b=b, fixed.a=a )
+dat <- sirt::sim.raschtype( rnorm(N), b=b, fixed.a=a )
 #*** estimate Rasch model
 mod1 <- TAM::tam.mml(resp=dat)
 #*** assess item fit by infit and outfit statistic
@@ -346,7 +347,7 @@ 
Examp
 library(sirt)
 mod1c <- mirt::mirt( dat, model=1, itemtype="Rasch", verbose=TRUE)
 print(mod1c)                      # model summary
-sirt::mirt.wrapper.coef(mod1c)    # estimated parameters
+sirt::mirt.wrapper.coef(mod1c)    # estimated parameters
 fit1c <- mirt::itemfit(mod1c, method="EAP")    # model fit in mirt package
 # compare results of TAM and mirt
 dfr <- cbind( "TAM"=fit1, "mirt"=fit1c[,-c(1:2)] )
diff --git a/docs/reference/tam.jml.html b/docs/reference/tam.jml.html
index aeb5079..1d4df33 100644
--- a/docs/reference/tam.jml.html
+++ b/docs/reference/tam.jml.html
@@ -74,7 +74,7 @@
       
       
         TAM
-        4.0-vv
+        4.1-vv
       
     
 
diff --git a/docs/reference/tam.latreg.html b/docs/reference/tam.latreg.html
index eee06f9..7e382f3 100644
--- a/docs/reference/tam.latreg.html
+++ b/docs/reference/tam.latreg.html
@@ -78,7 +78,7 @@
       
       
         TAM
-        4.0-vv
+        4.1-vv
       
     
 
diff --git a/docs/reference/tam.linking.html b/docs/reference/tam.linking.html
index 17d7547..c94dd25 100644
--- a/docs/reference/tam.linking.html
+++ b/docs/reference/tam.linking.html
@@ -78,7 +78,7 @@
       
       
         TAM
-        4.0-vv
+        4.1-vv
       
     
 
@@ -304,10 +304,9 @@ 
See a
     
Linking or equating of item response models can be also conducted with plink
 (Weeks, 2010), equate, equateIRT (Battauz, 2015), equateMultiple,
 kequate and irteQ packages.

-
See also the sirt::linking.haberman,
-sirt::invariance.alignment and
-sirt::linking.haebara functions
-in the sirt package.

+
See also the sirt::linking.haberman,
+sirt::invariance.alignment and sirt::linking.haebara functions
+in the sirt package.

 
     
Examples

     
if (FALSE) {
@@ -453,9 +452,9 @@ 
Examp
 I <- 30    # number of items
 b <- seq(-2,2, length=I)
 # data for group 1
-dat1 <- sirt::sim.raschtype( rnorm(N, mean=0, sd=1), b=b )
+dat1 <- sirt::sim.raschtype( rnorm(N, mean=0, sd=1), b=b )
 # data for group 2
-dat2 <- sirt::sim.raschtype( rnorm(N, mean=1, sd=.6), b=b )
+dat2 <- sirt::sim.raschtype( rnorm(N, mean=1, sd=.6), b=b )
 
 # fit group 1
 mod1 <- TAM::tam.mml.2pl( resp=dat1 )
diff --git a/docs/reference/tam.mml.3pl.html b/docs/reference/tam.mml.3pl.html
index 05170c6..3d6c15e 100644
--- a/docs/reference/tam.mml.3pl.html
+++ b/docs/reference/tam.mml.3pl.html
@@ -74,7 +74,7 @@
       
       
         TAM
-        4.0-vv
+        4.1-vv
       
     
 
diff --git a/docs/reference/tam.mml.html b/docs/reference/tam.mml.html
index 9742f50..c746446 100644
--- a/docs/reference/tam.mml.html
+++ b/docs/reference/tam.mml.html
@@ -79,7 +79,7 @@
       
       
         TAM
-        4.0-vv
+        4.1-vv
       
     
 
@@ -642,7 +642,7 @@ 
See a
 
Standard errors are estimated by a rather crude (but quick) approximation.
 Use tam.se for improved standard errors.

 
For model comparisons see anova.tam.

-
See sirt::tam2mirt for converting
+
See sirt::tam2mirt for converting
 tam objects into objects of class
 mirt::mirt in the mirt package.

 
@@ -2072,7 +2072,7 @@ 
Examp
 I <- 100       # number of items
 set.seed(987)
 # simulate data according to the Rasch model
-dat <- sirt::sim.raschtype( stats::rnorm(N), b=seq(-2,2,len=I)  )
+dat <- sirt::sim.raschtype( stats::rnorm(N), b=seq(-2,2,len=I)  )
 # estimate models
 mod1n <- TAM::tam.mml( resp=dat, control=list( acceleration="none") )  # no acceler.
 mod1y <- TAM::tam.mml( resp=dat, control=list( acceleration="Yu") )  # Yu acceler.
diff --git a/docs/reference/tam.modelfit.html b/docs/reference/tam.modelfit.html
index a987e49..356538e 100644
--- a/docs/reference/tam.modelfit.html
+++ b/docs/reference/tam.modelfit.html
@@ -84,7 +84,7 @@
       
       
         TAM
-        4.0-vv
+        4.1-vv
       
     
 
@@ -333,7 +333,7 @@ 
Examp
 I <- 20      # number of items
 # simulate responses
 library(sirt)
-dat <- sirt::sim.raschtype( rnorm(N), b=seq(-1.5,1.5,len=I) )
+dat <- sirt::sim.raschtype( stats::rnorm(N), b=seq(-1.5,1.5,len=I) )
 #*** estimation
 mod1 <- TAM::tam.mml( dat )
 summary(dat)
diff --git a/docs/reference/tam.np.html b/docs/reference/tam.np.html
index 894ac64..be6e95d 100644
--- a/docs/reference/tam.np.html
+++ b/docs/reference/tam.np.html
@@ -79,7 +79,7 @@
       
       
         TAM
-        4.0-vv
+        4.1-vv
       
     
 
@@ -361,7 +361,7 @@ 
Examp
 a <- rep(1,I)
 a[c(3,8)] <- c(.5, 2)
 theta <- stats::rnorm(N, sd=1)
-dat <- sirt::sim.raschtype(theta, b=b, fixed.a=a)
+dat <- sirt::sim.raschtype(theta, b=b, fixed.a=a)
 
 #- 1PL model
 mod1 <- TAM::tam.mml(dat)
diff --git a/docs/reference/tam.personfit.html b/docs/reference/tam.personfit.html
index 9a6406d..5be8ca6 100644
--- a/docs/reference/tam.personfit.html
+++ b/docs/reference/tam.personfit.html
@@ -72,7 +72,7 @@
       
       
         TAM
-        4.0-vv
+        4.1-vv
       
     
 
diff --git a/docs/reference/tam.pv.html b/docs/reference/tam.pv.html
index 3e59a5e..97f1871 100644
--- a/docs/reference/tam.pv.html
+++ b/docs/reference/tam.pv.html
@@ -84,7 +84,7 @@
       
       
         TAM
-        4.0-vv
+        4.1-vv
       
     
 
@@ -573,7 +573,7 @@ 
Examp
 theta <- .5*X[,1] + .4*X[,2] + rnorm( N, sd=.5 )
 # simulate item responses
 itemdiff <- seq( -2, 2, length=I)  # item difficulties
-dat <- sirt::sim.raschtype( theta, b=itemdiff )
+dat <- sirt::sim.raschtype( theta, b=itemdiff )
 
 #***********************
 #*** Model 0: Regression model with true variables
diff --git a/docs/reference/tam.se.html b/docs/reference/tam.se.html
index 219cd56..d20d6ce 100644
--- a/docs/reference/tam.se.html
+++ b/docs/reference/tam.se.html
@@ -73,7 +73,7 @@
       
       
         TAM
-        4.0-vv
+        4.1-vv
       
     
 
diff --git a/docs/reference/tam.threshold.html b/docs/reference/tam.threshold.html
index 41969de..01e3524 100644
--- a/docs/reference/tam.threshold.html
+++ b/docs/reference/tam.threshold.html
@@ -73,7 +73,7 @@
       
       
         TAM
-        4.0-vv
+        4.1-vv
       
     
 
diff --git a/docs/reference/tam.wle.html b/docs/reference/tam.wle.html
index 45c9572..baee2b6 100644
--- a/docs/reference/tam.wle.html
+++ b/docs/reference/tam.wle.html
@@ -76,7 +76,7 @@
       
       
         TAM
-        4.0-vv
+        4.1-vv
       
     
 
diff --git a/docs/reference/tam_NA_pattern.html b/docs/reference/tam_NA_pattern.html
index d17ebdc..38e23aa 100644
--- a/docs/reference/tam_NA_pattern.html
+++ b/docs/reference/tam_NA_pattern.html
@@ -73,7 +73,7 @@
       
       
         TAM
-        4.0-vv
+        4.1-vv
       
     
 
@@ -134,7 +134,7 @@ 
Arg
 
     
Value

 
-    
List containing identifiers and indices

+    
List containing pattern identifiers and indices

 
     
Examples

     
#############################################################################
@@ -147,6 +147,7 @@ 
Examp
 res <- TAM::tam_NA_pattern(dat)
 str(res)
 
+if (FALSE) {
 #############################################################################
 # EXAMPLE 2: Item response patterns
 #############################################################################
@@ -155,7 +156,8 @@ 
Examp
 dat <- data.read
 
 res <- TAM::tam_01_pattern(dat)
-str(res)

+str(res)
+}

   
   
 
diff --git a/docs/reference/tam_irf_3pl.html b/docs/reference/tam_irf_3pl.html
index c4796f0..2cab744 100644
--- a/docs/reference/tam_irf_3pl.html
+++ b/docs/reference/tam_irf_3pl.html
@@ -73,7 +73,7 @@
       
       
         TAM
-        4.0-vv
+        4.1-vv
       
     
 
diff --git a/docs/reference/tamaan.html b/docs/reference/tamaan.html
index 1f33048..7f16fd0 100644
--- a/docs/reference/tamaan.html
+++ b/docs/reference/tamaan.html
@@ -76,7 +76,7 @@
       
       
         TAM
-        4.0-vv
+        4.1-vv
       
     
 
@@ -199,7 +199,9 @@ 
See a
 for more examples.

 
     
Examples

-    
#############################################################################
+    
if (FALSE) {
+
+#############################################################################
 # EXAMPLE 1: Examples dichotomous data data.read
 #############################################################################
 
@@ -221,7 +223,6 @@ 
Examp
 mod1 <- TAM::tamaan( tammodel, resp=dat)
 summary(mod1)
 
-if (FALSE) {
 #*********************************************************************
 #*** Model 2: 2PL model with some selected items
 
diff --git a/docs/reference/tamaanify.html b/docs/reference/tamaanify.html
index 65d6718..3e0d40d 100644
--- a/docs/reference/tamaanify.html
+++ b/docs/reference/tamaanify.html
@@ -75,7 +75,7 @@
       
       
         TAM
-        4.0-vv
+        4.1-vv
       
     
 
@@ -266,7 +266,9 @@ 
See a
 
lavaanify.IRT

 
     
Examples

-    
#############################################################################
+    
if (FALSE) {
+
+#############################################################################
 # EXAMPLE 1: Examples dichotomous data data.read
 #############################################################################
 
@@ -315,7 +317,6 @@ 
Examp
 out <- TAM::tamaanify( tammodel, resp=dat)
 str(out$E)     # E design matrix for estimation with tam.mml.3pl function
 
-if (FALSE) {
 #*********************************************************************
 #*** Model 3: Linear constraints for item intercepts and item loadings
 tammodel <- "
diff --git a/docs/reference/tampv2datalist.html b/docs/reference/tampv2datalist.html
index 6e0c152..dd2f14c 100644
--- a/docs/reference/tampv2datalist.html
+++ b/docs/reference/tampv2datalist.html
@@ -75,7 +75,7 @@
       
       
         TAM
-        4.0-vv
+        4.1-vv
       
     
 
diff --git a/docs/reference/weighted_Stats.html b/docs/reference/weighted_Stats.html
index 5623edd..b13bb41 100644
--- a/docs/reference/weighted_Stats.html
+++ b/docs/reference/weighted_Stats.html
@@ -75,7 +75,7 @@
       
       
         TAM
-        4.0-vv
+        4.1-vv
       
     
 
diff --git a/inst/NEWS b/inst/NEWS
index e2f78c7..346adf8 100644
--- a/inst/NEWS
+++ b/inst/NEWS
@@ -41,20 +41,28 @@ http://www.edmeasurementsurveys.com/TAM/Tutorials/
 
 
 
-
 -------------------------------------------------------------
-VERSIONS TAM 4.0  |  2021-06-25  |  Last: TAM 4.0-1
+VERSIONS TAM 4.1  |  2022-05-15  |  Last: TAM 4.1-1
 -------------------------------------------------------------
 
 xxx   * ...
 
+
 DATA  * included/modified datasets: ---
 EXAMP * included/modified examples: ---
 
 
 
+-------------------------------------------------------------
+VERSIONS TAM 4.0  |  2022-05-13  |  Last: TAM 4.0-16
+-------------------------------------------------------------
 
+NOTE  * changed default output file name suffix in tam_osink()
+NOTE  * new CRAN release because of recent removal of the 
+        CDM package from CRAN
 
+DATA  * included/modified datasets: ---
+EXAMP * included/modified examples: ---
 
 -------------------------------------------------------------
 VERSIONS TAM 3.7  |  2021-06-24  |  Last: TAM 3.7-16
diff --git a/man/IRT.drawPV.Rd b/man/IRT.drawPV.Rd
index d0599ea..14a82a0 100644
--- a/man/IRT.drawPV.Rd
+++ b/man/IRT.drawPV.Rd
@@ -1,5 +1,5 @@
 %% File Name: IRT.drawPV.Rd
-%% File Version: 0.13
+%% File Version: 0.141
 
 \name{IRT.drawPV}
 \alias{IRT.drawPV}
@@ -62,7 +62,7 @@ Matrix with plausible values
 #############################################################################
 
 library(sirt)
-data(data.read,package="sirt")
+data(data.read, package="sirt")
 dat <- data.read
 
 # fit Rasch model
diff --git a/man/IRT.residuals.Rd b/man/IRT.residuals.Rd
index 70b7c72..cd9f286 100644
--- a/man/IRT.residuals.Rd
+++ b/man/IRT.residuals.Rd
@@ -1,5 +1,5 @@
 %% File Name: IRT.residuals.Rd
-%% File Version: 0.17
+%% File Version: 0.182
 
 \name{IRT.residuals}
 \alias{IRT.residuals}
@@ -92,12 +92,13 @@ See also \code{\link[TAM:predict.tam.mml]{predict.tam.mml}}.
 
 
 \examples{
+\dontrun{
 #############################################################################
 # EXAMPLE 1: Residuals data.read
 #############################################################################
 
 library(sirt)
-data(data.read,package="sirt")
+data(data.read, package="sirt")
 dat <- data.read
 
 # for Rasch model
@@ -106,6 +107,7 @@ mod <- TAM::tam.mml( dat )
 res <- TAM::IRT.residuals( mod )
 str(res)
 }
+}
 % Add one or more standard keywords, see file 'KEYWORDS' in the
 % R documentation directory.
 %% \keyword{Residuals}
diff --git a/man/IRT.truescore.Rd b/man/IRT.truescore.Rd
index 69ac7a9..f1cc23a 100644
--- a/man/IRT.truescore.Rd
+++ b/man/IRT.truescore.Rd
@@ -1,5 +1,5 @@
 %% File Name: IRT.truescore.Rd
-%% File Version: 0.21
+%% File Version: 0.221
 
 \name{IRT.truescore}
 \alias{IRT.truescore}
@@ -52,7 +52,7 @@ true scores \eqn{\tau( \theta ) }.
 %% ~Make other sections like Warning with \section{Warning }{....} ~
 
 \seealso{
-See also \code{\link[sirt:truescore.irt]{sirt::truescore.irt}}
+See also \code{sirt::truescore.irt}
 for a conversion function for generalized partial credit models.
 }
 
diff --git a/man/TAM-utilities.Rd b/man/TAM-utilities.Rd
index 909bf8e..3a474fe 100644
--- a/man/TAM-utilities.Rd
+++ b/man/TAM-utilities.Rd
@@ -1,5 +1,5 @@
 %% File Name: TAM-utilities.Rd
-%% File Version: 0.666
+%% File Version: 0.667
 
 \name{TAM-utilities}
 \alias{TAM-utilities}
@@ -66,7 +66,7 @@ tam_round_data_frame(obji, from=1, to=ncol(obji), digits=3, rownames_null=FALSE)
 ## round some columns in a data frame and print this data frame
 tam_round_data_frame_print(obji, from=1, to=ncol(obji), digits=3, rownames_null=FALSE)
 ## copy of CDM::osink
-tam_osink(file, suffix="__SUMMARY.Rout")
+tam_osink(file, suffix=".Rout")
 ## copy of CDM::csink
 tam_csink(file)
 
diff --git a/man/anova.tam.Rd b/man/anova.tam.Rd
index 383a54c..1202a11 100644
--- a/man/anova.tam.Rd
+++ b/man/anova.tam.Rd
@@ -1,5 +1,5 @@
 %% File Name: anova.tam.Rd
-%% File Version: 2.33
+%% File Version: 2.341
 
 \name{anova-logLik}
 \alias{anova.tam}
@@ -116,7 +116,7 @@ anova( mod1, mod2 )
 # EXAMPLE 2: Dataset reading (sirt package): 1- vs. 2-dimensional model
 #############################################################################
 
-data(data.read,package="sirt")
+data(data.read, package="sirt")
 
 # 1-dimensional model
 mod1 <- TAM::tam.mml.2pl(resp=data.read )
diff --git a/man/data.cqc.Rd b/man/data.cqc.Rd
index b7cff5f..4931464 100644
--- a/man/data.cqc.Rd
+++ b/man/data.cqc.Rd
@@ -99,7 +99,7 @@ variables of following format
 
 
 \seealso{
-See the \code{\link[sirt:R2conquest]{sirt::R2conquest}} function
+See the \code{sirt::R2conquest} function
 for running ConQuest software from within \R.
 
 See the \pkg{\link[WrightMap:WrightMap]{WrightMap}} package for functions
diff --git a/man/lavaanify.IRT.Rd b/man/lavaanify.IRT.Rd
index a4c582d..8d9cc54 100644
--- a/man/lavaanify.IRT.Rd
+++ b/man/lavaanify.IRT.Rd
@@ -1,5 +1,5 @@
 %% File Name: lavaanify.IRT.Rd
-%% File Version: 1.40
+%% File Version: 1.411
 
 \name{lavaanify.IRT}
 \alias{lavaanify.IRT}
@@ -85,11 +85,11 @@ syntax if nonlinear factors are used.}
 \code{\link[lavaan:lavaanify]{lavaan::lavaanify}}
 
 
-See \code{\link[sirt:tam2mirt]{sirt::tam2mirt}} for
+See \code{sirt::tam2mirt} for
 converting objects of class \code{tam} into \code{mirt}
 objects.
 
-See \code{\link[sirt:lavaan2mirt]{sirt::lavaan2mirt}}
+See \code{sirt::lavaan2mirt}
 for estimating models in the \pkg{mirt} package using \code{lavaan} syntax.
 
 See \code{\link{doparse}} for the \code{DO} and \code{DO2} statements.
diff --git a/man/msq.itemfit.Rd b/man/msq.itemfit.Rd
index ef90fec..9707423 100644
--- a/man/msq.itemfit.Rd
+++ b/man/msq.itemfit.Rd
@@ -1,5 +1,5 @@
 %% File Name: msq.itemfit.Rd
-%% File Version: 0.39
+%% File Version: 0.402
 
 \name{msq.itemfit}
 
@@ -85,6 +85,8 @@ See also \code{eRm::itemfit} or \code{\link[mirt:itemfit]{mirt::itemfit}}.
 
 
 \examples{
+\dontrun{
+
 #############################################################################
 # EXAMPLE 1: Simulated data Rasch model
 #############################################################################
@@ -109,7 +111,6 @@ wmod1 <- TAM::tam.wle(mod1)$theta
 fit1 <- TAM::msq.itemfit(mod1)
 summary( fit1 )
 
-\dontrun{
 #--- item fit using simulation in "tam.fit"
 fit0 <- TAM::tam.fit( mod1 )
 summary(fit0)
@@ -147,7 +148,6 @@ summary(fit2)
 # using WLEs
 fit2b <- TAM::msq.itemfitWLE( mod1, fitindices )
 summary(fit2b)
-}
 
 #############################################################################
 # EXAMPLE 2: data.read | fit statistics assessed for testlets
@@ -178,7 +178,6 @@ summary(res1)
 res2 <- TAM::msq.itemfitWLE( mod, fitindices )
 summary(res2)
 
-\dontrun{
 #############################################################################
 # EXAMPLE 3: Fit statistics for rater models
 #############################################################################
diff --git a/man/tam.fit.Rd b/man/tam.fit.Rd
index e9ca661..dea9ca9 100644
--- a/man/tam.fit.Rd
+++ b/man/tam.fit.Rd
@@ -1,5 +1,5 @@
 %% File Name: tam.fit.Rd
-%% File Version: 2.562
+%% File Version: 2.564
 
 \name{tam.fit}
 
@@ -110,8 +110,8 @@ for models fitted with JML.
 See \code{\link{tam.personfit}} for computing person fit statistics.
 
 Item fit and person fit based on estimated person parameters can also be
-calculated using the \code{\link[sirt:pcm.fit]{sirt::pcm.fit}} function
-in the \pkg{sirt} package (see Example 1 and Example 2).
+calculated using the \code{sirt::pcm.fit} function
+in the \bold{sirt} package (see Example 1 and Example 2).
 }
 %% ~~objects to See Also as \code{\link{help}}, ~~~
 
@@ -133,6 +133,8 @@ summary(fit1)
   ##   3         I3  1.022    0.330    0.185 1.012   0.366   0.179
   ##   4         I4  1.047    0.720    0.118 1.054   1.650   0.025
 
+\dontrun{
+
 #--------
 # infit and oufit based on estimated WLEs
 library(sirt)
@@ -146,7 +148,6 @@ fit1a <- sirt::pcm.fit(b=b1, theta=wle$theta, data.sim.rasch )
 fit1a$item       # item fit statistic
 fit1a$person     # person fit statistic
 
-\dontrun{
 #############################################################################
 # EXAMPLE 2: Partial credit model data.gpcm
 #############################################################################
diff --git a/man/tam.latreg.Rd b/man/tam.latreg.Rd
index 6881f92..76bf1d8 100644
--- a/man/tam.latreg.Rd
+++ b/man/tam.latreg.Rd
@@ -1,5 +1,5 @@
 %% File Name: tam.latreg.Rd
-%% File Version: 0.31
+%% File Version: 0.321
 
 \name{tam.latreg}
 \alias{tam.latreg}
@@ -146,7 +146,7 @@ See also \code{\link{tam.pv}} for plausible value imputation.
 \dontrun{
 #############################################################################
 # EXAMPLE 1: Unidimensional latent regression model with fitted IRT model in
-#            sirt package
+#            the sirt package
 #############################################################################
 
 library(sirt)
diff --git a/man/tam.linking.Rd b/man/tam.linking.Rd
index 8649382..498154c 100644
--- a/man/tam.linking.Rd
+++ b/man/tam.linking.Rd
@@ -1,5 +1,5 @@
 %% File Name: tam.linking.Rd
-%% File Version: 0.625
+%% File Version: 0.627
 
 \name{tam.linking}
 \alias{tam.linking}
@@ -153,10 +153,9 @@ Linking or equating of item response models can be also conducted with \pkg{plin
 (Weeks, 2010), \pkg{equate}, \pkg{equateIRT} (Battauz, 2015), \pkg{equateMultiple},
 \pkg{kequate} and \pkg{irteQ} packages.
 
-See also the \code{\link[sirt:linking.haberman]{sirt::linking.haberman}},
-\code{\link[sirt:invariance.alignment]{sirt::invariance.alignment}} and
-\code{\link[sirt:linking.haebara]{sirt::linking.haebara}} functions
-in the \pkg{sirt} package.
+See also the \code{sirt::linking.haberman},
+\code{sirt::invariance.alignment} and \code{sirt::linking.haebara} functions
+in the \bold{sirt} package.
 }
 
 \examples{
diff --git a/man/tam.mml.Rd b/man/tam.mml.Rd
index 3343d6c..0fe0517 100644
--- a/man/tam.mml.Rd
+++ b/man/tam.mml.Rd
@@ -1,5 +1,5 @@
 %% File Name: tam.mml.Rd
-%% File Version: 2.989
+%% File Version: 2.991
 
 \name{tam.mml}
 
@@ -589,7 +589,7 @@ Use \code{\link{tam.se}} for improved standard errors.
 
 For model comparisons see \code{\link{anova.tam}}.
 
-See \code{\link[sirt:tam2mirt]{sirt::tam2mirt}} for converting
+See \code{sirt::tam2mirt} for converting
 \code{tam} objects into objects of class
 \code{\link[mirt:mirt]{mirt::mirt}} in the \pkg{mirt} package.
 }
diff --git a/man/tam.modelfit.Rd b/man/tam.modelfit.Rd
index 83f9fbb..a15cc80 100644
--- a/man/tam.modelfit.Rd
+++ b/man/tam.modelfit.Rd
@@ -1,5 +1,5 @@
 %% File Name: tam.modelfit.Rd
-%% File Version: 2.384
+%% File Version: 2.385
 
 \name{tam.modelfit}
 \alias{tam.modelfit}
@@ -245,7 +245,7 @@ N <- 1000    # number of persons
 I <- 20      # number of items
 # simulate responses
 library(sirt)
-dat <- sirt::sim.raschtype( rnorm(N), b=seq(-1.5,1.5,len=I) )
+dat <- sirt::sim.raschtype( stats::rnorm(N), b=seq(-1.5,1.5,len=I) )
 #*** estimation
 mod1 <- TAM::tam.mml( dat )
 summary(dat)
diff --git a/man/tam_NA_pattern.Rd b/man/tam_NA_pattern.Rd
index ddef46d..7a7dcfc 100644
--- a/man/tam_NA_pattern.Rd
+++ b/man/tam_NA_pattern.Rd
@@ -1,5 +1,5 @@
 %% File Name: tam_NA_pattern.Rd
-%% File Version: 0.05
+%% File Version: 0.062
 
 \name{tam_NA_pattern}
 \alias{tam_NA_pattern}
@@ -22,9 +22,7 @@ tam_01_pattern(x)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{
-\item{x}{
-Matrix or data frame
-}
+\item{x}{Matrix or data frame}
 }
 
 
@@ -34,7 +32,7 @@ Matrix or data frame
 
 
 \value{
-List containing identifiers and indices
+List containing pattern identifiers and indices
 }
 
 %\references{
@@ -65,6 +63,7 @@ dat <- data.sim.rasch.missing
 res <- TAM::tam_NA_pattern(dat)
 str(res)
 
+\dontrun{
 #############################################################################
 # EXAMPLE 2: Item response patterns
 #############################################################################
@@ -75,6 +74,7 @@ dat <- data.read
 res <- TAM::tam_01_pattern(dat)
 str(res)
 }
+}
 % Add one or more standard keywords, see file 'KEYWORDS' in the
 % R documentation directory.
 % \keyword{DO statements}
diff --git a/man/tamaan.Rd b/man/tamaan.Rd
index 45a0af8..dd4018f 100644
--- a/man/tamaan.Rd
+++ b/man/tamaan.Rd
@@ -1,5 +1,5 @@
 %% File Name: tamaan.Rd
-%% File Version: 0.56
+%% File Version: 0.571
 
 \name{tamaan}
 \alias{tamaan}
@@ -101,6 +101,8 @@ for more examples.
 
 
 \examples{
+\dontrun{
+
 #############################################################################
 # EXAMPLE 1: Examples dichotomous data data.read
 #############################################################################
@@ -123,7 +125,6 @@ ITEM TYPE:
 mod1 <- TAM::tamaan( tammodel, resp=dat)
 summary(mod1)
 
-\dontrun{
 #*********************************************************************
 #*** Model 2: 2PL model with some selected items
 
diff --git a/man/tamaanify.Rd b/man/tamaanify.Rd
index 263e11e..4499346 100644
--- a/man/tamaanify.Rd
+++ b/man/tamaanify.Rd
@@ -1,5 +1,5 @@
 %% File Name: tamaanify.Rd
-%% File Version: 0.553
+%% File Version: 0.554
 
 \name{tamaanify}
 \alias{tamaanify}
@@ -195,6 +195,8 @@ are included in \code{\link{tam.mml}} and \code{\link{tam.mml.3pl}}.
 
 
 \examples{
+\dontrun{
+
 #############################################################################
 # EXAMPLE 1: Examples dichotomous data data.read
 #############################################################################
@@ -244,7 +246,6 @@ LAVAAN MODEL:
 out <- TAM::tamaanify( tammodel, resp=dat)
 str(out$E)     # E design matrix for estimation with tam.mml.3pl function
 
-\dontrun{
 #*********************************************************************
 #*** Model 3: Linear constraints for item intercepts and item loadings
 tammodel <- "
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
index fe9266a..e4bf88d 100644
--- a/src/RcppExports.cpp
+++ b/src/RcppExports.cpp
@@ -1,5 +1,5 @@
 //// File Name: RcppExports.cpp
-//// File Version: 4.000001
+//// File Version: 4.001001
 // Generated by using Rcpp::compileAttributes() -> do not edit by hand
 // Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
@@ -7,6 +7,11 @@
 
 using namespace Rcpp; using namespace arma;
 
+#ifdef RCPP_USE_GLOBAL_ROSTREAM
+Rcpp::Rostream&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
+Rcpp::Rostream& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
+#endif
+
 // tam_rcpp_calc_exp
 Rcpp::List tam_rcpp_calc_exp(int NP, Rcpp::NumericVector rprobs, Rcpp::NumericVector A, Rcpp::NumericMatrix INDEXIPNO, Rcpp::NumericVector INDEXIPLIST2, Rcpp::NumericVector ESTXSIINDEX, int C, Rcpp::NumericMatrix ITEMWT, int NR, int TP);
 RcppExport SEXP _TAM_tam_rcpp_calc_exp(SEXP NPSEXP, SEXP rprobsSEXP, SEXP ASEXP, SEXP INDEXIPNOSEXP, SEXP INDEXIPLIST2SEXP, SEXP ESTXSIINDEXSEXP, SEXP CSEXP, SEXP ITEMWTSEXP, SEXP NRSEXP, SEXP TPSEXP) {
diff --git a/src/init.c b/src/init.c
index c4c9516..a1d33ad 100644
--- a/src/init.c
+++ b/src/init.c
@@ -1,5 +1,5 @@
 //// File Name: init.c
-//// File Version: 4.000001
+//// File Version: 4.001001
 #include 
 #include 
 #include  // for NULL
diff --git a/src/tam_rcpp_mml_2pl.cpp b/src/tam_rcpp_mml_2pl.cpp
index 4c1951b..9d0f528 100644
--- a/src/tam_rcpp_mml_2pl.cpp
+++ b/src/tam_rcpp_mml_2pl.cpp
@@ -1,5 +1,5 @@
 //// File Name: tam_rcpp_mml_2pl.cpp
-//// File Version: 0.515
+//// File Version: 0.516
 
 
 #include 
@@ -38,7 +38,7 @@ Rcpp::List tam_rcpp_mml_2pl_mstep_item_slopes_suffstat( Rcpp::NumericVector rpro
     double temp1=0;
     double temp2=0;
     double probs_temp=0;
-    if ( ( irtmodel[0] == "GPCM" ) | ( irtmodel[0] == "GPCM.design" ) ){
+    if ( ( irtmodel[0] == "GPCM" ) || ( irtmodel[0] == "GPCM.design" ) ){
         for (int tt=0; tt
@@ -121,7 +121,7 @@ Rcpp::List tam_rcpp_modelfit_counts( Rcpp::NumericMatrix resp0,
                 hwtii[tt] = hwtiifull[tt];
                 //**** expected counts
                 for (int nn=0;nn