From f9bcebbec317e869e0e7b5d5a3012c761f0e27de Mon Sep 17 00:00:00 2001
From: corentinchoisy <corentin.choisy@proton.me>
Date: Tue, 3 Jun 2025 15:53:56 +0200
Subject: [PATCH] added na.action setting in pcm

---
 R/pcm.R    | 4 ++--
 man/pcm.Rd | 2 ++
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/R/pcm.R b/R/pcm.R
index 97b6aa8..8edc36f 100644
--- a/R/pcm.R
+++ b/R/pcm.R
@@ -14,6 +14,7 @@
 #' @param verbose set to TRUE to print a detailed output, FALSE otherwise
 #' @param fit string determining the optimization algorithm. Values "ucminf" or "nlminb" ar recommended
 #' @param method.theta string determining the estimation method for individual latent variable values. Either "eap", "mle" or "wle"
+#' @param na.action function for treatment of NAs to be passed to model estimation
 #' @return A data.frame containing various model outputs
 #' @import vcrpart
 #' @import PP
@@ -270,7 +271,6 @@ pcm <- function(df=NULL,items=NULL,grp=NULL,dif.items=NULL,type.dif=NULL,weights
     }
 
   }
-  if (is.null(grpo)) {
     if (method.theta=="eap") {
       theta <- c(-1*ranef(mod,norm=F)+ ifelse(is.null(grpo),0, ifelse(grp==1,beta,0) ) )
     } else if (method.theta=="wle") {
@@ -278,7 +278,7 @@ pcm <- function(df=NULL,items=NULL,grp=NULL,dif.items=NULL,type.dif=NULL,weights
     } else if (method.theta=="mle") {
       theta <- PP::PP_gpcm(as.matrix(df[,items]),t(restab),rep(1,length(items)),type="mle")$resPP$resPP[,1]
     }
-  }
+
 
   resid <- apply(matrix(1:nbitems,ncol=length(nbitems)),1, function(k) sapply(1:nrow(df), function(j) resi(theta[j],restab[k,],df[j,items[k]],beta=0)))
   colnames(resid) <- items_o
diff --git a/man/pcm.Rd b/man/pcm.Rd
index 1aa1a0e..253b854 100644
--- a/man/pcm.Rd
+++ b/man/pcm.Rd
@@ -35,6 +35,8 @@ pcm(
 \item{fit}{string determining the optimization algorithm. Values "ucminf" or "nlminb" ar recommended}
 
 \item{method.theta}{string determining the estimation method for individual latent variable values. Either "eap", "mle" or "wle"}
+
+\item{na.action}{function for treatment of NAs to be passed to model estimation}
 }
 \value{
 A data.frame containing various model outputs