3.18-2

alexanderrobitzsch · Jan 10, 2024 · eba4fbc · eba4fbc
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: miceadds
 Type: Package
 Title: Some Additional Multiple Imputation Functions, Especially for 'mice'
-Version: 3.17-34
-Date: 2023-10-20 20:14:09.576992
+Version: 3.18-2
+Date: 2024-01-10 09:23:28
 Author: 
     Alexander Robitzsch [aut,cre] (<https://orcid.org/0000-0002-8226-3132>),
     Simon Grund [aut] (<https://orcid.org/0000-0002-1290-8986>),
@@ -47,7 +47,7 @@ Enhances:
     simputation
 URL: 
     https://github.com/alexanderrobitzsch/miceadds,
-    https://sites.google.com/site/alexanderrobitzsch2/software
+    https://sites.google.com/view/alexander-robitzsch/software
 License: 
     GPL (>= 2)
 BugReports: 

diff --git a/NAMESPACE b/NAMESPACE
@@ -166,8 +166,8 @@ importFrom(Rcpp, sourceCpp)
 #############################
 ## exports
 
-export(complete.mids.1chain)
-export(complete.mids.nmi)
+# export(complete.mids.1chain)
+# export(complete.mids.nmi)
 export(create.designMatrices.waldtest)
 export(crlrem)
 export(cwc)
@@ -371,6 +371,8 @@ S3method(coef, mipo.nmi)
 S3method(coef, ml_mcmc)
 S3method(coef, pool_mi)
 S3method(coef, lmer_vcov)
+S3method(complete, mids.1chain)
+S3method(complete, mids.nmi)
 S3method(MIcombine, NestedImputationResultList)
 S3method(plot, mids.1chain)
 S3method(plot, ml_mcmc)

diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -1,5 +1,5 @@
 ## File Name: RcppExports.R
-## File Version: 3.017034
+## File Version: 3.018002
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 

diff --git a/R/complete.miceadds.R b/R/complete.miceadds.R
@@ -1,27 +1,26 @@
 ## File Name: complete.miceadds.R
-## File Version: 0.11
+## File Version: 0.124
 
-
-#######################################################
-# complete function for nested multiple imputation
-complete.mids.nmi <- function( x, action=c(1,1) )
+#*** complete function for nested multiple imputation
+complete.mids.nmi <- function( data, action=c(1,1), ... )
 {
+    x <- data
     if ( x$type=="mice" ){
         x1 <- x$imp
-        data <- mice::complete( x1[[ action[1] ]], action=action[2] )
+        data <- mice::complete( data=x1[[ action[1] ]], action=action[2], ... )
     }
     if ( x$type=="mice.1chain" ){
-        data <- complete.mids.1chain( x$imp[[ action[1] ]], action=action[2] )
+        data <- complete.mids.1chain( x$imp[[ action[1] ]], action=action[2], ...)
     }
     return(data)
 }
-#######################################################
 
 
-#######################################################
-# complete function for objects of class mids.1chain
-complete.mids.1chain <- function( x, action=1 )
+#*** complete function for objects of class mids.1chain
+complete.mids.1chain <- function( data, action=1, ...)
 {
-    mice::complete( x$midsobj, action=action )
+    x <- data
+    data <- mice::complete( data=x$midsobj, action=action, ...)
+    return(data)
 }
-#######################################################
+
diff --git a/R/datalist2mids.R b/R/datalist2mids.R
@@ -1,5 +1,5 @@
 ## File Name: datalist2mids.R
-## File Version: 0.41
+## File Version: 0.432
 
 datalist2mids <- function( dat.list, progress=FALSE )
 {

diff --git a/R/mice.1chain.R b/R/mice.1chain.R
@@ -1,5 +1,5 @@
 ## File Name: mice.1chain.R
-## File Version: 0.672
+## File Version: 0.673
 
 #*** apply mice algorithm in a single chain
 mice.1chain <- function(data, burnin=10, iter=20, Nimp=10,
@@ -59,7 +59,7 @@ mice.1chain <- function(data, burnin=10, iter=20, Nimp=10,
         implist[[mm+1]] <- imp1 <- mice::mice( data, maxit=maxit_temp, m=1,
                     method=method, where=where, visitSequence=visitSequence,
                     blots=blots, post=post, defaultMethod=defaultMethod,
-                    printFlag=printFlag, seed=seed, 
+                    printFlag=printFlag, seed=seed,
                     data.init=mice::complete(implist[[mm]], action=1), ... )
         datlist[[mm]] <- dat0 <- mice::complete( imp1, 1 )
         chainMean <- rbind( chainMean, t( imp1$chainMean[,,1] ) )

diff --git a/R/systime.R b/R/systime.R
@@ -1,11 +1,12 @@
 ## File Name: systime.R
-## File Version: 0.11
+## File Version: 0.124
 
 
 #-- several variants for getting system time
 systime <- function()
 {
     s1 <- paste(Sys.time())
+    s1 <- substring(s1,1,19)
     res <- c( s1, substring( s1, 1,10) )
     res <- c(res, gsub("-","",res[2] ) )
     s1a <- substring( s1, 1, 16 )

diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@ all necessary information on the used librarys, the R version, and the OS it is
 
 The manual can be found here [https://alexanderrobitzsch.github.io/miceadds/](https://alexanderrobitzsch.github.io/miceadds/) 
 
-#### CRAN version `miceadds` 3.16-18 (2023-01-06)
+#### CRAN version `miceadds` 3.17-44 (2024-01-08)
 
 
 [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version-last-release/miceadds)](https://cran.r-project.org/package=miceadds)
@@ -24,9 +24,9 @@ The CRAN version can be installed from within R using:
 utils::install.packages("miceadds")
 ```
 
-#### GitHub version `miceadds` 3.17-34 (2023-10-20)
+#### GitHub version `miceadds` 3.18-2 (2024-01-10)
 
-[![](https://img.shields.io/badge/github%20version-3.17--34-orange.svg)](https://github.com/alexanderrobitzsch/miceadds)&#160;&#160;
+[![](https://img.shields.io/badge/github%20version-3.18--2-orange.svg)](https://github.com/alexanderrobitzsch/miceadds)&#160;&#160;
 
 The version hosted [here](https://github.com/alexanderrobitzsch/miceadds) is the development version of `miceadds`. 
 The GitHub version can be installed from within R using:

diff --git a/inst/CITATION b/inst/CITATION
@@ -25,7 +25,7 @@ citHeader( paste0( "To cite the '", pkg , "' package in publications use:") )
 bibentry(key = paste0(pkg, "_", meta$Version), 
          bibtype = "Manual",
          title = paste0( pkg , ": " , pkg_title ) ,
-         author = personList( person_list1 ),
+         author = c( person_list1 ),
          year = year,
          note = vers,
          url =  paste0( "https://CRAN.R-project.org/package=", pkg) ,

diff --git a/inst/NEWS b/inst/NEWS
@@ -44,21 +44,34 @@ CHANGELOG miceadds
 
 
 --------------------------------------------------------------------------
-VERSIONS miceadds 3.17  |  2023-10-20  |  Last: miceadds 3.17-34
+VERSIONS miceadds 3.18  |  2024-01-10  |  Last: miceadds 3.18-2
+--------------------------------------------------------------------------
+
+xxx   * ---
+
+
+DATA  * ---
+EXAMP * ---
+
+
+
+--------------------------------------------------------------------------
+VERSIONS miceadds 3.17  |  2024-01-08  |  Last: miceadds 3.17-44
 --------------------------------------------------------------------------
 
 ADDED * added argument 'derived_vars' in mice.impute.pls() for including
         derived variables in PLS dimension reduction
         (requested by Karoline Sachse)
 FIXED * fixed specification issues in mice.1chain()
-
+NOTE  * rechanged functionality of systime() due to changes of the 
+        Sys.time() function since R 4.3.1
+NOTE  * complete functions in miceadds are now declared as a method in
+        the manual. Moreover, renamed argument 'x' into 'data'
+        (requested by Kurt Hornik from the CRAN team)
 
 DATA  * ---
 EXAMP * mice.impute.pls (1), lm.cluster (3)
 
-
-
-
 --------------------------------------------------------------------------
 VERSIONS miceadds 3.16  |  2023-01-06  |  Last: miceadds 3.16-18
 --------------------------------------------------------------------------

diff --git a/man/complete.miceadds.Rd b/man/complete.miceadds.Rd
@@ -1,5 +1,5 @@
 %% File Name: complete.miceadds.Rd
-%% File Version: 0.20
+%% File Version: 0.214
 
 \name{complete.miceadds}
 \alias{complete.mids.nmi}
@@ -17,14 +17,18 @@ Creates imputed dataset from a \code{mids.nmi} or \code{mids.1chain} object.
 }
 
 \usage{
-complete.mids.nmi( x, action=c(1,1) )
+\method{complete}{mids.nmi}(data, action=c(1,1), ...)
 
-complete.mids.1chain( x, action=1 )
+\method{complete}{mids.1chain}(data, action=1, ...)
 }
 
+% complete.mids.nmi( x, action=c(1,1) )
+
+% complete.mids.1chain( x, action=1 )
+
 %- maybe also 'usage' for other objects documented here.
 \arguments{
-\item{x}{
+\item{data}{
 Object of class \code{mids.nmi} (for \code{complete.mids.nmi}) or
 \code{mids.1chain} (for \code{complete.mids.1chain})
 }
@@ -33,6 +37,7 @@ A vector of length two indicating to indices of between and within
 imputed dataset for for \code{complete.mids.nmi} and an integer for the
 index of imputed dataset for \code{complete.mids.1chain}.
 }
+\item{\dots}{More arguments to be passed}
 }
 
 %\details{