3.17-6

alexanderrobitzsch · Feb 20, 2023 · fd560a9 · fd560a9
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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: 3.17-1
-Date: 2023-01-07 17:20:57
+Version: 3.17-6
+Date: 2023-02-20 15:12:34
 Author: 
     Alexander Robitzsch [aut,cre] (<https://orcid.org/0000-0002-8226-3132>),
     Simon Grund [aut] (<https://orcid.org/0000-0002-1290-8986>),

diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -1,5 +1,5 @@
 ## File Name: RcppExports.R
-## File Version: 3.017001
+## File Version: 3.017006
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 

diff --git a/R/mice.impute.pls.R b/R/mice.impute.pls.R
@@ -1,5 +1,5 @@
 ## File Name: mice.impute.pls.R
-## File Version: 3.745
+## File Version: 3.752
 
 
 mice.impute.pls <- function(y, ry, x, type, pls.facs=NULL,
@@ -54,6 +54,9 @@ mice.impute.pls <- function(y, ry, x, type, pls.facs=NULL,
     # define minimal correlation for interactions
     min.int.cor <- mice_imputation_extract_list_arguments( min.int.cor, vname, 0 )
 
+    # proportion of explained variance in PCA
+    pcamaxcols <- mice_imputation_extract_list_arguments( pcamaxcols, vname,  1e9 )
+
     #*** print progress | print section 1
     res <- mice_imputation_pls_print_progress1( pls.print.progress=pls.print.progress,
                     vname=vname, print.dims=print.dims, y=y, ry=ry, x=x, type=type )

diff --git a/R/mice_imputation_pls_do_impute.R b/R/mice_imputation_pls_do_impute.R
@@ -1,5 +1,5 @@
 ## File Name: mice_imputation_pls_do_impute.R
-## File Version: 0.207
+## File Version: 0.212
 
 mice_imputation_pls_do_impute <- function( x, y, ry, imputationWeights,
     use_weights, pls.impMethod, pls.print.progress,
@@ -8,7 +8,6 @@ mice_imputation_pls_do_impute <- function( x, y, ry, imputationWeights,
     # clean missing values
     x <- as.matrix(x)
     x <- mice_imputation_pls_clean_missings(x=x, eps=1e-12)
-
     colnames(x) <- gsub(" ", "", colnames(x) )
 
     #*** logical whether an imputation should be conducted
@@ -63,6 +62,7 @@ mice_imputation_pls_do_impute <- function( x, y, ry, imputationWeights,
             x1 <- mice_imputation_pls_pmm_match(yhatobs=yhatobs, yhatmis=yhatmis,
                         y=y, ry=ry, donors=donors)
         }
+
         if ( ! ( pls.impMethod %in% imp_methods_special) ){
             if (use_boot){
                 warning( paste0("Argument 'use_boot' cannot be used for imputation ",

diff --git a/R/mice_imputation_pls_pca_reduction.R b/R/mice_imputation_pls_pca_reduction.R
@@ -1,11 +1,13 @@
 ## File Name: mice_imputation_pls_pca_reduction.R
-## File Version: 0.13
+## File Version: 0.147
 
 
 mice_imputation_pls_pca_reduction <- function(x, pcamaxcols,
     pls.print.progress, imputationWeights=NULL, use_weights=FALSE)
 {
-    if (! use_weights ){ imputationWeights <- NULL }
+    if (! use_weights ){
+        imputationWeights <- NULL
+    }
     if ( ncol(x) > pcamaxcols ){
         a0 <- Sys.time()
         NX <- nrow(x)
@@ -25,7 +27,11 @@ mice_imputation_pls_pca_reduction <- function(x, pcamaxcols,
         xpca <- pca.covridge(x=x, wt=imputationWeights)
         varexpl <- xpca$sdev^2
         varexpl <- cumsum( varexpl / sum( varexpl) * 100 )
-        xdims <- which( varexpl > 100*pcamaxcols )[1]
+        if (pcamaxcols<1){
+            xdims <- which( varexpl > 100*pcamaxcols )[1]
+        } else {
+            xdims <- pcamaxcols
+        }
         if (pls.print.progress){
             cat( " ->", xdims, "extracted dimensions\n")
             cat("Explained variance:", round( varexpl[ xdims], 2 ), " % " )
@@ -35,7 +41,7 @@ mice_imputation_pls_pca_reduction <- function(x, pcamaxcols,
         if (pls.print.progress){
             cat("\nTime needed:", a1-a0, "\n")
         }
-    }
+    }  # PCA dimension reduction
     #--- output
     return(x)
 }
diff --git a/R/syn_da_create_formula.R b/R/syn_da_create_formula.R
@@ -1,5 +1,5 @@
 ## File Name: syn_da_create_formula.R
-## File Version: 0.03
+## File Version: 0.04
 
 syn_da_create_formula <- function(wv, ord_vars)
 {

diff --git a/README.md b/README.md
@@ -24,9 +24,9 @@ The CRAN version can be installed from within R using:
 utils::install.packages("miceadds")
 ```
 
-#### GitHub version `miceadds` 3.17-1 (2023-01-07)
+#### GitHub version `miceadds` 3.17-6 (2023-02-20)
 
-[![](https://img.shields.io/badge/github%20version-3.17--1-orange.svg)](https://github.com/alexanderrobitzsch/miceadds)&#160;&#160;
+[![](https://img.shields.io/badge/github%20version-3.17--6-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/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: 2023-01-07T16:32Z
+last_built: 2023-02-20T14:24Z
 
diff --git a/docs/reference/mice.impute.pls.html b/docs/reference/mice.impute.pls.html
diff --git a/inst/NEWS b/inst/NEWS
@@ -44,7 +44,7 @@ CHANGELOG miceadds
 
 
 --------------------------------------------------------------------------
-VERSIONS miceadds 3.17  |  2023-01-07  |  Last: miceadds 3.17-1
+VERSIONS miceadds 3.17  |  2023-02-20  |  Last: miceadds 3.17-6
 --------------------------------------------------------------------------
 
 xxx   * ---

diff --git a/man/mice.impute.pls.Rd b/man/mice.impute.pls.Rd
@@ -1,5 +1,5 @@
 %% File Name: mice.impute.pls.Rd
-%% File Version: 2.383
+%% File Version: 2.384
 
 \name{mice.impute.pls}
 \alias{mice.impute.pls}
@@ -81,7 +81,7 @@ Vector of sample weights to be used in imputation models.
 }
   \item{pcamaxcols}{
 Amount of variance explained by principal components (must be a number between
-0 and 1)
+0 and 1) or number of factors used in PCA (an integer larger than 1).
 }
   \item{min.int.cor}{
 Minimum absolute correlation for an interaction of two predictors

diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
@@ -1,5 +1,5 @@
 //// File Name: RcppExports.cpp
-//// File Version: 3.017001
+//// File Version: 3.017006
 // Generated by using Rcpp::compileAttributes() -> do not edit by hand
 // Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393