improve VIF and actions

.github/workflows/pkgdown.yaml

@@ -1,6 +1,6 @@
 on:
   push:
-    branches: master
+    branches: main
 
 name: pkgdown
 

.github/workflows/test-coverage.yaml

@@ -1,10 +1,10 @@
 on:
   push:
     branches:
-      - master
+      - main
   pull_request:
     branches:
-      - master
+      - main
 
 name: test-coverage
 

NAMESPACE

@@ -10,8 +10,6 @@ importFrom(data.table, as.data.table)
 importFrom(data.table, setDT)
 
 useDynLib(miceFast,.registration=TRUE)
-export(corrData)
-export(miceFast)
 
 export(neibo)
 

NEWS.md

@@ -2,6 +2,7 @@
 
 * fixed CRAN Notes.
 * style the cpp code.
+* VIF() should be more stable.
 
 # miceFast 0.8.2
 

R/VIF.R

@@ -88,10 +88,10 @@ VIF <- function(x, posit_y, posit_x, correct = FALSE) {
 VIF.data.frame <- function(x, posit_y, posit_x, correct = FALSE) {
   x_small <- x[, c(posit_y, posit_x)]
   x_small[[1]] <- as.numeric(x_small[[1]])
-  xx <- model.matrix.lm(~.-1, x_small, na.action = "na.pass")
+  xx <- model.matrix.lm(~., x_small, na.action = "na.pass")
   aa <- attributes(xx)$assign
-  ll <- 2:ncol(xx)
-  VIF_(xx, 1, ll, aa[ll], correct)
+  ll <- 3:ncol(xx)
+  VIF_(xx, 2, ll, aa[ll], correct)
 }
 
 #' @describeIn  VIF
@@ -109,6 +109,7 @@ VIF.data.table <- function(x, posit_y, posit_x, correct = FALSE) {
 
 VIF.matrix <- function(x, posit_y, posit_x, correct = FALSE) {
   x_small <- x[, c(posit_y, posit_x)]
+  stopifnot(is.numeric(x_small))
   ncol_x <- ncol(x_small)
   VIF_(x_small, 1, 2:ncol_x, 2:ncol_x, correct)
 }

src/R_funs.cpp

@@ -1,6 +1,6 @@
 #include <RcppArmadillo.h>
-#include "miceFast.h"
 #include <math.h>
+#include "miceFast.h"
 
 arma::uvec get_index_full_R(arma::mat &x, int posit_y, arma::uvec posit_x) {
   arma::colvec y_col = x.col(posit_y);

vignettes/miceFast-intro.Rmd

@@ -86,23 +86,21 @@ upset_NA(air_miss, 6)
 
 ### Intro: dplyr
 
-```{r,echo=TRUE}
+```{r, echo=TRUE}
 # VIF - values bigger than 10 (around) suggest that there might be a collinearity problem.
 # VIF is high for Solar.R and x_character which is obvious - x_character is a factor version of numeric Solar.R
-air_miss %>%
-  do(vifs = VIF(.,
-    posit_y = "Ozone",
-    posit_x = c(
-      "Solar.R",
-      "Wind",
-      "Temp",
-      "x_character",
-      "Day",
-      "weights",
-      "groups"
-    )
-  )) %>%
-  unlist()
+VIF(air_miss,
+  posit_y = "Ozone",
+  posit_x = c(
+    "Solar.R",
+    "Wind",
+    "Temp",
+    "x_character",
+    "Day",
+    "weights",
+    "groups"
+  )
+)
 
 # IMPUTATIONS
 air_miss <- air_miss %>%