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add plot_pred compatibility with mids object and add test #132

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add plot_pred compatibility with mids object and add test #132

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e367963
add plot_pred compatibility with `mids` object and add test
pepijnvink Dec 7, 2023
60d7bf2
Update plot_pred.R
pepijnvink Dec 14, 2023
231e632
add warning
pepijnvink Dec 14, 2023
3def200
Change `Method` to `method`
pepijnvink Dec 14, 2023
58d832c
Merge branch 'main' into pr/132
hanneoberman Dec 21, 2023
22f0828
Message formatting
hanneoberman Dec 21, 2023
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14 changes: 12 additions & 2 deletions R/plot_pred.R
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
#' Plot the predictor matrix of an imputation model
#'
#' @param data A predictor matrix for `mice`, typically generated with [mice::make.predictorMatrix] or [mice::quickpred].
#' @param data A predictor matrix for `mice`, typically generated with [mice::make.predictorMatrix] or [mice::quickpred], or an object of class [`mice::mids`].

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file=R/plot_pred.R,line=3,col=151,[line_length_linter] Lines should not be more than 150 characters. This line is 159 characters.
#' @param vrb String, vector, or unquoted expression with variable name(s), default is "all".
#' @param method Character string or vector with imputation methods.
#' @param label Logical indicating whether predictor matrix values should be displayed.
Expand All @@ -20,7 +20,17 @@
label = TRUE,
square = TRUE,
rotate = FALSE) {
verify_data(data, pred = TRUE)
verify_data(data, pred = TRUE, imp = TRUE)
if (mice::is.mids(data)) {
if (!is.null(method)) {
cli::cli_warn(c(
"!" = "`Method` is ignored when `data` is of class `mids`.",
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"i" = "The `method` vector from the `mids` object will be used."
))
}
method <- data$method
data <- data$predictorMatrix
}
p <- nrow(data)
if (!is.null(method) && is.character(method)) {
if (length(method) == 1) {
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15 changes: 13 additions & 2 deletions R/utils.R
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@
#'
#' @keywords internal
#' @noRd
verify_data <- function(data,

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file=R/utils.R,line=38,col=1,[cyclocomp_linter] Functions should have cyclomatic complexity of less than 30, this has 40.
df = FALSE,
imp = FALSE,
pred = FALSE) {
Expand All @@ -52,7 +52,7 @@
}
if (df && imp) {
if (!(is.data.frame(data) ||
is.matrix(data) || mice::is.mids(data))) {

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file=R/utils.R,line=55,col=10,[indentation_linter] Indentation should be 12 spaces but is 10 spaces.
cli::cli_abort(
c(
"The 'data' argument requires an object of class 'data.frame', 'matrix', or 'mids'.",
Expand All @@ -62,7 +62,7 @@
)
}
}
if (imp && !df) {
if (imp && !df && !pred) {
if (!mice::is.mids(data)) {
cli::cli_abort(
c(
Expand All @@ -73,7 +73,18 @@
)
}
}
if (pred) {
if (imp && pred){

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file=R/utils.R,line=76,col=19,[brace_linter] There should be a space before an opening curly brace.

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if (!(is.matrix(data) || mice::is.mids(data))) {
cli::cli_abort(
c(
"The 'data' argument requires an object of class 'matrix', or 'mids'.",
"i" = "Input object is of class {class(data)}."
),
call. = FALSE
)
}
}
if (pred && !imp) {
if (!is.matrix(data)) {
cli::cli_abort(
c(
Expand Down
2 changes: 1 addition & 1 deletion man/plot_pred.Rd
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2 changes: 2 additions & 0 deletions tests/testthat/test-plot_pred.R
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
# create test objects
dat <- mice::nhanes
pred <- mice::quickpred(dat)
imp <- mice::mice(dat, printFlag = FALSE)

# tests
test_that("plot_pred creates ggplot object", {
Expand All @@ -18,6 +19,7 @@ test_that("plot_pred creates ggplot object", {
expect_s3_class(plot_pred(rbind(
cbind(pred, "with space" = 0), "with space" = 0
)), "ggplot")
expect_s3_class(plot_pred(imp, vrb = c("age", "bmi")), "ggplot")
})

test_that("plot_pred with incorrect argument(s)", {
Expand Down
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