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Warn user for invalid formula #562

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merged 3 commits into from
Nov 21, 2024
Merged

Warn user for invalid formula #562

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5403938
Warn user for invalif formula
strengejacke Nov 21, 2024
01aca65
add tests
strengejacke Nov 21, 2024
9bd1f6b
fix tests
strengejacke Nov 21, 2024
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Type: Package
Package: datawizard
Title: Easy Data Wrangling and Statistical Transformations
Version: 0.13.0.12
Version: 0.13.0.13
Authors@R: c(
person("Indrajeet", "Patil", , "[email protected]", role = "aut",
comment = c(ORCID = "0000-0003-1995-6531")),
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6 changes: 6 additions & 0 deletions R/standardize.models.R
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Expand Up @@ -78,6 +78,12 @@
return(x)
}

# check model formula. Some notations don't work when standardizing data
if (!insight::formula_ok(x, verbose = verbose)) {
insight::format_alert(insight::color_text("Model cannot be standardized.", "red"))
return(x)
}
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data_std <- NULL # needed to avoid note
.standardize_models(x,
robust = robust, two_sd = two_sd,
Expand All @@ -96,10 +102,10 @@
weights = TRUE,
verbose = TRUE,
include_response = TRUE,
update_expr,

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file=R/standardize.models.R,line=105,col=33,[function_argument_linter] Arguments without defaults should come before arguments with defaults.
...) {
m_info <- .get_model_info(x, ...)
data <- insight::get_data(x, source = "mf", verbose = FALSE)

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file=R/standardize.models.R,line=108,col=3,[object_overwrite_linter] 'data' is an exported object from package 'utils'. Avoid re-using such symbols.

if (isTRUE(attr(data, "is_subset"))) {
insight::format_error("Cannot standardize a model fit with a 'subset = '.")
Expand Down Expand Up @@ -365,7 +371,7 @@


if (!is.null(covs)) {
covs <- mapply(.rescale_fixed_values, covs, names(covs),

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file=R/standardize.models.R,line=374,col=13,[undesirable_function_linter] Avoid undesirable function "mapply".
SIMPLIFY = FALSE,
MoreArgs = list(
y_data = y_data, m_data = m_data,
Expand All @@ -391,7 +397,7 @@
#
# control.value <- temp_vals[1]
# treat.value <- temp_vals[2]
# if (verbose) insight::format_alert("control and treatment values have been rescaled to their standardized scales.")

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file=R/standardize.models.R,line=400,col=121,[line_length_linter] Lines should not be more than 120 characters. This line is 121 characters.
# }

if (verbose && !all(c(control.value, treat.value) %in% c(0, 1))) {
Expand All @@ -402,7 +408,7 @@
}


text <- utils::capture.output({

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file=R/standardize.models.R,line=411,col=3,[object_overwrite_linter] 'text' is an exported object from package 'graphics'. Avoid re-using such symbols.
model_std <- stats::update(x,
model.y = y_std, model.m = m_std,
# control.value = control.value, treat.value = treat.value
Expand Down Expand Up @@ -476,7 +482,7 @@

# check if model has a response variable that should not be standardized.
info$is_linear &&
!info$family == "inverse.gaussian" &&

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file=R/standardize.models.R,line=485,col=5,[comparison_negation_linter] Use x != y, not !(x == y).
!info$is_survival &&
!info$is_censored

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22 changes: 22 additions & 0 deletions tests/testthat/test-standardize_models.R
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Expand Up @@ -31,6 +31,28 @@ test_that("standardize | errors", {
})


test_that("standardize | problematic formulas", {
data(mtcars)
m <- lm(mpg ~ hp, data = mtcars)
expect_equal(
coef(standardise(m)),
c(`(Intercept)` = -3.14935717633686e-17, hp = -0.776168371826586),
tolerance = 1e-4
)

colnames(mtcars)[1] <- "1_mpg"
m <- lm(`1_mpg` ~ hp, data = mtcars)
expect_message(expect_warning(standardise(m), regex = "Looks like"))

data(mtcars)
m <- lm(mtcars$mpg ~ mtcars$hp)
expect_message(expect_warning(standardise(m), regex = "model formulas"))

m <- lm(mtcars[, 1] ~ hp, data = mtcars)
expect_message(expect_warning(standardise(m), regex = "indexed data"))
})
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# Transformations ---------------------------------------------------------
test_that("transformations", {
skip_if_not_installed("effectsize")
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