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694 fix stats ancova old versions@main #695

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merged 2 commits into from
Aug 30, 2022
Merged

694 fix stats ancova old versions@main #695

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7a4134b
fix class error
Melkiades Aug 30, 2022
3c564ce
fixing bug 2
Melkiades Aug 30, 2022
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3 changes: 2 additions & 1 deletion NEWS.md
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Expand Up @@ -39,7 +39,8 @@
* Renamed `test-assertthat.R` to `test-utils_checkmate.R`.

### Bug Fixes
* Fixed bugs from tests that rely on `stats::ancova`. They are probably due to an external update.
* Fixed bugs from tests that rely on `stats::ancova`. Adding more general solutions. They
are probably due to an external update.
* Fixed tests to respect the new standard print for `NA`.
* Fixed error in tests coming from changes in `formatters::var_labels()`.
* Identified bug in `prop_diff` functions. Coding of responses have been corrected (TRUE is a success).
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2 changes: 1 addition & 1 deletion R/coxph.R
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Expand Up @@ -320,7 +320,7 @@ s_cox_univariate <- function(formula,
lrt <- Map(
f = function(without_interaction,
with_interaction) {
stats::anova(without_interaction$mod, with_interaction$mod)[2, "Pr(>|Chi|)"]
stats::anova(without_interaction$mod, with_interaction$mod)[2, 4] # Pr(>|Chi|)
},
without_interaction = fit[2:(length(covariates) + 1)],
with_interaction = fit[-(1:(length(covariates) + 1))] # nolint
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6 changes: 5 additions & 1 deletion tests/testthat/test-summarize_ancova.R
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Expand Up @@ -8,6 +8,10 @@ testthat::test_that("h_ancova works with healthy input", {
) %>%
as.data.frame()

# Fixing class differences between versions
exp_class <- "data.frame"
if (inherits(result, "summary_emm")) exp_class <- c("summary_emm", exp_class)

expected <- structure(
data.frame(
Species = as.factor(c("setosa", "versicolor", "virginica")),
Expand All @@ -17,7 +21,7 @@ testthat::test_that("h_ancova works with healthy input", {
lower.CL = c(5.488497, 5.585349, 5.112255),
upper.CL = c(6.821149, 5.849469, 5.700498)
),
class = c("summary_emm", "data.frame"),
class = exp_class,
estName = "emmean",
clNames = c("lower.CL", "upper.CL"),
pri.vars = "Species",
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