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Decorators: Accepts new snapshot from testthat::test() #1304

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merged 2 commits into from
Dec 17, 2024
Merged

Decorators: Accepts new snapshot from testthat::test() #1304

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379a390
fix: new snapshots
averissimo Dec 16, 2024
9dadf47
Merge branch '1187_decorate_output@main' into snapshots@1187_decorate…
averissimo Dec 17, 2024
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26 changes: 12 additions & 14 deletions tests/testthat/_snaps/tm_a_gee.md
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Original file line number Diff line number Diff line change
Expand Up @@ -13,9 +13,9 @@

$table
{
result_table <- tern.gee::as.rtable(model_fit, type = "cov")
subtitles(result_table) <- NULL
main_footer(result_table) <- NULL
table <- tern.gee::as.rtable(model_fit, type = "cov")
subtitles(table) <- NULL
main_footer(table) <- NULL
}


Expand All @@ -34,9 +34,9 @@

$table
{
result_table <- tern.gee::as.rtable(data.frame(Coefficient = model_fit$coefficients))
subtitles(result_table) <- NULL
main_footer(result_table) <- NULL
table <- tern.gee::as.rtable(data.frame(Coefficient = model_fit$coefficients))
subtitles(table) <- NULL
main_footer(table) <- NULL
}


Expand All @@ -56,13 +56,12 @@
$table
{
lsmeans_fit_model <- tern.gee::lsmeans(model_fit, 0.95)
result_table <- rtables::basic_table(show_colcounts = TRUE) %>%
table <- rtables::basic_table(show_colcounts = TRUE) %>%
rtables::split_cols_by(var = "ARM", ref_group = model_fit$ref_level) %>%
tern.gee::summarize_gee_logistic() %>% rtables::build_table(df = lsmeans_fit_model,
alt_counts_df = ANL_ADSL)
subtitles(result_table) <- NULL
main_footer(result_table) <- NULL
result_table
subtitles(table) <- NULL
main_footer(table) <- NULL
}


Expand All @@ -82,13 +81,12 @@
$table
{
lsmeans_fit_model <- tern.gee::lsmeans(model_fit, 0.95)
result_table <- rtables::basic_table(show_colcounts = TRUE) %>%
table <- rtables::basic_table(show_colcounts = TRUE) %>%
rtables::split_cols_by(var = "ARM", ref_group = model_fit$ref_level) %>%
tern.gee::summarize_gee_logistic() %>% rtables::build_table(df = lsmeans_fit_model,
alt_counts_df = ANL_ADSL)
subtitles(result_table) <- NULL
main_footer(result_table) <- NULL
result_table
subtitles(table) <- NULL
main_footer(table) <- NULL
}


10 changes: 4 additions & 6 deletions tests/testthat/_snaps/tm_a_mmrm.md
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Expand Up @@ -62,9 +62,8 @@

$cov_matrix
{
cov_matrix <- tern.mmrm::as.rtable(fit_mmrm, type = "cov")
subtitles(cov_matrix) <- NULL
cov_matrix
covariance_table <- tern.mmrm::as.rtable(fit_mmrm, type = "cov")
subtitles(covariance_table) <- NULL
}


Expand All @@ -80,9 +79,8 @@

$cov_matrix
{
cov_matrix <- tern.mmrm::as.rtable(fit_mmrm, type = "cov")
subtitles(cov_matrix) <- NULL
cov_matrix
covariance_table <- tern.mmrm::as.rtable(fit_mmrm, type = "cov")
subtitles(covariance_table) <- NULL
}


Expand Down
12 changes: 4 additions & 8 deletions tests/testthat/_snaps/tm_g_ci.md
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Expand Up @@ -4,15 +4,14 @@
res
Output
{
gg <- ggplot2::ggplot(data = ANL, mapping = ggplot2::aes(x = ARMCD,
plot <- ggplot2::ggplot(data = ANL, mapping = ggplot2::aes(x = ARMCD,
y = AVAL, color = SEX, lty = SEX, shape = SEX)) + ggplot2::stat_summary(fun.data = stat_mean_ci,
geom = "errorbar", width = 0.1, position = ggplot2::position_dodge(width = 0.5)) +
ggplot2::stat_summary(fun = mean, geom = "point", position = ggplot2::position_dodge(width = 0.5)) +
ggplot2::labs(title = "Confidence Interval Plot by Treatment Group",
caption = "Mean and 95% CIs for mean are displayed.",
x = "Treatment Group", y = "Value", color = "", lty = "",
shape = "")
print(gg)
}

# 3. Confidence Interval Plot (using different stratification variable)
Expand All @@ -21,7 +20,7 @@
res
Output
{
gg <- ggplot2::ggplot(data = ANL, mapping = ggplot2::aes(x = ARMCD,
plot <- ggplot2::ggplot(data = ANL, mapping = ggplot2::aes(x = ARMCD,
y = AVAL, color = STRATA2, lty = STRATA2, shape = STRATA2)) +
ggplot2::stat_summary(fun.data = stat_mean_ci, geom = "errorbar",
width = 0.1, position = ggplot2::position_dodge(width = 0.5)) +
Expand All @@ -30,7 +29,6 @@
caption = "Mean and 95% CIs for mean are displayed.",
x = "Treatment Group", y = "Value", color = "", lty = "",
shape = "")
print(gg)
}

# 4. Median and 95% CIs for median
Expand All @@ -39,7 +37,7 @@
res
Output
{
gg <- ggplot2::ggplot(data = ANL, mapping = ggplot2::aes(x = ARMCD,
plot <- ggplot2::ggplot(data = ANL, mapping = ggplot2::aes(x = ARMCD,
y = AVAL, color = STRATA1, lty = STRATA1, shape = STRATA1)) +
ggplot2::stat_summary(fun.data = stat_median_ci, geom = "errorbar",
width = 0.1, position = ggplot2::position_dodge(width = 0.5)) +
Expand All @@ -48,7 +46,6 @@
caption = "Median and 95% CIs for median are displayed.",
x = "Treatment Group", y = "Value", color = "", lty = "",
shape = "")
print(gg)
}

# 5. Using different alpha level
Expand All @@ -57,14 +54,13 @@
res
Output
{
gg <- ggplot2::ggplot(data = ANL, mapping = ggplot2::aes(x = ARMCD,
plot <- ggplot2::ggplot(data = ANL, mapping = ggplot2::aes(x = ARMCD,
y = AVAL, color = SEX, lty = SEX, shape = SEX)) + ggplot2::stat_summary(fun.data = function(x) stat_mean_ci(x,
conf_level = 0.9), geom = "errorbar", width = 0.1, position = ggplot2::position_dodge(width = 0.5)) +
ggplot2::stat_summary(fun = mean, geom = "point", position = ggplot2::position_dodge(width = 0.5)) +
ggplot2::labs(title = "Confidence Interval Plot by Treatment Group",
caption = "Mean and 90% CIs for mean are displayed.",
x = "Treatment Group", y = "Value", color = "", lty = "",
shape = "")
print(gg)
}

4 changes: 2 additions & 2 deletions tests/testthat/_snaps/tm_g_forest_rsp.md
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Expand Up @@ -35,7 +35,7 @@
as_list = TRUE)

$plot[[2]]
p <- cowplot::plot_grid(f[["table"]] + ggplot2::labs(title = "Forest Plot of Best Overall Response for "),
plot <- cowplot::plot_grid(f[["table"]] + ggplot2::labs(title = "Forest Plot of Best Overall Response for "),
f[["plot"]] + ggplot2::labs(caption = ""), align = "h", axis = "tblr",
rel_widths = c(1 - 0.25, 0.25))

Expand Down Expand Up @@ -80,7 +80,7 @@
as_list = TRUE)

$plot[[2]]
p <- cowplot::plot_grid(f[["table"]] + ggplot2::labs(title = "Forest Plot of Best Overall Response for "),
plot <- cowplot::plot_grid(f[["table"]] + ggplot2::labs(title = "Forest Plot of Best Overall Response for "),
f[["plot"]] + ggplot2::labs(caption = ""), align = "h", axis = "tblr",
rel_widths = c(1 - 0.25, 0.25))

Expand Down
4 changes: 2 additions & 2 deletions tests/testthat/_snaps/tm_g_forest_tte.md
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Expand Up @@ -38,7 +38,7 @@
as_list = TRUE)

$plot[[2]]
p <- cowplot::plot_grid(f[["table"]] + ggplot2::labs(title = "Forest Plot of Survival Duration for \nStratified by STRATA2",
plot <- cowplot::plot_grid(f[["table"]] + ggplot2::labs(title = "Forest Plot of Survival Duration for \nStratified by STRATA2",
subtitle = NULL), f[["plot"]] + ggplot2::labs(caption = ""),
align = "h", axis = "tblr", rel_widths = c(1 - 0.25, 0.25))

Expand Down Expand Up @@ -85,7 +85,7 @@
as_list = TRUE)

$plot[[2]]
p <- cowplot::plot_grid(f[["table"]] + ggplot2::labs(title = "Forest Plot of Survival Duration for \nStratified by STRATA2",
plot <- cowplot::plot_grid(f[["table"]] + ggplot2::labs(title = "Forest Plot of Survival Duration for \nStratified by STRATA2",
subtitle = NULL), f[["plot"]] + ggplot2::labs(caption = ""),
align = "h", axis = "tblr", rel_widths = c(1 - 0.25, 0.25))

Expand Down
3 changes: 0 additions & 3 deletions tests/testthat/_snaps/tm_g_km.md
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Expand Up @@ -52,7 +52,6 @@
g_km_counter <- g_km_counter_generator()
plot_list <- lapply(anl, g_km_counter)
plot <- cowplot::plot_grid(plotlist = plot_list, ncol = 1)
plot
}


Expand Down Expand Up @@ -114,7 +113,6 @@
g_km_counter <- g_km_counter_generator()
plot_list <- lapply(anl, g_km_counter)
plot <- cowplot::plot_grid(plotlist = plot_list, ncol = 1)
plot
}


Expand Down Expand Up @@ -177,7 +175,6 @@
g_km_counter <- g_km_counter_generator()
plot_list <- lapply(anl, g_km_counter)
plot <- cowplot::plot_grid(plotlist = plot_list, ncol = 1)
plot
}


2 changes: 0 additions & 2 deletions tests/testthat/_snaps/tm_g_lineplot.md
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Expand Up @@ -24,7 +24,6 @@
legend_title = NULL, ggtheme = ggplot2::theme_minimal(),
control = control_analyze_vars(conf_level = 0.95), subtitle_add_paramcd = FALSE,
subtitle_add_unit = FALSE)
plot
}


Expand Down Expand Up @@ -54,7 +53,6 @@
legend_title = NULL, ggtheme = ggplot2::theme_minimal(),
control = control_analyze_vars(conf_level = 0.9), subtitle_add_paramcd = FALSE,
subtitle_add_unit = FALSE)
plot
}


9 changes: 3 additions & 6 deletions tests/testthat/_snaps/tm_t_abnormality.md
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Expand Up @@ -38,9 +38,8 @@

$table
{
result <- rtables::build_table(lyt = lyt, df = anl, alt_counts_df = adsl) %>%
table <- rtables::build_table(lyt = lyt, df = anl, alt_counts_df = adsl) %>%
rtables::prune_table()
result
}


Expand Down Expand Up @@ -83,9 +82,8 @@

$table
{
result <- rtables::build_table(lyt = lyt, df = anl, alt_counts_df = adsl) %>%
table <- rtables::build_table(lyt = lyt, df = anl, alt_counts_df = adsl) %>%
rtables::prune_table()
result
}


Expand Down Expand Up @@ -129,9 +127,8 @@

$table
{
result <- rtables::build_table(lyt = lyt, df = anl, alt_counts_df = adsl) %>%
table <- rtables::build_table(lyt = lyt, df = anl, alt_counts_df = adsl) %>%
rtables::prune_table()
result
}


6 changes: 2 additions & 4 deletions tests/testthat/_snaps/tm_t_abnormality_by_worst_grade.md
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Expand Up @@ -40,8 +40,7 @@

$table
{
result <- rtables::build_table(lyt = lyt, df = anl, alt_counts_df = adsl)
result
table <- rtables::build_table(lyt = lyt, df = anl, alt_counts_df = adsl)
}


Expand Down Expand Up @@ -87,8 +86,7 @@

$table
{
result <- rtables::build_table(lyt = lyt, df = anl, alt_counts_df = myadsl)
result
table <- rtables::build_table(lyt = lyt, df = anl, alt_counts_df = myadsl)
}


21 changes: 7 additions & 14 deletions tests/testthat/_snaps/tm_t_ancova.md
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Expand Up @@ -30,8 +30,7 @@

$table
{
result <- rtables::build_table(lyt = lyt, df = adqs, alt_counts_df = adsl)
result
table <- rtables::build_table(lyt = lyt, df = adqs, alt_counts_df = adsl)
}


Expand Down Expand Up @@ -68,8 +67,7 @@

$table
{
result <- rtables::build_table(lyt = lyt, df = adqs, alt_counts_df = adsl)
result
table <- rtables::build_table(lyt = lyt, df = adqs, alt_counts_df = adsl)
}


Expand Down Expand Up @@ -107,8 +105,7 @@

$table
{
result <- rtables::build_table(lyt = lyt, df = adqs, alt_counts_df = adsl)
result
table <- rtables::build_table(lyt = lyt, df = adqs, alt_counts_df = adsl)
}


Expand Down Expand Up @@ -148,8 +145,7 @@

$table
{
result <- rtables::build_table(lyt = lyt, df = adqs, alt_counts_df = adsl)
result
table <- rtables::build_table(lyt = lyt, df = adqs, alt_counts_df = adsl)
}


Expand Down Expand Up @@ -187,8 +183,7 @@

$table
{
result <- rtables::build_table(lyt = lyt, df = adqs, alt_counts_df = adsl)
result
table <- rtables::build_table(lyt = lyt, df = adqs, alt_counts_df = adsl)
}


Expand Down Expand Up @@ -225,8 +220,7 @@

$table
{
result <- rtables::build_table(lyt = lyt, df = adqs, alt_counts_df = adsl)
result
table <- rtables::build_table(lyt = lyt, df = adqs, alt_counts_df = adsl)
}


Expand Down Expand Up @@ -263,8 +257,7 @@

$table
{
result <- rtables::build_table(lyt = lyt, df = adqs, alt_counts_df = adsl)
result
table <- rtables::build_table(lyt = lyt, df = adqs, alt_counts_df = adsl)
}


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