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Add in missing analysis function option for custom statistics #1400

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Merged
merged 4 commits into from
Feb 26, 2025
Merged

Add in missing analysis function option for custom statistics #1400

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05b4071
Not using custom_stats_in param
edelarua Feb 25, 2025
1a3841f
Not using custom_stat_functions
edelarua Feb 25, 2025
75df6b4
Not using custom_stat_functions, update formatting
edelarua Feb 25, 2025
95a5e61
count_values done
edelarua Feb 25, 2025
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9 changes: 7 additions & 2 deletions R/abnormal.R
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Original file line number Diff line number Diff line change
Expand Up @@ -109,10 +109,15 @@ a_count_abnormal <- function(df,
extra_afun_params <- retrieve_extra_afun_params(names(dots_extra_args$.additional_fun_parameters))
dots_extra_args$.additional_fun_parameters <- NULL

# Check for user-defined functions
default_and_custom_stats_list <- .split_std_from_custom_stats(.stats)
.stats <- default_and_custom_stats_list$all_stats
custom_stat_functions <- default_and_custom_stats_list$custom_stats

# Apply statistics function
x_stats <- .apply_stat_functions(
default_stat_fnc = s_count_abnormal,
custom_stat_fnc_list = NULL,
custom_stat_fnc_list = custom_stat_functions,
args_list = c(
df = list(df),
extra_afun_params,
Expand All @@ -121,7 +126,7 @@ a_count_abnormal <- function(df,
)

# Fill in formatting defaults
.stats <- get_stats("abnormal", stats_in = .stats)
.stats <- get_stats("abnormal", stats_in = .stats, custom_stats_in = names(custom_stat_functions))
levels_per_stats <- lapply(x_stats, names)
.formats <- get_formats_from_stats(.stats, .formats, levels_per_stats)
.labels <- get_labels_from_stats(.stats, .labels, levels_per_stats)
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9 changes: 7 additions & 2 deletions R/abnormal_by_baseline.R
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Original file line number Diff line number Diff line change
Expand Up @@ -136,10 +136,15 @@ a_count_abnormal_by_baseline <- function(df,
extra_afun_params <- retrieve_extra_afun_params(names(dots_extra_args$.additional_fun_parameters))
dots_extra_args$.additional_fun_parameters <- NULL

# Check for user-defined functions
default_and_custom_stats_list <- .split_std_from_custom_stats(.stats)
.stats <- default_and_custom_stats_list$all_stats
custom_stat_functions <- default_and_custom_stats_list$custom_stats

# Apply statistics function
x_stats <- .apply_stat_functions(
default_stat_fnc = s_count_abnormal_by_baseline,
custom_stat_fnc_list = NULL,
custom_stat_fnc_list = custom_stat_functions,
args_list = c(
df = list(df),
extra_afun_params,
Expand All @@ -148,7 +153,7 @@ a_count_abnormal_by_baseline <- function(df,
)

# Fill in formatting defaults
.stats <- get_stats("abnormal_by_baseline", stats_in = .stats)
.stats <- get_stats("abnormal_by_baseline", stats_in = .stats, custom_stats_in = names(custom_stat_functions))
levels_per_stats <- lapply(x_stats, names)
.formats <- get_formats_from_stats(.stats, .formats, levels_per_stats)
.labels <- get_labels_from_stats(
Expand Down
9 changes: 7 additions & 2 deletions R/abnormal_by_marked.R
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Original file line number Diff line number Diff line change
Expand Up @@ -120,10 +120,15 @@ a_count_abnormal_by_marked <- function(df,
extra_afun_params <- retrieve_extra_afun_params(names(dots_extra_args$.additional_fun_parameters))
dots_extra_args$.additional_fun_parameters <- NULL

# Check for user-defined functions
default_and_custom_stats_list <- .split_std_from_custom_stats(.stats)
.stats <- default_and_custom_stats_list$all_stats
custom_stat_functions <- default_and_custom_stats_list$custom_stats

# Apply statistics function
x_stats <- .apply_stat_functions(
default_stat_fnc = s_count_abnormal_by_marked,
custom_stat_fnc_list = NULL,
custom_stat_fnc_list = custom_stat_functions,
args_list = c(
df = list(df),
extra_afun_params,
Expand All @@ -132,7 +137,7 @@ a_count_abnormal_by_marked <- function(df,
)

# Fill in formatting defaults
.stats <- get_stats("abnormal_by_marked", stats_in = .stats)
.stats <- get_stats("abnormal_by_marked", stats_in = .stats, custom_stats_in = names(custom_stat_functions))
levels_per_stats <- lapply(x_stats, names)
.formats <- get_formats_from_stats(.stats, .formats, levels_per_stats)
.labels <- get_labels_from_stats(.stats, .labels, levels_per_stats)
Expand Down
9 changes: 7 additions & 2 deletions R/abnormal_by_worst_grade.R
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Original file line number Diff line number Diff line change
Expand Up @@ -107,10 +107,15 @@ a_count_abnormal_by_worst_grade <- function(df,
extra_afun_params <- retrieve_extra_afun_params(names(dots_extra_args$.additional_fun_parameters))
dots_extra_args$.additional_fun_parameters <- NULL

# Check for user-defined functions
default_and_custom_stats_list <- .split_std_from_custom_stats(.stats)
.stats <- default_and_custom_stats_list$all_stats
custom_stat_functions <- default_and_custom_stats_list$custom_stats

# Apply statistics function
x_stats <- .apply_stat_functions(
default_stat_fnc = s_count_abnormal_by_worst_grade,
custom_stat_fnc_list = NULL,
custom_stat_fnc_list = custom_stat_functions,
args_list = c(
df = list(df),
extra_afun_params,
Expand All @@ -119,7 +124,7 @@ a_count_abnormal_by_worst_grade <- function(df,
)

# Fill in formatting defaults
.stats <- get_stats("abnormal_by_worst_grade", stats_in = .stats)
.stats <- get_stats("abnormal_by_worst_grade", stats_in = .stats, custom_stats_in = names(custom_stat_functions))
levels_per_stats <- lapply(x_stats, names)
.formats <- get_formats_from_stats(.stats, .formats, levels_per_stats)
.labels <- get_labels_from_stats(.stats, .labels, levels_per_stats)
Expand Down
13 changes: 11 additions & 2 deletions R/abnormal_lab_worsen_by_baseline.R
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Original file line number Diff line number Diff line change
Expand Up @@ -88,10 +88,15 @@ a_count_abnormal_lab_worsen_by_baseline <- function(df,
extra_afun_params <- retrieve_extra_afun_params(names(dots_extra_args$.additional_fun_parameters))
dots_extra_args$.additional_fun_parameters <- NULL

# Check for user-defined functions
default_and_custom_stats_list <- .split_std_from_custom_stats(.stats)
.stats <- default_and_custom_stats_list$all_stats
custom_stat_functions <- default_and_custom_stats_list$custom_stats

# Apply statistics function
x_stats <- .apply_stat_functions(
default_stat_fnc = s_count_abnormal_lab_worsen_by_baseline,
custom_stat_fnc_list = NULL,
custom_stat_fnc_list = custom_stat_functions,
args_list = c(
df = list(df),
extra_afun_params,
Expand All @@ -100,7 +105,11 @@ a_count_abnormal_lab_worsen_by_baseline <- function(df,
)

# Fill in formatting defaults
.stats <- get_stats("abnormal_lab_worsen_by_baseline", stats_in = .stats)
.stats <- get_stats(
"abnormal_lab_worsen_by_baseline",
stats_in = .stats,
custom_stats_in = names(custom_stat_functions)
)
levels_per_stats <- lapply(x_stats, names)
.formats <- get_formats_from_stats(.stats, .formats, levels_per_stats)
.labels <- get_labels_from_stats(.stats, .labels, levels_per_stats)
Expand Down
2 changes: 1 addition & 1 deletion R/summarize_ancova.R
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Original file line number Diff line number Diff line change
Expand Up @@ -237,7 +237,7 @@ a_ancova <- function(df,
)

# Fill in formatting defaults
.stats <- c(get_stats("summarize_ancova", stats_in = .stats), names(custom_stat_functions))
.stats <- get_stats("summarize_ancova", stats_in = .stats, custom_stats_in = names(custom_stat_functions))
x_stats <- x_stats[.stats]
.formats <- get_formats_from_stats(.stats, .formats)
.labels <- get_labels_from_stats(
Expand Down
6 changes: 1 addition & 5 deletions R/summarize_change.R
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Original file line number Diff line number Diff line change
Expand Up @@ -88,11 +88,7 @@ a_change_from_baseline <- function(df,
)

# Fill in with formatting defaults if needed
.stats <- get_stats(
"analyze_vars_numeric",
stats_in = .stats,
custom_stats_in = names(custom_stat_functions),
)
.stats <- get_stats("analyze_vars_numeric", stats_in = .stats, custom_stats_in = names(custom_stat_functions))
.formats <- get_formats_from_stats(.stats, .formats)
.labels <- get_labels_from_stats(.stats, .labels)
.indent_mods <- get_indents_from_stats(.stats, .indent_mods)
Expand Down
2 changes: 1 addition & 1 deletion R/summarize_glm_count.R
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Original file line number Diff line number Diff line change
Expand Up @@ -303,7 +303,7 @@ a_glm_count <- function(df,
)

# Fill in formatting defaults
.stats <- c(get_stats("summarize_glm_count", stats_in = .stats), names(custom_stat_functions))
.stats <- get_stats("summarize_glm_count", stats_in = .stats, custom_stats_in = names(custom_stat_functions))
.formats <- get_formats_from_stats(.stats, .formats)
.labels <- get_labels_from_stats(.stats, .labels)
.indent_mods <- get_indents_from_stats(.stats, .indent_mods)
Expand Down