Refactoring of analyze_vars with specifics for .stat_names
#1361
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| all obs | ||
| ————————————————————— | ||
| n 4 | ||
| Mean (SD) 2.5 (1.3) |
| n 5 | ||
| a 2 (40%) | ||
| b 1 (20%) | ||
| NA 2 (40%) |
| 8 mean_ci (4.57, 5.69) 0 Mean 95% CI | ||
| 9 mean_sei (4.89, 5.38) 0 Mean -/+ 1xSE | ||
| 10 mean_sdi (4.35, 5.91) 0 Mean -/+ 1xSD | ||
| 2 sum 48.7 0 Sum |
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Why this calc changed?
| #' | ||
| #' @return A `list` with modified elements `x`, `.formats`, `.labels`, and `.indent_mods`. | ||
| #' @return A `list` with modified elements `stat_out`, `.formats`, `.labels`, `.levels`, and `.indent_mods`. |
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to fix: ungroup_stats should be removed in favor of get_*_from_stats
| empty_pval <- "pval" %in% names(stat_out) && length(stat_out[["pval"]]) == 0 | ||
| empty_pval_counts <- "pval_counts" %in% names(stat_out) && length(stat_out[["pval_counts"]]) == 0 | ||
| stat_out <- unlist(stat_out, recursive = FALSE) | ||
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| # If p-value is empty it is removed by unlist and needs to be re-added | ||
| if (empty_pval) x[["pval"]] <- character() | ||
| if (empty_pval_counts) x[["pval_counts"]] <- character() |
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these are if pval is NULL?
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pval handling to be refactored
| n 5 | ||
| FALSE 1 (20%) | ||
| TRUE 2 (40%) | ||
| NA 2 (40%) |
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| if (na.rm) { | ||
| if (na_rm) { |
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na_rm can be reverted into na.rm if you think it is just creating issues downstream
| # Compare with reference group | ||
| if (isTRUE(compare_with_ref_group)) { |
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compare functions have been deprecated and merged in here
| ) | ||
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| y$n_blq <- sum(grepl("BLQ|LTR|<[1-9]|<PCLLOQ", x)) | ||
| y$n_blq <- list("n_blq" = c("n_blq" = sum(grepl("BLQ|LTR|<[1-9]|<PCLLOQ", x)))) |
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useful to get_stat_names
| dots_extra_args <- list(...) | ||
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| # Check if there are user-defined functions | ||
| default_and_custom_stats_list <- .split_std_from_custom_stats(.stats) |
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it is possible to add custom stats
| .N_col, # nolint | ||
| .N_row, # nolint | ||
| .var = NULL, | ||
| .df_row = NULL, | ||
| .ref_group = NULL, | ||
| .in_ref_col = FALSE, | ||
| compare = FALSE, |
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all these vars are broadcasted from analyze through ...
| # Auto format handling | ||
| .formats <- apply_auto_formatting(.formats, x_stats, .df_row, .var) | ||
| # Get and check statistical names from defaults | ||
| .stat_names <- get_stat_names(x_stats, .stat_names_in) # note is x_stats |
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core stat_names modification
| @@ -140,7 +141,7 @@ afun_riskdiff <- function(df, | |||
| stat <- ifelse("count_fraction" %in% names(s_x), "count_fraction", "unique") | |||
| if ("flag_variables" %in% names(s_args)) { | |||
| var_nms <- s_args$flag_variables | |||
| } else if (!is.null(names(s_x[[stat]]))) { | |||
| } else if (is.list(s_x[[stat]]) && !is.null(names(s_x[[stat]]))) { | |||
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now statistics are character vectors
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*named numeric vectors
| @@ -351,6 +387,72 @@ get_indents_from_stats <- function(stats, indents_in = NULL, row_nms = NULL) { | |||
| out | |||
| } | |||
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| # Function to loop over each stat and levels to set correct values | |||
| .adjust_stats_desc_by_in_def <- function(levels_per_stats, user_in, tern_defaults) { | |||
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This is only to be extra sure that you can change the labels in anyway you want (to do add this for formats and indentation)
| @@ -1361,7 +1603,7 @@ | |||
| ---------------------------- | |||
| row_name formatted_cell indent_mod row_label | |||
| 1 pval <0.0001 3 pvalue | |||
| 2 median_ci -0.41 - 1.10 3 Median 95% CI | |||
Pull Request
Fixes #1352