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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,113 @@ | ||
| #' Collapse region | ||
| #' | ||
| #' Collapse data for duplicate regions. | ||
| #' | ||
| #' @param df_in dataset | ||
| #' @param fld_id | ||
| #' @param fld_value field with value, defaults to 'value' | ||
| #' @param collapse_fxn function to collapse duplicate regions into one (example: China, Macau, Hong Kong) | ||
| #' @param collapse_wts table with weights if weighted mean function is chosen | ||
| #' | ||
| #' @details This function collapses duplicate regions (example: China, Macau, Hong Kong) | ||
| #' | ||
| #' @keywords ohi | ||
| #' @export | ||
| collapse_2_rgn <- function(df_in, | ||
| fld_value, | ||
| fld_id = 'rgn_id', | ||
| collapse_fxn = c('sum','mean','weighted_mean')[1], | ||
| collapse_wts = NULL) { | ||
| ### Expectation: a data frame, with columns for rgn_id, maybe rgn_name, and some value. | ||
| ### Group by rgn_id and unique fields; summarize value column(s) according to collapse_fxn. | ||
| ### collapse_csv? collapse_flds_join (not used...?)? | ||
| ### collapse_wts will be a .csv or a df with rgn_id and another column to be used for weighting. | ||
| ### What if other variables not captured by "fld_unique"? | ||
| ### DETAIL. Return a data.frame (vs add_rgn_id which writes to a csv) | ||
| ### and perform extra checks, including collapsing on duplicates. | ||
| ### Note: The original fld_name lost because possible to collapse multiple | ||
| ### countries into a single region. | ||
|
|
||
| ### check for valid arguments stopifnot(fld_name %in% names(d)) | ||
| ### ? should be warning for these? | ||
| stopifnot(fld_id %in% names(df_in)) | ||
| stopifnot(fld_value %in% names(df_in)) | ||
| stopifnot(all(fld_keep %in% names(df_in))) | ||
| # stopifnot(sum(duplicated(df_in[ , fld_keep])) == 0) | ||
|
|
||
| fld_keep_rgn_id <- c(fld_id, setdiff(c(fld_keep), fld_id)) | ||
|
|
||
| ### are there duplicates? create index of duplicated records | ||
| i_dupes <- duplicated(df_in[, fld_keep_rgn_id], fromLast = FALSE) | | ||
| duplicated(df_in[, fld_keep_rgn_id], fromLast = TRUE) | ||
|
|
||
| if (sum(i_dupes) == 0) { | ||
| ### No duplicates - return dataframe as is. | ||
| cat(sprintf('No duplicates found in %s. \n', paste(fld_keep_rgn_id, collapse = ', '))) | ||
| df_out <- df_in | ||
| } else { | ||
| ### Duplicates found; collapse using function | ||
| cat(sprintf('\nDuplicate values found for %s. \n', paste(fld_keep_rgn_id, collapse = ', '))) | ||
| cat(sprintf('Resolving by collapsing %s with collapse_fxn: %s after first removing all NAs from duplicates...\n', | ||
| fld_id, collapse_fxn)) | ||
|
|
||
| fld_dropped <- names(df_in)[!names(df_in) %in% c(fld_value, fld_keep_rgn_id)] | ||
| message(sprintf('Dropping variables: %s\n', paste(fld_dropped, collapse = ', '))) | ||
| message(' Use argument fld_keep to prevent variables from being dropped.\n') | ||
|
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||
| ### create a data.frame of just the duplicated records, for collapsing | ||
| df_in_dup <- df_in[i_dupes, ] %>% | ||
| dplyr::arrange(rgn_id, rgn_name) | ||
| print(df_in_dup) | ||
|
|
||
| ### set tmp_value to be the value, to protect original value | ||
| df_in_dup$tmp_value <- df_in_dup[[fld_value]] | ||
|
|
||
| if (collapse_fxn == "sum") { | ||
| df_in_collapsed <- df_in_dup %>% | ||
| dplyr::filter(!is.na(tmp_value)) %>% | ||
| dplyr::group_by_(.dots = as.list(fld_keep_rgn_id)) %>% | ||
| dplyr::summarize(tmp_value = sum(tmp_value)) | ||
| ### NOTE: since NAs removed above, no need here... similar below | ||
| } else if(collapse_fxn == "mean") { | ||
| df_in_collapsed <- df_in_dup %>% | ||
| dplyr::filter(!is.na(tmp_value)) %>% | ||
| dplyr::group_by_(.dots=as.list(fld_keep_rgn_id)) %>% | ||
| dplyr::summarize(tmp_value = mean(tmp_value)) | ||
| } else if(collapse_fxn == "weighted_mean") { | ||
| wts_df <- switch(class(collapse_wts), | ||
| 'character' = read.csv(collapse_wts, stringsAsFactors = FALSE), | ||
| 'data.frame' = collapse_wts, | ||
| 'NULL' = stop('Must set weighting values for weighted mean'), | ||
| as.data.frame(collapse_wts)) | ||
|
|
||
| flds_matched <- intersect(names(wts_df), names(df_in_dup)) | ||
| fld_collapse <- setdiff(names(wts_df), names(df_in_dup)) | ||
| stopifnot(length(fld_collapse) == 1) | ||
| wts_df['tmp_weight'] <- wts_df[fld_collapse] | ||
| wts_df <- wts_df[, c(flds_matched, "tmp_weight")] | ||
| df_in_collapsed <- df_in_dup %>% | ||
| dplyr::left_join(wts_df, by = flds_matched) %>% | ||
| dplyr::filter(!is.na(tmp_value) & !is.na(tmp_weight)) %>% | ||
| dplyr::group_by_(.dots = as.list(fld_keep_rgn_id)) %>% | ||
| dplyr::summarize(tmp_value = sum(tmp_value * tmp_weight)/sum(tmp_weight)) | ||
| } else { | ||
| stop("collapse_fxn needs to be a string of one of the following: sum, mean, weighted_mean.") | ||
| } | ||
|
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||
| ### clean up tmp_value field, quick check | ||
| df_in_collapsed <- df_in_collapsed %>% | ||
| dplyr::rename_(.dots = setNames('tmp_value', fld_value)) | ||
| head(df_in_collapsed) | ||
|
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| df_out <- rbind(df_in[!i_dupes, c(fld_keep_rgn_id, fld_value)], | ||
| df_in_collapsed) | ||
| } | ||
|
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| ### limit to same subset of fields for consistent behavior regardless of duplicates presents | ||
| df_out <- df_out[, c(fld_keep_rgn_id, fld_value)] | ||
|
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| ### check to ensure no duplicates remaining in kept fields | ||
| stopifnot(duplicated(df_out[, c(fld_keep_rgn_id)]) == 0) | ||
|
|
||
| return(as.data.frame(df_out)) | ||
| } |
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