R/cartograph_key.R

In patelm9/cartographR2:

cartograph_key <-
        function(parent_dataframe) {
                cartograph <-
                        dplyr::bind_rows(
                                data.frame(bifurcation = "1",
                                           sequence = "1",
                                           dplyr_function = "filter_at",
                                           dplyr_function_arg = "vars(CUI), any_vars(!is.na(.))",
                                           status = "MAPPED_TO_SINGLE_CUI",
                                           definition = "concept mapped to a single cui that fully encapsulates meaning of the native concept",
                                           parent = "PARENT"),
                                data.frame(bifurcation = "2",
                                           sequence = "1",
                                           dplyr_function = "filter_at",
                                           dplyr_function_arg = "vars(CUI_FLAG), any_vars(!is.na(.))",
                                           status = "FLAGGED",
                                           definition = "concept mapped to a single cui that fully encapsulates meaning of the native concept",
                                           parent = "MAPPED_TO_SINGLE_CUI"),
                                data.frame(bifurcation = "2",
                                           sequence = "2",
                                           dplyr_function = "filter_at",
                                           dplyr_function_arg = "vars(CUI_FLAG), any_vars(is.na(.))",
                                           status = "FINAL",
                                           definition = "concept mapped to a single cui that fully encapsulates meaning of the native concept",
                                           parent = "MAPPED_TO_SINGLE_CUI"),
                                data.frame(bifurcation = "1",
                                           sequence = "2",
                                           dplyr_function = "filter_at",
                                           dplyr_function_arg = "vars(CUI_01), any_vars(!is.na(.))",
                                           status = "MAPPED_TO_COORDINATE_CUIS",
                                           definition = "concept mapped to a multiple cuis that varies in coverage and overlap of meaning of the native concept",
                                           parent = "PARENT"),
                                data.frame(bifurcation = "1",
                                           sequence = "3",
                                           dplyr_function = "filter_at",
                                           dplyr_function_arg = "vars(CUI, CUI_01), all_vars(is.na(.))",
                                           status = "UNMAPPED",
                                           definition = "concepts that have not been mapped",
                                           parent = "PARENT"),
                                data.frame(bifurcation = "2",
                                           sequence = "1",
                                           dplyr_function = "filter_at",
                                           dplyr_function_arg = "vars(contains('DENOVO')), any_vars(!(is.na(.)))",
                                           status = "DENOVO",
                                           definition = "concepts that may need denovo concept creation due to their meaning",
                                           parent = "UNMAPPED"),
                                data.frame(bifurcation = "2",
                                           sequence = "2",
                                           dplyr_function = "filter_at",
                                           dplyr_function_arg = "vars(contains('FOLLOWUP')), any_vars(!(is.na(.)))",
                                           status = "FOLLOWUP",
                                           definition = "concepts that may need denovo concept creation due to their meaning",
                                           parent = "UNMAPPED"),
                                data.frame(bifurcation = "1",
                                           sequence = "4",
                                           dplyr_function = "setdiff",
                                           dplyr_function_arg = "PARENT, dplyr::bind_rows(MAPPED_TO_SINGLE_CUI, MAPPED_TO_COORDINATE_CUIS, UNMAPPED)",
                                           status = "ORPHAN",
                                           definition = "concepts lost in this bifurcation",
                                           parent = "PARENT"),
                                data.frame(bifurcation = "2",
                                           sequence = "3",
                                           dplyr_function = "setdiff",
                                           dplyr_function_arg = "MAPPED_TO_SINGLE_CUI, dplyr::bind_rows(FLAGGED, FINAL)",
                                           status = "ORPHAN",
                                           definition = "concepts lost in this bifurcation",
                                           parent = "MAPPED_TO_SINGLE_CUI"),
                                data.frame(bifurcation = "2",
                                           sequence = "3",
                                           dplyr_function = "setdiff",
                                           dplyr_function_arg = "UNMAPPED, dplyr::bind_rows(DENOVO, FOLLOWUP)",
                                           status = "ORPHAN",
                                           definition = "concepts lost in this bifurcation",
                                           parent = "UNMAPPED")
                        ) %>%
                        dplyr::mutate_at(vars(bifurcation, sequence), as.integer) %>%
                        dplyr::arrange(bifurcation, parent, sequence)
                
                
        }