source('utilities.R') ################################################################################ library(medicalcoder) # build and test the longitudinal flagging of conditions. The renal code will # be provided twice, once as poa and once as not poa. This should flag on the # encounter as expected. the duplication is here to see if there is a any bug # in the code that would get messed up by a 0 and a 1 poa for a conditon on an # encounter. # C78.4: Cancer # - Charlson (Quan 2005) # - mst # - Elixhauser (AHRQ 2025) # - does not need to be POA to count for Elixhauser # - CANCER_METS # - PCCC v3.1 # - malignancy_dxpr_only # - malignancy_dxpr_tech_only # - malignancy_dxpr_and_tech # - malignancy_dxpr_or_tech # # I50.40: heart failure, or cardiovasular disease # - Charlson (Quan 2005) # - chf # - Elixhauser (AHRQ 2025) # - does need to be POA to count for Elixhauser # - HF # - PCCC v3.1 # - cvd_dxpr_only # - cvd_dxpr_tech_only # - cvd_dxpr_and_tech # - cvd_dxpr_or_tech # # N18.4: renal # - Charlson (Quan 2005) # - rnd # - Elixhauser (AHRQ 2025) # - does need to be POA to count for Elixhauser # - RENLFL_SEV # - PCCC v3.1 # - renal_dxpr_only # - renal_dxpr_tech_only # - renal_dxpr_and_tech # - renal_dxpr_or_tech record <- structure( list( patid = c("A", "A", "A", "A", "A", "A", "A", "A", "A", "B", "B", "B", "B", "B", "B", "B"), encid = c(1L, 2L, 3L, 4L, 4L, 5L, 5L, 6L, 7L, 1L, 1L, 1L, 2L, 3L, 4L, 5L), code = c(NA, "C78.4", "I50.40", "N18.4", "N18.4", "C78.4", "I50.40", NA, "-", NA, "N18.4", "N18.4", NA, NA, "N18.4", NA), poa = c(NA, 0L, 1L, 1L, 0L, 1L, 0L, NA, 1L, NA, 1L, 0L, NA, NA, 0L, NA) ), class = "data.frame", row.names = c(NA, -16L) ) # set the data in an unsorted order to verify that the output will be sorted and # as expected. set.seed(42) rws <- c(sample(seq_len(nrow(record))), sample(seq_len(nrow(record))), sample(seq_len(nrow(record)))) record <- record[rws, ] recordDT <- record recordTBL <- record class(recordDT) <- c("data.table", class(recordDT)) class(recordTBL) <- c("tbl_df", "tbl", class(recordTBL)) ################################################################################ # Expected results expected_zeros <- rep(0L, 12L) expected_patid <- rep(c("A", "B"), times = c(7, 5)) expected_encid <- c(1:7, 1:5) ################################################################################ # arguments for the comorbidities call args <- list( data = record, icd.codes = "code", id.vars = c("patid", "encid"), icdv = 10L, dx = 1L, full.codes = TRUE, compact.codes = FALSE ) CMRBS <- list( charlson_current_0 = do.call(comorbidities, c(args, list(method = "charlson_quan2005", flag.method = "current", primarydx = 0L, poa = 0))), charlson_current_1 = do.call(comorbidities, c(args, list(method = "charlson_quan2005", flag.method = "current", primarydx = 0L, poa = 1))), charlson_current_v = do.call(comorbidities, c(args, list(method = "charlson_quan2005", flag.method = "current", primarydx = 0L, poa.var = "poa"))), charlson_cumulative_0 = do.call(comorbidities, c(args, list(method = "charlson_quan2005", flag.method = "cumulative", primarydx = 0L, poa = 0))), charlson_cumulative_1 = do.call(comorbidities, c(args, list(method = "charlson_quan2005", flag.method = "cumulative", primarydx = 0L, poa = 1))), charlson_cumulative_v = do.call(comorbidities, c(args, list(method = "charlson_quan2005", flag.method = "cumulative", primarydx = 0L, poa.var = "poa"))), pccc_current_0 = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "current", poa = 0))), pccc_current_1 = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "current", poa = 1))), pccc_current_v = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "current", poa.var = "poa"))), pccc_cumulative_0 = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "cumulative", poa = 0))), pccc_cumulative_1 = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "cumulative", poa = 1))), pccc_cumulative_v = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "cumulative", poa.var = "poa"))), spccc_current_0 = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "current", poa = 0, subconditions = TRUE))), spccc_current_1 = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "current", poa = 1, subconditions = TRUE))), spccc_current_v = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "current", poa.var = "poa", subconditions = TRUE))), spccc_cumulative_0 = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "cumulative", poa = 0, subconditions = TRUE))), spccc_cumulative_1 = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "cumulative", poa = 1, subconditions = TRUE))), spccc_cumulative_v = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "cumulative", poa.var = "poa", subconditions = TRUE))), elixhauser_current_0 = do.call(comorbidities, c(args, list(method = "elixhauser_ahrq2025", flag.method = "current", primarydx = 0L, poa = 0))), elixhauser_current_1 = do.call(comorbidities, c(args, list(method = "elixhauser_ahrq2025", flag.method = "current", primarydx = 0L, poa = 1))), elixhauser_current_v = do.call(comorbidities, c(args, list(method = "elixhauser_ahrq2025", flag.method = "current", primarydx = 0L, poa.var = "poa"))), elixhauser_cumulative_0 = do.call(comorbidities, c(args, list(method = "elixhauser_ahrq2025", flag.method = "cumulative", primarydx = 0L, poa = 0))), elixhauser_cumulative_1 = do.call(comorbidities, c(args, list(method = "elixhauser_ahrq2025", flag.method = "cumulative", primarydx = 0L, poa = 1))), elixhauser_cumulative_v = do.call(comorbidities, c(args, list(method = "elixhauser_ahrq2025", flag.method = "cumulative", primarydx = 0L, poa.var = "poa"))) ) args[["data"]] <- recordDT CMRBSDT <- list( charlson_current_0 = do.call(comorbidities, c(args, list(method = "charlson_quan2005", flag.method = "current", primarydx = 0L, poa = 0))), charlson_current_1 = do.call(comorbidities, c(args, list(method = "charlson_quan2005", flag.method = "current", primarydx = 0L, poa = 1))), charlson_current_v = do.call(comorbidities, c(args, list(method = "charlson_quan2005", flag.method = "current", primarydx = 0L, poa.var = "poa"))), charlson_cumulative_0 = do.call(comorbidities, c(args, list(method = "charlson_quan2005", flag.method = "cumulative", primarydx = 0L, poa = 0))), charlson_cumulative_1 = do.call(comorbidities, c(args, list(method = "charlson_quan2005", flag.method = "cumulative", primarydx = 0L, poa = 1))), charlson_cumulative_v = do.call(comorbidities, c(args, list(method = "charlson_quan2005", flag.method = "cumulative", primarydx = 0L, poa.var = "poa"))), pccc_current_0 = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "current", poa = 0))), pccc_current_1 = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "current", poa = 1))), pccc_current_v = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "current", poa.var = "poa"))), pccc_cumulative_0 = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "cumulative", poa = 0))), pccc_cumulative_1 = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "cumulative", poa = 1))), pccc_cumulative_v = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "cumulative", poa.var = "poa"))), spccc_current_0 = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "current", poa = 0, subconditions = TRUE))), spccc_current_1 = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "current", poa = 1, subconditions = TRUE))), spccc_current_v = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "current", poa.var = "poa", subconditions = TRUE))), spccc_cumulative_0 = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "cumulative", poa = 0, subconditions = TRUE))), spccc_cumulative_1 = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "cumulative", poa = 1, subconditions = TRUE))), spccc_cumulative_v = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "cumulative", poa.var = "poa", subconditions = TRUE))), elixhauser_current_0 = do.call(comorbidities, c(args, list(method = "elixhauser_ahrq2025", flag.method = "current", primarydx = 0L, poa = 0))), elixhauser_current_1 = do.call(comorbidities, c(args, list(method = "elixhauser_ahrq2025", flag.method = "current", primarydx = 0L, poa = 1))), elixhauser_current_v = do.call(comorbidities, c(args, list(method = "elixhauser_ahrq2025", flag.method = "current", primarydx = 0L, poa.var = "poa"))), elixhauser_cumulative_0 = do.call(comorbidities, c(args, list(method = "elixhauser_ahrq2025", flag.method = "cumulative", primarydx = 0L, poa = 0))), elixhauser_cumulative_1 = do.call(comorbidities, c(args, list(method = "elixhauser_ahrq2025", flag.method = "cumulative", primarydx = 0L, poa = 1))), elixhauser_cumulative_v = do.call(comorbidities, c(args, list(method = "elixhauser_ahrq2025", flag.method = "cumulative", primarydx = 0L, poa.var = "poa"))) ) args[["data"]] <- recordTBL CMRBSTBL <- list( charlson_current_0 = do.call(comorbidities, c(args, list(method = "charlson_quan2005", flag.method = "current", primarydx = 0L, poa = 0))), charlson_current_1 = do.call(comorbidities, c(args, list(method = "charlson_quan2005", flag.method = "current", primarydx = 0L, poa = 1))), charlson_current_v = do.call(comorbidities, c(args, list(method = "charlson_quan2005", flag.method = "current", primarydx = 0L, poa.var = "poa"))), charlson_cumulative_0 = do.call(comorbidities, c(args, list(method = "charlson_quan2005", flag.method = "cumulative", primarydx = 0L, poa = 0))), charlson_cumulative_1 = do.call(comorbidities, c(args, list(method = "charlson_quan2005", flag.method = "cumulative", primarydx = 0L, poa = 1))), charlson_cumulative_v = do.call(comorbidities, c(args, list(method = "charlson_quan2005", flag.method = "cumulative", primarydx = 0L, poa.var = "poa"))), pccc_current_0 = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "current", poa = 0))), pccc_current_1 = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "current", poa = 1))), pccc_current_v = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "current", poa.var = "poa"))), pccc_cumulative_0 = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "cumulative", poa = 0))), pccc_cumulative_1 = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "cumulative", poa = 1))), pccc_cumulative_v = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "cumulative", poa.var = "poa"))), spccc_current_0 = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "current", poa = 0, subconditions = TRUE))), spccc_current_1 = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "current", poa = 1, subconditions = TRUE))), spccc_current_v = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "current", poa.var = "poa", subconditions = TRUE))), spccc_cumulative_0 = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "cumulative", poa = 0, subconditions = TRUE))), spccc_cumulative_1 = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "cumulative", poa = 1, subconditions = TRUE))), spccc_cumulative_v = do.call(comorbidities, c(args, list(method = "pccc_v3.1", flag.method = "cumulative", poa.var = "poa", subconditions = TRUE))), elixhauser_current_0 = do.call(comorbidities, c(args, list(method = "elixhauser_ahrq2025", flag.method = "current", primarydx = 0L, poa = 0))), elixhauser_current_1 = do.call(comorbidities, c(args, list(method = "elixhauser_ahrq2025", flag.method = "current", primarydx = 0L, poa = 1))), elixhauser_current_v = do.call(comorbidities, c(args, list(method = "elixhauser_ahrq2025", flag.method = "current", primarydx = 0L, poa.var = "poa"))), elixhauser_cumulative_0 = do.call(comorbidities, c(args, list(method = "elixhauser_ahrq2025", flag.method = "cumulative", primarydx = 0L, poa = 0))), elixhauser_cumulative_1 = do.call(comorbidities, c(args, list(method = "elixhauser_ahrq2025", flag.method = "cumulative", primarydx = 0L, poa = 1))), elixhauser_cumulative_v = do.call(comorbidities, c(args, list(method = "elixhauser_ahrq2025", flag.method = "cumulative", primarydx = 0L, poa.var = "poa"))) ) CMRBS <- list(DF = CMRBS, DT = CMRBSDT, TBL = CMRBSTBL) ################################################################################ # for the testing - check for the expected results and then remove the object # from the CMRBS until it is empty. # PCCC Subconditions # # The PCCC with subconditions should have the same comorbidities as the objects # without subconditions. for (i in seq_len(length(CMRBS))) { for (x in grep("^pccc_", names(CMRBS[[i]]), value = TRUE)) { check <- all.equal( target = CMRBS[[i]][[x]], current = CMRBS[[i]][[paste0("s", x)]][["conditions"]], check.attributes = FALSE ) if (check) { CMRBS[[i]][[paste0("s", x)]][["conditions"]] <- NULL } else { stop(sprintf('CMRBS[[%d]][[s%s]][["conditions"]] is not all.equal to CMRBS[[%s]]', i, x, x)) } } } # Check each of the subconditions. For the following conditions, all of which # should not be flagged, the number of rows in the output should be zero. for (i in seq_len(length(CMRBS))) { for (cnd in c("respiratory", "neuromusc", "neonatal", "misc", "metabolic", "hemato_immu", "gi", "congeni_genetic")) { stopifnot( nrow(CMRBS[[i]][["spccc_current_0"]][["subconditions"]][[cnd]]) == 0L, nrow(CMRBS[[i]][["spccc_current_1"]][["subconditions"]][[cnd]]) == 0L, nrow(CMRBS[[i]][["spccc_current_v"]][["subconditions"]][[cnd]]) == 0L, nrow(CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]][[cnd]]) == 0L, nrow(CMRBS[[i]][["spccc_cumulative_1"]][["subconditions"]][[cnd]]) == 0L, nrow(CMRBS[[i]][["spccc_cumulative_v"]][["subconditions"]][[cnd]]) == 0L ) CMRBS[[i]][["spccc_current_0"]][["subconditions"]][[cnd]] <- NULL CMRBS[[i]][["spccc_current_1"]][["subconditions"]][[cnd]] <- NULL CMRBS[[i]][["spccc_current_v"]][["subconditions"]][[cnd]] <- NULL CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]][[cnd]] <- NULL CMRBS[[i]][["spccc_cumulative_1"]][["subconditions"]][[cnd]] <- NULL CMRBS[[i]][["spccc_cumulative_v"]][["subconditions"]][[cnd]] <- NULL } } # Specific checks for cvd for (i in seq_len(length(CMRBS))) { stopifnot(identical(nrow(CMRBS[[i]][["spccc_current_0"]][["subconditions"]][["cvd"]]), 0L)) CMRBS[[i]][["spccc_current_0"]][["subconditions"]][["cvd"]] <- NULL stopifnot( identical(CMRBS[[i]][["spccc_current_1"]][["subconditions"]][["cvd"]][["patid"]], c("A", "A")), identical(CMRBS[[i]][["spccc_current_1"]][["subconditions"]][["cvd"]][["encid"]], c(3L, 5L)), identical(CMRBS[[i]][["spccc_current_1"]][["subconditions"]][["cvd"]][["cardiomyopathies"]], c(0L, 0L)), identical(CMRBS[[i]][["spccc_current_1"]][["subconditions"]][["cvd"]][["conduction_disorder"]], c(0L, 0L)), identical(CMRBS[[i]][["spccc_current_1"]][["subconditions"]][["cvd"]][["device_and_technology_use"]], c(0L, 0L)), identical(CMRBS[[i]][["spccc_current_1"]][["subconditions"]][["cvd"]][["dysrhythmias"]], c(0L, 0L)), identical(CMRBS[[i]][["spccc_current_1"]][["subconditions"]][["cvd"]][["endocardium_diseases"]], c(0L, 0L)), identical(CMRBS[[i]][["spccc_current_1"]][["subconditions"]][["cvd"]][["heart_and_great_vessel_malformations"]], c(0L, 0L)), identical(CMRBS[[i]][["spccc_current_1"]][["subconditions"]][["cvd"]][["transplantation"]], c(0L, 0L)), identical(CMRBS[[i]][["spccc_current_1"]][["subconditions"]][["cvd"]][["other"]], c(1L, 1L)) ) CMRBS[[i]][["spccc_current_1"]][["subconditions"]][["cvd"]] <- NULL stopifnot( identical(CMRBS[[i]][["spccc_current_v"]][["subconditions"]][["cvd"]][["patid"]], c("A")), identical(CMRBS[[i]][["spccc_current_v"]][["subconditions"]][["cvd"]][["encid"]], c(3L)), identical(CMRBS[[i]][["spccc_current_v"]][["subconditions"]][["cvd"]][["cardiomyopathies"]], c(0L)), identical(CMRBS[[i]][["spccc_current_v"]][["subconditions"]][["cvd"]][["conduction_disorder"]], c(0L)), identical(CMRBS[[i]][["spccc_current_v"]][["subconditions"]][["cvd"]][["device_and_technology_use"]], c(0L)), identical(CMRBS[[i]][["spccc_current_v"]][["subconditions"]][["cvd"]][["dysrhythmias"]], c(0L)), identical(CMRBS[[i]][["spccc_current_v"]][["subconditions"]][["cvd"]][["endocardium_diseases"]], c(0L)), identical(CMRBS[[i]][["spccc_current_v"]][["subconditions"]][["cvd"]][["heart_and_great_vessel_malformations"]], c(0L)), identical(CMRBS[[i]][["spccc_current_v"]][["subconditions"]][["cvd"]][["transplantation"]], c(0L)), identical(CMRBS[[i]][["spccc_current_v"]][["subconditions"]][["cvd"]][["other"]], c(1L)) ) CMRBS[[i]][["spccc_current_v"]][["subconditions"]][["cvd"]] <- NULL stopifnot( identical(CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]][["cvd"]][["patid"]], rep("A", 4)), identical(CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]][["cvd"]][["encid"]], 4:7), identical(CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]][["cvd"]][["other"]], rep(c(1L), 4L)), identical(CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]][["cvd"]][["cardiomyopathies"]], rep(c(0L), 4L)), identical(CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]][["cvd"]][["conduction_disorder"]], rep(c(0L), 4L)), identical(CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]][["cvd"]][["device_and_technology_use"]], rep(c(0L), 4L)), identical(CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]][["cvd"]][["dysrhythmias"]], rep(c(0L), 4L)), identical(CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]][["cvd"]][["endocardium_diseases"]], rep(c(0L), 4L)), identical(CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]][["cvd"]][["heart_and_great_vessel_malformations"]], rep(c(0L), 4L)), identical(CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]][["cvd"]][["transplantation"]], rep(c(0L), 4L)), identical(CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]][["cvd"]][["other"]], rep(c(1L), 4L)) ) CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]][["cvd"]] <- NULL stopifnot( identical(CMRBS[[i]][["spccc_cumulative_1"]][["subconditions"]][["cvd"]][["patid"]], rep("A", 5)), identical(CMRBS[[i]][["spccc_cumulative_1"]][["subconditions"]][["cvd"]][["encid"]], 3:7), identical(CMRBS[[i]][["spccc_cumulative_1"]][["subconditions"]][["cvd"]][["cardiomyopathies"]], rep(c(0L), 5L)), identical(CMRBS[[i]][["spccc_cumulative_1"]][["subconditions"]][["cvd"]][["conduction_disorder"]], rep(c(0L), 5L)), identical(CMRBS[[i]][["spccc_cumulative_1"]][["subconditions"]][["cvd"]][["device_and_technology_use"]], rep(c(0L), 5L)), identical(CMRBS[[i]][["spccc_cumulative_1"]][["subconditions"]][["cvd"]][["dysrhythmias"]], rep(c(0L), 5L)), identical(CMRBS[[i]][["spccc_cumulative_1"]][["subconditions"]][["cvd"]][["endocardium_diseases"]], rep(c(0L), 5L)), identical(CMRBS[[i]][["spccc_cumulative_1"]][["subconditions"]][["cvd"]][["heart_and_great_vessel_malformations"]], rep(c(0L), 5L)), identical(CMRBS[[i]][["spccc_cumulative_1"]][["subconditions"]][["cvd"]][["transplantation"]], rep(c(0L), 5L)), identical(CMRBS[[i]][["spccc_cumulative_1"]][["subconditions"]][["cvd"]][["other"]], rep(c(1L), 5L)) ) CMRBS[[i]][["spccc_cumulative_1"]][["subconditions"]][["cvd"]] <- NULL stopifnot( identical(CMRBS[[i]][["spccc_cumulative_v"]][["subconditions"]][["cvd"]][["patid"]], rep("A", 5)), identical(CMRBS[[i]][["spccc_cumulative_v"]][["subconditions"]][["cvd"]][["encid"]], 3:7), identical(CMRBS[[i]][["spccc_cumulative_v"]][["subconditions"]][["cvd"]][["cardiomyopathies"]], rep(c(0L), 5L)), identical(CMRBS[[i]][["spccc_cumulative_v"]][["subconditions"]][["cvd"]][["conduction_disorder"]], rep(c(0L), 5L)), identical(CMRBS[[i]][["spccc_cumulative_v"]][["subconditions"]][["cvd"]][["device_and_technology_use"]], rep(c(0L), 5L)), identical(CMRBS[[i]][["spccc_cumulative_v"]][["subconditions"]][["cvd"]][["dysrhythmias"]], rep(c(0L), 5L)), identical(CMRBS[[i]][["spccc_cumulative_v"]][["subconditions"]][["cvd"]][["endocardium_diseases"]], rep(c(0L), 5L)), identical(CMRBS[[i]][["spccc_cumulative_v"]][["subconditions"]][["cvd"]][["heart_and_great_vessel_malformations"]], rep(c(0L), 5L)), identical(CMRBS[[i]][["spccc_cumulative_v"]][["subconditions"]][["cvd"]][["transplantation"]], rep(c(0L), 5L)), identical(CMRBS[[i]][["spccc_cumulative_v"]][["subconditions"]][["cvd"]][["other"]], rep(c(1L), 5L)) ) CMRBS[[i]][["spccc_cumulative_v"]][["subconditions"]][["cvd"]] <- NULL } ################################################################################ # for cancer/malignancy for (i in seq_len(length(CMRBS))) { stopifnot(identical(nrow(CMRBS[[i]][["spccc_current_0"]][["subconditions"]][["malignancy"]]), 0L)) CMRBS[[i]][["spccc_current_0"]][["subconditions"]][["malignancy"]] <- NULL stopifnot( identical(CMRBS[[i]][["spccc_current_1"]][["subconditions"]][["malignancy"]][["patid"]], c("A", "A")), identical(CMRBS[[i]][["spccc_current_1"]][["subconditions"]][["malignancy"]][["encid"]], c(2L, 5L)), identical(CMRBS[[i]][["spccc_current_1"]][["subconditions"]][["malignancy"]][["neoplasms"]], c(1L, 1L)), identical(CMRBS[[i]][["spccc_current_1"]][["subconditions"]][["malignancy"]][["transplantation"]], c(0L, 0L)) ) CMRBS[[i]][["spccc_current_1"]][["subconditions"]][["malignancy"]] <- NULL stopifnot( identical(CMRBS[[i]][["spccc_current_v"]][["subconditions"]][["malignancy"]][["patid"]], c("A")), identical(CMRBS[[i]][["spccc_current_v"]][["subconditions"]][["malignancy"]][["encid"]], c(5L)), identical(CMRBS[[i]][["spccc_current_v"]][["subconditions"]][["malignancy"]][["neoplasms"]], c(1L)), identical(CMRBS[[i]][["spccc_current_v"]][["subconditions"]][["malignancy"]][["transplantation"]], c(0L)) ) CMRBS[[i]][["spccc_current_v"]][["subconditions"]][["malignancy"]] <- NULL stopifnot( identical(CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]][["malignancy"]][["patid"]], rep("A", 5)), identical(CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]][["malignancy"]][["encid"]], 3:7), identical(CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]][["malignancy"]][["neoplasms"]], rep(1L, 5)), identical(CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]][["malignancy"]][["transplantation"]], rep(0L, 5)) ) CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]][["malignancy"]] <- NULL stopifnot( identical(CMRBS[[i]][["spccc_cumulative_1"]][["subconditions"]][["malignancy"]][["patid"]], rep("A", 6)), identical(CMRBS[[i]][["spccc_cumulative_1"]][["subconditions"]][["malignancy"]][["encid"]], 2:7), identical(CMRBS[[i]][["spccc_cumulative_1"]][["subconditions"]][["malignancy"]][["neoplasms"]], rep(1L, 6)), identical(CMRBS[[i]][["spccc_cumulative_1"]][["subconditions"]][["malignancy"]][["transplantation"]], rep(0L, 6)) ) CMRBS[[i]][["spccc_cumulative_1"]][["subconditions"]][["malignancy"]] <- NULL stopifnot( identical(CMRBS[[i]][["spccc_cumulative_v"]][["subconditions"]][["malignancy"]][["patid"]], rep("A", 5)), identical(CMRBS[[i]][["spccc_cumulative_v"]][["subconditions"]][["malignancy"]][["encid"]], 3:7), identical(CMRBS[[i]][["spccc_cumulative_v"]][["subconditions"]][["malignancy"]][["neoplasms"]], rep(1L, 5)), identical(CMRBS[[i]][["spccc_cumulative_v"]][["subconditions"]][["malignancy"]][["transplantation"]], rep(0L, 5)) ) CMRBS[[i]][["spccc_cumulative_v"]][["subconditions"]][["malignancy"]] <- NULL } ################################################################################ # for renal for (i in seq_len(length(CMRBS))) { stopifnot(identical(nrow(CMRBS[[i]][["spccc_current_0"]][["subconditions"]][["renal"]]), 0L)) CMRBS[[i]][["spccc_current_0"]][["subconditions"]][["renal"]] <- NULL stopifnot( identical(CMRBS[[i]][["spccc_current_1"]][["subconditions"]][["renal"]][["patid"]], c("A", "B", "B")), identical(CMRBS[[i]][["spccc_current_1"]][["subconditions"]][["renal"]][["encid"]], c(4L, 1L, 4L)), identical(CMRBS[[i]][["spccc_current_1"]][["subconditions"]][["renal"]][["chronic_renal_failure"]], c(1L, 1L, 1L)), identical(CMRBS[[i]][["spccc_current_1"]][["subconditions"]][["renal"]][["chronic_bladder_diseases"]], c(0L, 0L, 0L)), identical(CMRBS[[i]][["spccc_current_1"]][["subconditions"]][["renal"]][["congenital_anomalies"]], c(0L, 0L, 0L)), identical(CMRBS[[i]][["spccc_current_1"]][["subconditions"]][["renal"]][["device_and_technology_use"]], c(0L, 0L, 0L)), identical(CMRBS[[i]][["spccc_current_1"]][["subconditions"]][["renal"]][["other"]], c(0L, 0L, 0L)), identical(CMRBS[[i]][["spccc_current_1"]][["subconditions"]][["renal"]][["transplantation"]], c(0L, 0L, 0L)) ) CMRBS[[i]][["spccc_current_1"]][["subconditions"]][["renal"]] <- NULL stopifnot( identical(CMRBS[[i]][["spccc_current_v"]][["subconditions"]][["renal"]][["patid"]], c("A", "B")), identical(CMRBS[[i]][["spccc_current_v"]][["subconditions"]][["renal"]][["encid"]], c(4L, 1L)), identical(CMRBS[[i]][["spccc_current_v"]][["subconditions"]][["renal"]][["chronic_renal_failure"]], c(1L, 1L)), identical(CMRBS[[i]][["spccc_current_v"]][["subconditions"]][["renal"]][["chronic_bladder_diseases"]], c(0L, 0L)), identical(CMRBS[[i]][["spccc_current_v"]][["subconditions"]][["renal"]][["congenital_anomalies"]], c(0L, 0L)), identical(CMRBS[[i]][["spccc_current_v"]][["subconditions"]][["renal"]][["device_and_technology_use"]], c(0L, 0L)), identical(CMRBS[[i]][["spccc_current_v"]][["subconditions"]][["renal"]][["other"]], c(0L, 0L)), identical(CMRBS[[i]][["spccc_current_v"]][["subconditions"]][["renal"]][["transplantation"]], c(0L, 0L)) ) CMRBS[[i]][["spccc_current_v"]][["subconditions"]][["renal"]] <- NULL stopifnot( identical(CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]][["renal"]][["patid"]], rep(c("A", "B"), times = c(3, 4))), identical(CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]][["renal"]][["encid"]], c(5:7, 2:5)), identical(CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]][["renal"]][["chronic_renal_failure"]], rep(1L, 7)), identical(CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]][["renal"]][["chronic_bladder_diseases"]], rep(0L, 7L)), identical(CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]][["renal"]][["congenital_anomalies"]], rep(0L, 7L)), identical(CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]][["renal"]][["device_and_technology_use"]], rep(0L, 7L)), identical(CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]][["renal"]][["other"]], rep(0L, 7L)), identical(CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]][["renal"]][["transplantation"]], rep(0L, 7L)) ) CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]][["renal"]] <- NULL stopifnot( identical(CMRBS[[i]][["spccc_cumulative_1"]][["subconditions"]][["renal"]][["patid"]], rep(c("A", "B"), times = c(4, 5))), identical(CMRBS[[i]][["spccc_cumulative_1"]][["subconditions"]][["renal"]][["encid"]], c(4:7, 1:5)), identical(CMRBS[[i]][["spccc_cumulative_1"]][["subconditions"]][["renal"]][["chronic_renal_failure"]], rep(1L, 9L)), identical(CMRBS[[i]][["spccc_cumulative_1"]][["subconditions"]][["renal"]][["chronic_bladder_diseases"]], rep(0L, 9L)), identical(CMRBS[[i]][["spccc_cumulative_1"]][["subconditions"]][["renal"]][["congenital_anomalies"]], rep(0L, 9L)), identical(CMRBS[[i]][["spccc_cumulative_1"]][["subconditions"]][["renal"]][["device_and_technology_use"]], rep(0L, 9L)), identical(CMRBS[[i]][["spccc_cumulative_1"]][["subconditions"]][["renal"]][["other"]], rep(0L, 9L)), identical(CMRBS[[i]][["spccc_cumulative_1"]][["subconditions"]][["renal"]][["transplantation"]], rep(0L, 9L)) ) CMRBS[[i]][["spccc_cumulative_1"]][["subconditions"]][["renal"]] <- NULL stopifnot( identical(CMRBS[[i]][["spccc_cumulative_v"]][["subconditions"]][["renal"]][["patid"]], rep(c("A", "B"), times = c(4, 5))), identical(CMRBS[[i]][["spccc_cumulative_v"]][["subconditions"]][["renal"]][["encid"]], c(4:7, 1:5)), identical(CMRBS[[i]][["spccc_cumulative_v"]][["subconditions"]][["renal"]][["chronic_renal_failure"]], rep(1L, 9)), identical(CMRBS[[i]][["spccc_cumulative_v"]][["subconditions"]][["renal"]][["chronic_bladder_diseases"]], rep(0L, 9L)), identical(CMRBS[[i]][["spccc_cumulative_v"]][["subconditions"]][["renal"]][["congenital_anomalies"]], rep(0L, 9L)), identical(CMRBS[[i]][["spccc_cumulative_v"]][["subconditions"]][["renal"]][["device_and_technology_use"]], rep(0L, 9L)), identical(CMRBS[[i]][["spccc_cumulative_v"]][["subconditions"]][["renal"]][["other"]], rep(0L, 9L)), identical(CMRBS[[i]][["spccc_cumulative_v"]][["subconditions"]][["renal"]][["transplantation"]], rep(0L, 9L)) ) CMRBS[[i]][["spccc_cumulative_v"]][["subconditions"]][["renal"]] <- NULL } ################################################################################ # remove the subcondtions after verifying they are all empty for( i in seq_len(length(CMRBS)) ) { stopifnot(identical(length(CMRBS[[i]][["spccc_current_0"]][["subconditions"]]), 0L)) CMRBS[[i]][["spccc_current_0"]][["subconditions"]] <- NULL stopifnot(identical(length(CMRBS[[i]][["spccc_current_0"]]), 0L)) CMRBS[[i]][["spccc_current_0"]] <- NULL stopifnot(identical(length(CMRBS[[i]][["spccc_current_1"]][["subconditions"]]), 0L)) CMRBS[[i]][["spccc_current_1"]][["subconditions"]] <- NULL stopifnot(identical(length(CMRBS[[i]][["spccc_current_1"]]), 0L)) CMRBS[[i]][["spccc_current_1"]] <- NULL stopifnot(identical(length(CMRBS[[i]][["spccc_current_v"]][["subconditions"]]), 0L)) CMRBS[[i]][["spccc_current_v"]][["subconditions"]] <- NULL stopifnot(identical(length(CMRBS[[i]][["spccc_current_v"]]), 0L)) CMRBS[[i]][["spccc_current_v"]] <- NULL stopifnot(identical(length(CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]]), 0L)) CMRBS[[i]][["spccc_cumulative_0"]][["subconditions"]] <- NULL stopifnot(identical(length(CMRBS[[i]][["spccc_cumulative_0"]]), 0L)) CMRBS[[i]][["spccc_cumulative_0"]] <- NULL stopifnot(identical(length(CMRBS[[i]][["spccc_cumulative_1"]][["subconditions"]]), 0L)) CMRBS[[i]][["spccc_cumulative_1"]][["subconditions"]] <- NULL stopifnot(identical(length(CMRBS[[i]][["spccc_cumulative_1"]]), 0L)) CMRBS[[i]][["spccc_cumulative_1"]] <- NULL stopifnot(identical(length(CMRBS[[i]][["spccc_cumulative_v"]][["subconditions"]]), 0L)) CMRBS[[i]][["spccc_cumulative_v"]][["subconditions"]] <- NULL stopifnot(identical(length(CMRBS[[i]][["spccc_cumulative_v"]]), 0L)) CMRBS[[i]][["spccc_cumulative_v"]] <- NULL } ################################################################################ # Check the conditions for charlson current poa 0 for (i in seq_len(length(CMRBS))) { stopifnot(identical(CMRBS[[i]][["charlson_current_0"]][["age_score"]], rep(NA_integer_, 12))) CMRBS[[i]][["charlson_current_0"]][["age_score"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_current_0"]][["patid"]], expected_patid)) CMRBS[[i]][["charlson_current_0"]][["patid"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_current_0"]][["encid"]], expected_encid)) CMRBS[[i]][["charlson_current_0"]][["encid"]] <- NULL stopifnot(all(CMRBS[[i]][["charlson_current_0"]] == 0)) CMRBS[[i]][["charlson_current_0"]] <- NULL } ################################################################################ # Check the conditions for pccc current poa 0 for (i in seq_len(length(CMRBS))) { stopifnot(identical(CMRBS[[i]][["pccc_current_0"]][["patid"]], expected_patid)) CMRBS[[i]][["pccc_current_0"]][["patid"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_current_0"]][["encid"]], expected_encid)) CMRBS[[i]][["pccc_current_0"]][["encid"]] <- NULL stopifnot(all(CMRBS[[i]][["pccc_current_0"]] == 0)) CMRBS[[i]][["pccc_current_0"]] <- NULL } ################################################################################ # Check the conditions for elixhauser current poa 0 for (i in seq_len(length(CMRBS))) { stopifnot(identical(CMRBS[[i]][["elixhauser_current_0"]][["patid"]], expected_patid)) CMRBS[[i]][["elixhauser_current_0"]][["patid"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_current_0"]][["encid"]], expected_encid)) CMRBS[[i]][["elixhauser_current_0"]][["encid"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_current_0"]][["CANCER_METS"]], c(0L, 1L, 0L, 0L, 1L, rep(0L, 7)))) CMRBS[[i]][["elixhauser_current_0"]][["CANCER_METS"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_current_0"]][["mortality_index"]], 22L * c(0L, 1L, 0L, 0L, 1L, rep(0L, 7)))) CMRBS[[i]][["elixhauser_current_0"]][["mortality_index"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_current_0"]][["readmission_index"]], 11L * c(0L, 1L, 0L, 0L, 1L, rep(0L, 7)))) CMRBS[[i]][["elixhauser_current_0"]][["readmission_index"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_current_0"]][["cmrb_flag"]], c(0L, 1L, 0L, 0L, 1L, rep(0L, 7)))) CMRBS[[i]][["elixhauser_current_0"]][["cmrb_flag"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_current_0"]][["num_cmrb"]], c(0L, 1L, 0L, 0L, 1L, rep(0L, 7)))) CMRBS[[i]][["elixhauser_current_0"]][["num_cmrb"]] <- NULL stopifnot(all(CMRBS[[i]][["elixhauser_current_0"]] == 0)) CMRBS[[i]][["elixhauser_current_0"]] <- NULL } ################################################################################ # Charlson, current, poa 1 for (i in seq_len(length(CMRBS))) { stopifnot(identical(CMRBS[[i]][["charlson_current_1"]][["patid"]], expected_patid)) CMRBS[[i]][["charlson_current_1"]][["patid"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_current_1"]][["encid"]], expected_encid)) CMRBS[[i]][["charlson_current_1"]][["encid"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_current_1"]][["age_score"]], rep(NA_integer_, 12))) CMRBS[[i]][["charlson_current_1"]][["age_score"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_current_1"]][["chf"]], c(0L, 0L, 1L, 0L, 1L, rep(0L, 7L)))) CMRBS[[i]][["charlson_current_1"]][["chf"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_current_1"]][["mst"]], c(0L, 1L, 0L, 0L, 1L, rep(0L, 7L)))) CMRBS[[i]][["charlson_current_1"]][["mst"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_current_1"]][["rnd"]], c(0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 0L))) CMRBS[[i]][["charlson_current_1"]][["rnd"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_current_1"]][["cmrb_flag"]], c(0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 0L))) CMRBS[[i]][["charlson_current_1"]][["cmrb_flag"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_current_1"]][["num_cmrb"]], c(0L, 1L, 1L, 1L, 2L, 0L, 0L, 1L, 0L, 0L, 1L, 0L))) CMRBS[[i]][["charlson_current_1"]][["num_cmrb"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_current_1"]][["cci"]], c(0L, 6L, 1L, 2L, 7L, 0L, 0L, 2L, 0L, 0L, 2L, 0L))) CMRBS[[i]][["charlson_current_1"]][["cci"]] <- NULL stopifnot(all(CMRBS[[i]][["charlson_current_1"]] == 0)) CMRBS[[i]][["charlson_current_1"]] <- NULL } ################################################################################ # charlson_current_v for (i in seq_len(length(CMRBS))) { stopifnot(identical(CMRBS[[i]][["charlson_current_v"]][["patid"]], expected_patid)) CMRBS[[i]][["charlson_current_v"]][["patid"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_current_v"]][["encid"]], expected_encid)) CMRBS[[i]][["charlson_current_v"]][["encid"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_current_v"]][["age_score"]], rep(NA_integer_, 12L))) CMRBS[[i]][["charlson_current_v"]][["age_score"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_current_v"]][["chf"]], c(rep(0L, 2L), 1L, rep(0L, 9L)))) CMRBS[[i]][["charlson_current_v"]][["chf"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_current_v"]][["rnd"]], c(rep(0L, 3L), 1L, rep(0L, 3L), 1L, rep(0L, 4L)))) CMRBS[[i]][["charlson_current_v"]][["rnd"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_current_v"]][["mst"]], c(rep(0L, 4L), 1L, rep(0L, 7L)))) CMRBS[[i]][["charlson_current_v"]][["mst"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_current_v"]][["num_cmrb"]], c(0L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L))) CMRBS[[i]][["charlson_current_v"]][["num_cmrb"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_current_v"]][["cmrb_flag"]], c(0L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L))) CMRBS[[i]][["charlson_current_v"]][["cmrb_flag"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_current_v"]][["cci"]], c(0L, 0L, 1L, 2L, 6L, 0L, 0L, 2L, 0L, 0L, 0L, 0L))) CMRBS[[i]][["charlson_current_v"]][["cci"]] <- NULL stopifnot(all(CMRBS[[i]][["charlson_current_v"]] == 0)) CMRBS[[i]][["charlson_current_v"]] <- NULL } ################################################################################ # charlson_cumulative_0 for (i in seq_len(length(CMRBS))) { stopifnot(identical(CMRBS[[i]][["charlson_cumulative_0"]][["patid"]], expected_patid)) CMRBS[[i]][["charlson_cumulative_0"]][["patid"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_cumulative_0"]][["encid"]], expected_encid)) CMRBS[[i]][["charlson_cumulative_0"]][["encid"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_cumulative_0"]][["age_score"]], rep(NA_integer_, 12L))) CMRBS[[i]][["charlson_cumulative_0"]][["age_score"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_cumulative_0"]][["chf"]], c(0L, 0L, 0L, rep(1L, 4L), rep(0L, 5L)))) CMRBS[[i]][["charlson_cumulative_0"]][["chf"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_cumulative_0"]][["rnd"]], c(rep(0L, 4L), rep(1L, 3L), 0L, rep(1L, 4L)))) CMRBS[[i]][["charlson_cumulative_0"]][["rnd"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_cumulative_0"]][["mst"]], c(0L, 0L, rep(1L, 5L), rep(0L, 5)))) CMRBS[[i]][["charlson_cumulative_0"]][["mst"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_cumulative_0"]][["num_cmrb"]], c(0L, 0L, 1L, 2L, 3L, 3L, 3L, 0L, 1L, 1L, 1L, 1L))) CMRBS[[i]][["charlson_cumulative_0"]][["num_cmrb"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_cumulative_0"]][["cmrb_flag"]], c(0L, 0L, 1L, 1L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L))) CMRBS[[i]][["charlson_cumulative_0"]][["cmrb_flag"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_cumulative_0"]][["cci"]], c(0L, 0L, 6L, 7L, 9L, 9L, 9L, 0L, 2L, 2L, 2L, 2L))) CMRBS[[i]][["charlson_cumulative_0"]][["cci"]] <- NULL stopifnot(all(CMRBS[[i]][["charlson_cumulative_0"]] == 0)) CMRBS[[i]][["charlson_cumulative_0"]] <- NULL } ################################################################################ # charlson_cumulative_1 for (i in seq_len(length(CMRBS))) { stopifnot(identical(CMRBS[[i]][["charlson_cumulative_1"]][["patid"]], expected_patid)) CMRBS[[i]][["charlson_cumulative_1"]][["patid"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_cumulative_1"]][["encid"]], expected_encid)) CMRBS[[i]][["charlson_cumulative_1"]][["encid"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_cumulative_1"]][["age_score"]], rep(NA_integer_, 12L))) CMRBS[[i]][["charlson_cumulative_1"]][["age_score"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_cumulative_1"]][["chf"]], c(0L, 0L, rep(1L, 5L), rep(0L, 5L)))) CMRBS[[i]][["charlson_cumulative_1"]][["chf"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_cumulative_1"]][["rnd"]], c(rep(0L, 3L), rep(1L, 4L), rep(1L, 5L)))) CMRBS[[i]][["charlson_cumulative_1"]][["rnd"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_cumulative_1"]][["mst"]], c(0L, rep(1L, 6L), rep(0L, 5)))) CMRBS[[i]][["charlson_cumulative_1"]][["mst"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_cumulative_1"]][["num_cmrb"]], c(0L, 1L, 2L, 3L, 3L, 3L, 3L, rep(1L, 5L)))) CMRBS[[i]][["charlson_cumulative_1"]][["num_cmrb"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_cumulative_1"]][["cmrb_flag"]], c(0L, rep(1L, 11L)))) CMRBS[[i]][["charlson_cumulative_1"]][["cmrb_flag"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_cumulative_1"]][["cci"]], c(0L, 6L, 7L, 9L, 9L, 9L, 9L, 2L, 2L, 2L, 2L, 2L))) CMRBS[[i]][["charlson_cumulative_1"]][["cci"]] <- NULL stopifnot(all(CMRBS[[i]][["charlson_cumulative_1"]] == 0)) CMRBS[[i]][["charlson_cumulative_1"]] <- NULL } ################################################################################ # charlson_cumulative_v for (i in seq_len(length(CMRBS))) { stopifnot(identical(CMRBS[[i]][["charlson_cumulative_v"]][["patid"]], expected_patid)) CMRBS[[i]][["charlson_cumulative_v"]][["patid"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_cumulative_v"]][["encid"]], expected_encid)) CMRBS[[i]][["charlson_cumulative_v"]][["encid"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_cumulative_v"]][["age_score"]], rep(NA_integer_, 12L))) CMRBS[[i]][["charlson_cumulative_v"]][["age_score"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_cumulative_v"]][["chf"]], c(0L, 0L, rep(1L, 5L), rep(0L, 5L)))) CMRBS[[i]][["charlson_cumulative_v"]][["chf"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_cumulative_v"]][["rnd"]], c(rep(0L, 3L), rep(1L, 4L), rep(1L, 5L)))) CMRBS[[i]][["charlson_cumulative_v"]][["rnd"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_cumulative_v"]][["mst"]], c(0L, 0L, rep(1L, 5L), rep(0L, 5)))) CMRBS[[i]][["charlson_cumulative_v"]][["mst"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_cumulative_v"]][["num_cmrb"]], c(0L, 0L, 2L, 3L, 3L, 3L, 3L, rep(1L, 5L)))) CMRBS[[i]][["charlson_cumulative_v"]][["num_cmrb"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_cumulative_v"]][["cmrb_flag"]], c(0L, 0L, rep(1L, 10L)))) CMRBS[[i]][["charlson_cumulative_v"]][["cmrb_flag"]] <- NULL stopifnot(identical(CMRBS[[i]][["charlson_cumulative_v"]][["cci"]], c(0L, 0L, 7L, 9L, 9L, 9L, 9L, 2L, 2L, 2L, 2L, 2L))) CMRBS[[i]][["charlson_cumulative_v"]][["cci"]] <- NULL stopifnot(all(CMRBS[[i]][["charlson_cumulative_v"]] == 0)) CMRBS[[i]][["charlson_cumulative_v"]] <- NULL } ################################################################################ # pccc_current_1 for (i in seq_len(length(CMRBS))) { stopifnot(identical(CMRBS[[i]][["pccc_current_1"]][["patid"]], expected_patid)) CMRBS[[i]][["pccc_current_1"]][["patid"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_current_1"]][["encid"]], expected_encid)) CMRBS[[i]][["pccc_current_1"]][["encid"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_current_1"]][["cvd_dxpr_or_tech"]], c(0L, 0L, 1L, 0L, 1L, rep(0L, 7L)))) CMRBS[[i]][["pccc_current_1"]][["cvd_dxpr_or_tech"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_current_1"]][["cvd_dxpr_only"]], c(0L, 0L, 1L, 0L, 1L, rep(0L, 7L)))) CMRBS[[i]][["pccc_current_1"]][["cvd_dxpr_only"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_current_1"]][["malignancy_dxpr_or_tech"]], c(0L, 1L, 0L, 0L, 1L, rep(0L, 7L)))) CMRBS[[i]][["pccc_current_1"]][["malignancy_dxpr_or_tech"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_current_1"]][["malignancy_dxpr_only"]], c(0L, 1L, 0L, 0L, 1L, rep(0L, 7L)))) CMRBS[[i]][["pccc_current_1"]][["malignancy_dxpr_only"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_current_1"]][["renal_dxpr_or_tech"]], c(0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 0L))) CMRBS[[i]][["pccc_current_1"]][["renal_dxpr_or_tech"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_current_1"]][["renal_dxpr_only"]], c(0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 0L))) CMRBS[[i]][["pccc_current_1"]][["renal_dxpr_only"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_current_1"]][["cmrb_flag"]], c(0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 0L))) CMRBS[[i]][["pccc_current_1"]][["cmrb_flag"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_current_1"]][["num_cmrb"]], c(0L, 1L, 1L, 1L, 2L, 0L, 0L, 1L, 0L, 0L, 1L, 0L))) CMRBS[[i]][["pccc_current_1"]][["num_cmrb"]] <- NULL stopifnot(all(CMRBS[[i]][["pccc_current_1"]] == 0)) CMRBS[[i]][["pccc_current_1"]] <- NULL } ################################################################################ # pccc_current_v for (i in seq_len(length(CMRBS))) { stopifnot(identical(CMRBS[[i]][["pccc_current_v"]][["patid"]], expected_patid)) CMRBS[[i]][["pccc_current_v"]][["patid"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_current_v"]][["encid"]], expected_encid)) CMRBS[[i]][["pccc_current_v"]][["encid"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_current_v"]][["cvd_dxpr_or_tech"]], c(0L, 0L, 1L, 0L, 0L, rep(0L, 7L)))) CMRBS[[i]][["pccc_current_v"]][["cvd_dxpr_or_tech"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_current_v"]][["cvd_dxpr_only"]], c(0L, 0L, 1L, 0L, 0L, rep(0L, 7L)))) CMRBS[[i]][["pccc_current_v"]][["cvd_dxpr_only"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_current_v"]][["malignancy_dxpr_or_tech"]], c(0L, 0L, 0L, 0L, 1L, rep(0L, 7L)))) CMRBS[[i]][["pccc_current_v"]][["malignancy_dxpr_or_tech"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_current_v"]][["malignancy_dxpr_only"]], c(0L, 0L, 0L, 0L, 1L, rep(0L, 7L)))) CMRBS[[i]][["pccc_current_v"]][["malignancy_dxpr_only"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_current_v"]][["renal_dxpr_or_tech"]], c(0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L))) CMRBS[[i]][["pccc_current_v"]][["renal_dxpr_or_tech"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_current_v"]][["renal_dxpr_only"]], c(0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L))) CMRBS[[i]][["pccc_current_v"]][["renal_dxpr_only"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_current_v"]][["cmrb_flag"]], c(0L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L))) CMRBS[[i]][["pccc_current_v"]][["cmrb_flag"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_current_v"]][["num_cmrb"]], c(0L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L))) CMRBS[[i]][["pccc_current_v"]][["num_cmrb"]] <- NULL stopifnot(all(CMRBS[[i]][["pccc_current_v"]] == 0)) CMRBS[[i]][["pccc_current_v"]] <- NULL } ################################################################################ # pccc_cumulative_0 for (i in seq_len(length(CMRBS))) { stopifnot(identical(CMRBS[[i]][["pccc_cumulative_0"]][["patid"]], expected_patid)) CMRBS[[i]][["pccc_cumulative_0"]][["patid"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_cumulative_0"]][["encid"]], expected_encid)) CMRBS[[i]][["pccc_cumulative_0"]][["encid"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_cumulative_0"]][["cvd_dxpr_or_tech"]], c(0L, 0L, 0L, rep(1L, 4L), rep(0L, 5L)))) CMRBS[[i]][["pccc_cumulative_0"]][["cvd_dxpr_or_tech"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_cumulative_0"]][["cvd_dxpr_only"]], c(0L, 0L, 0L, rep(1L, 4L), rep(0L, 5L)))) CMRBS[[i]][["pccc_cumulative_0"]][["cvd_dxpr_only"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_cumulative_0"]][["renal_dxpr_or_tech"]], c(rep(0L, 4L), rep(1L, 3L), 0L, rep(1L, 4L)))) CMRBS[[i]][["pccc_cumulative_0"]][["renal_dxpr_or_tech"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_cumulative_0"]][["renal_dxpr_only"]], c(rep(0L, 4L), rep(1L, 3L), 0L, rep(1L, 4L)))) CMRBS[[i]][["pccc_cumulative_0"]][["renal_dxpr_only"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_cumulative_0"]][["malignancy_dxpr_or_tech"]], c(0L, 0L, rep(1L, 5L), rep(0L, 5)))) CMRBS[[i]][["pccc_cumulative_0"]][["malignancy_dxpr_or_tech"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_cumulative_0"]][["malignancy_dxpr_only"]], c(0L, 0L, rep(1L, 5L), rep(0L, 5)))) CMRBS[[i]][["pccc_cumulative_0"]][["malignancy_dxpr_only"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_cumulative_0"]][["num_cmrb"]], c(0L, 0L, 1L, 2L, 3L, 3L, 3L, 0L, 1L, 1L, 1L, 1L))) CMRBS[[i]][["pccc_cumulative_0"]][["num_cmrb"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_cumulative_0"]][["cmrb_flag"]], c(0L, 0L, 1L, 1L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L))) CMRBS[[i]][["pccc_cumulative_0"]][["cmrb_flag"]] <- NULL stopifnot(all(CMRBS[[i]][["pccc_cumulative_0"]] == 0)) CMRBS[[i]][["pccc_cumulative_0"]] <- NULL } ################################################################################ # pccc_cumulative_1 for (i in seq_len(length(CMRBS))) { stopifnot(identical(CMRBS[[i]][["pccc_cumulative_1"]][["patid"]], expected_patid)) CMRBS[[i]][["pccc_cumulative_1"]][["patid"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_cumulative_1"]][["encid"]], expected_encid)) CMRBS[[i]][["pccc_cumulative_1"]][["encid"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_cumulative_1"]][["cvd_dxpr_or_tech"]], c(0L, 0L, rep(1L, 5L), rep(0L, 5L)))) CMRBS[[i]][["pccc_cumulative_1"]][["cvd_dxpr_or_tech"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_cumulative_1"]][["renal_dxpr_or_tech"]], c(rep(0L, 3L), rep(1L, 4L), rep(1L, 5L)))) CMRBS[[i]][["pccc_cumulative_1"]][["renal_dxpr_or_tech"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_cumulative_1"]][["malignancy_dxpr_or_tech"]], c(0L, rep(1L, 6L), rep(0L, 5)))) CMRBS[[i]][["pccc_cumulative_1"]][["malignancy_dxpr_or_tech"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_cumulative_1"]][["cvd_dxpr_only"]], c(0L, 0L, rep(1L, 5L), rep(0L, 5L)))) CMRBS[[i]][["pccc_cumulative_1"]][["cvd_dxpr_only"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_cumulative_1"]][["renal_dxpr_only"]], c(rep(0L, 3L), rep(1L, 4L), rep(1L, 5L)))) CMRBS[[i]][["pccc_cumulative_1"]][["renal_dxpr_only"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_cumulative_1"]][["malignancy_dxpr_only"]], c(0L, rep(1L, 6L), rep(0L, 5)))) CMRBS[[i]][["pccc_cumulative_1"]][["malignancy_dxpr_only"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_cumulative_1"]][["num_cmrb"]], c(0L, 1L, 2L, 3L, 3L, 3L, 3L, rep(1L, 5L)))) CMRBS[[i]][["pccc_cumulative_1"]][["num_cmrb"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_cumulative_1"]][["cmrb_flag"]], c(0L, rep(1L, 11L)))) CMRBS[[i]][["pccc_cumulative_1"]][["cmrb_flag"]] <- NULL stopifnot(all(CMRBS[[i]][["pccc_cumulative_1"]] == 0)) CMRBS[[i]][["pccc_cumulative_1"]] <- NULL } ################################################################################ # pccc_cumulative_v for (i in seq_len(length(CMRBS))) { stopifnot(identical(CMRBS[[i]][["pccc_cumulative_v"]][["patid"]], expected_patid)) CMRBS[[i]][["pccc_cumulative_v"]][["patid"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_cumulative_v"]][["encid"]], expected_encid)) CMRBS[[i]][["pccc_cumulative_v"]][["encid"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_cumulative_v"]][["cvd_dxpr_or_tech"]], c(0L, 0L, rep(1L, 5L), rep(0L, 5L)))) CMRBS[[i]][["pccc_cumulative_v"]][["cvd_dxpr_or_tech"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_cumulative_v"]][["renal_dxpr_or_tech"]], c(rep(0L, 3L), rep(1L, 4L), rep(1L, 5L)))) CMRBS[[i]][["pccc_cumulative_v"]][["renal_dxpr_or_tech"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_cumulative_v"]][["malignancy_dxpr_or_tech"]], c(0L, 0L, rep(1L, 5L), rep(0L, 5)))) CMRBS[[i]][["pccc_cumulative_v"]][["malignancy_dxpr_or_tech"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_cumulative_v"]][["cvd_dxpr_only"]], c(0L, 0L, rep(1L, 5L), rep(0L, 5L)))) CMRBS[[i]][["pccc_cumulative_v"]][["cvd_dxpr_only"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_cumulative_v"]][["renal_dxpr_only"]], c(rep(0L, 3L), rep(1L, 4L), rep(1L, 5L)))) CMRBS[[i]][["pccc_cumulative_v"]][["renal_dxpr_only"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_cumulative_v"]][["malignancy_dxpr_only"]], c(0L, 0L, rep(1L, 5L), rep(0L, 5)))) CMRBS[[i]][["pccc_cumulative_v"]][["malignancy_dxpr_only"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_cumulative_v"]][["num_cmrb"]], c(0L, 0L, 2L, 3L, 3L, 3L, 3L, rep(1L, 5L)))) CMRBS[[i]][["pccc_cumulative_v"]][["num_cmrb"]] <- NULL stopifnot(identical(CMRBS[[i]][["pccc_cumulative_v"]][["cmrb_flag"]], c(0L, 0L, rep(1L, 10L)))) CMRBS[[i]][["pccc_cumulative_v"]][["cmrb_flag"]] <- NULL stopifnot(all(CMRBS[[i]][["pccc_cumulative_v"]] == 0)) CMRBS[[i]][["pccc_cumulative_v"]] <- NULL } ################################################################################ # elixhauser_current_1 for (i in seq_len(length(CMRBS))) { stopifnot(identical(CMRBS[[i]][["elixhauser_current_1"]][["patid"]], expected_patid)) CMRBS[[i]][["elixhauser_current_1"]][["patid"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_current_1"]][["encid"]], expected_encid)) CMRBS[[i]][["elixhauser_current_1"]][["encid"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_current_1"]][["cmrb_flag"]], c(0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 0L))) CMRBS[[i]][["elixhauser_current_1"]][["cmrb_flag"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_current_1"]][["num_cmrb"]], c(0L, 1L, 1L, 1L, 2L, 0L, 0L, 1L, 0L, 0L, 1L, 0L))) CMRBS[[i]][["elixhauser_current_1"]][["num_cmrb"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_current_1"]][["RENLFL_SEV"]], c(0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 0L))) CMRBS[[i]][["elixhauser_current_1"]][["RENLFL_SEV"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_current_1"]][["HF"]], c(0L, 0L, 1L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L))) CMRBS[[i]][["elixhauser_current_1"]][["HF"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_current_1"]][["CANCER_METS"]], c(0L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L))) CMRBS[[i]][["elixhauser_current_1"]][["CANCER_METS"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_current_1"]][["mortality_index"]], c(0L, 22L, 14L, 7L, 36L, 0L, 0L, 7L, 0L, 0L, 7L, 0L))) CMRBS[[i]][["elixhauser_current_1"]][["mortality_index"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_current_1"]][["readmission_index"]], c(0L, 11L, 7L, 8L, 18L, 0L, 0L, 8L, 0L, 0L, 8L, 0L))) CMRBS[[i]][["elixhauser_current_1"]][["readmission_index"]] <- NULL stopifnot(all(CMRBS[[i]][["elixhauser_current_1"]] == 0)) CMRBS[[i]][["elixhauser_current_1"]] <- NULL } ################################################################################ # elixhauser_current_v for (i in seq_len(length(CMRBS))) { stopifnot(identical(CMRBS[[i]][["elixhauser_current_v"]][["patid"]], expected_patid)) CMRBS[[i]][["elixhauser_current_v"]][["patid"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_current_v"]][["encid"]], expected_encid)) CMRBS[[i]][["elixhauser_current_v"]][["encid"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_current_v"]][["cmrb_flag"]], c(0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L))) CMRBS[[i]][["elixhauser_current_v"]][["cmrb_flag"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_current_v"]][["num_cmrb"]], c(0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L))) CMRBS[[i]][["elixhauser_current_v"]][["num_cmrb"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_current_v"]][["RENLFL_SEV"]], c(0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L))) CMRBS[[i]][["elixhauser_current_v"]][["RENLFL_SEV"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_current_v"]][["HF"]], c(0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L))) CMRBS[[i]][["elixhauser_current_v"]][["HF"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_current_v"]][["CANCER_METS"]], c(0L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L))) CMRBS[[i]][["elixhauser_current_v"]][["CANCER_METS"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_current_v"]][["mortality_index"]], c(0L, 22L, 14L, 7L, 22L, 0L, 0L, 7L, 0L, 0L, 0L, 0L))) CMRBS[[i]][["elixhauser_current_v"]][["mortality_index"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_current_v"]][["readmission_index"]], c(0L, 11L, 7L, 8L, 11L, 0L, 0L, 8L, 0L, 0L, 0L, 0L))) CMRBS[[i]][["elixhauser_current_v"]][["readmission_index"]] <- NULL stopifnot(all(CMRBS[[i]][["elixhauser_current_v"]] == 0)) CMRBS[[i]][["elixhauser_current_v"]] <- NULL } ################################################################################ # elixhauser_cumulative_0 for (i in seq_len(length(CMRBS))) { stopifnot(identical(CMRBS[[i]][["elixhauser_cumulative_0"]][["patid"]], expected_patid)) CMRBS[[i]][["elixhauser_cumulative_0"]][["patid"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_cumulative_0"]][["encid"]], expected_encid)) CMRBS[[i]][["elixhauser_cumulative_0"]][["encid"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_cumulative_0"]][["cmrb_flag"]], c(0L, 1L, 1L, 1L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L))) CMRBS[[i]][["elixhauser_cumulative_0"]][["cmrb_flag"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_cumulative_0"]][["num_cmrb"]], c(0L, 1L, 1L, 2L, 3L, 3L, 3L, 0L, 1L, 1L, 1L, 1L))) CMRBS[[i]][["elixhauser_cumulative_0"]][["num_cmrb"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_cumulative_0"]][["RENLFL_SEV"]], c(0L, 0L, 0L, 0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L))) CMRBS[[i]][["elixhauser_cumulative_0"]][["RENLFL_SEV"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_cumulative_0"]][["HF"]], c(0L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L))) CMRBS[[i]][["elixhauser_cumulative_0"]][["HF"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_cumulative_0"]][["CANCER_METS"]], c(0L, 1L, 1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L))) CMRBS[[i]][["elixhauser_cumulative_0"]][["CANCER_METS"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_cumulative_0"]][["mortality_index"]], c(0L, 22L, 22L, 36L, 43L, 43L, 43L, 0L, 7L, 7L, 7L, 7L))) CMRBS[[i]][["elixhauser_cumulative_0"]][["mortality_index"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_cumulative_0"]][["readmission_index"]], c(0L, 11L, 11L, 18L, 26L, 26L, 26L, 0L, 8L, 8L, 8L, 8L))) CMRBS[[i]][["elixhauser_cumulative_0"]][["readmission_index"]] <- NULL stopifnot(all(CMRBS[[i]][["elixhauser_cumulative_0"]] == 0)) CMRBS[[i]][["elixhauser_cumulative_0"]] <- NULL } ################################################################################ # elixhauser_cumulative_1 for (i in seq_len(length(CMRBS))) { stopifnot(identical(CMRBS[[i]][["elixhauser_cumulative_1"]][["patid"]], expected_patid)) CMRBS[[i]][["elixhauser_cumulative_1"]][["patid"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_cumulative_1"]][["encid"]], expected_encid)) CMRBS[[i]][["elixhauser_cumulative_1"]][["encid"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_cumulative_1"]][["cmrb_flag"]], c(0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L))) CMRBS[[i]][["elixhauser_cumulative_1"]][["cmrb_flag"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_cumulative_1"]][["num_cmrb"]], c(0L, 1L, 2L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 1L, 1L))) CMRBS[[i]][["elixhauser_cumulative_1"]][["num_cmrb"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_cumulative_1"]][["RENLFL_SEV"]], c(0L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L))) CMRBS[[i]][["elixhauser_cumulative_1"]][["RENLFL_SEV"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_cumulative_1"]][["HF"]], c(0L, 0L, 1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L))) CMRBS[[i]][["elixhauser_cumulative_1"]][["HF"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_cumulative_1"]][["CANCER_METS"]], c(0L, 1L, 1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L))) CMRBS[[i]][["elixhauser_cumulative_1"]][["CANCER_METS"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_cumulative_1"]][["mortality_index"]], c(0L, 22L, 36L, 43L, 43L, 43L, 43L, 7L, 7L, 7L, 7L, 7L))) CMRBS[[i]][["elixhauser_cumulative_1"]][["mortality_index"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_cumulative_1"]][["readmission_index"]], c(0L, 11L, 18L, 26L, 26L, 26L, 26L, 8L, 8L, 8L, 8L, 8L))) CMRBS[[i]][["elixhauser_cumulative_1"]][["readmission_index"]] <- NULL stopifnot(all(CMRBS[[i]][["elixhauser_cumulative_1"]] == 0)) CMRBS[[i]][["elixhauser_cumulative_1"]] <- NULL } ################################################################################ # elixhauser_cumulative_v for (i in seq_len(length(CMRBS))) { stopifnot(identical(CMRBS[[i]][["elixhauser_cumulative_v"]][["patid"]], expected_patid)) CMRBS[[i]][["elixhauser_cumulative_v"]][["patid"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_cumulative_v"]][["encid"]], expected_encid)) CMRBS[[i]][["elixhauser_cumulative_v"]][["encid"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_cumulative_v"]][["cmrb_flag"]], c(0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L))) CMRBS[[i]][["elixhauser_cumulative_v"]][["cmrb_flag"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_cumulative_v"]][["num_cmrb"]], c(0L, 1L, 2L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 1L, 1L))) CMRBS[[i]][["elixhauser_cumulative_v"]][["num_cmrb"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_cumulative_v"]][["RENLFL_SEV"]], c(0L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L))) CMRBS[[i]][["elixhauser_cumulative_v"]][["RENLFL_SEV"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_cumulative_v"]][["HF"]], c(0L, 0L, 1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L))) CMRBS[[i]][["elixhauser_cumulative_v"]][["HF"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_cumulative_v"]][["CANCER_METS"]], c(0L, 1L, 1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L))) CMRBS[[i]][["elixhauser_cumulative_v"]][["CANCER_METS"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_cumulative_v"]][["mortality_index"]], c(0L, 22L, 36L, 43L, 43L, 43L, 43L, 7L, 7L, 7L, 7L, 7L))) CMRBS[[i]][["elixhauser_cumulative_v"]][["mortality_index"]] <- NULL stopifnot(identical(CMRBS[[i]][["elixhauser_cumulative_v"]][["readmission_index"]], c(0L, 11L, 18L, 26L, 26L, 26L, 26L, 8L, 8L, 8L, 8L, 8L))) CMRBS[[i]][["elixhauser_cumulative_v"]][["readmission_index"]] <- NULL stopifnot(all(CMRBS[[i]][["elixhauser_cumulative_v"]] == 0)) CMRBS[[i]][["elixhauser_cumulative_v"]] <- NULL } ################################################################################ #summary(CMRBS) stopifnot(identical(length(CMRBS[["DF"]]), 0L)) CMRBS[["DF"]] <- NULL stopifnot(identical(length(CMRBS[["DT"]]), 0L)) CMRBS[["DT"]] <- NULL stopifnot(identical(length(CMRBS[["TBL"]]), 0L)) CMRBS[["TBL"]] <- NULL stopifnot(identical(length(CMRBS), 0L)) ################################################################################ # End of File # ################################################################################