R Under development (unstable) (2025-05-13 r88200 ucrt) -- "Unsuffered Consequences"
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> # Overview of tests for ccc():
> #   ICD 9
> #     X invalid input (not real ICD codes)
> #     X check output for saved file - if it changes, I want to know
> #     X missing diagnoses list
> #     X missing procedure list
> #     X missing ID column
> #     X no input
> #     X need to test each category of CCC - one code from each category
> #       Neuro
> #       ....
> #     performance test?
> #
> ###############################################################################
> #
> # run tests with Ctrl/Cmd + Shift + T or devtools::test()
> # for manually running, execute
> library(pccc)
> 
> # set useFancyQuotes = FALSE so that in both interactive and non-interactive
> # modes output will be consistent.  Without this the double quote will be
> # unicode 34 in non-interactie and unicode 8802 in interactive.
> options(useFancyQuotes = FALSE)
> 
> 
> # context("PCCC - ccc ICD9 function tests")
> 
> # Basic checks of standard output ---------------------------------------------
> 
> # "Correct number of rows (1 per patient) returned?"
> df <-
+   ccc(pccc_icd9_dataset[, c(1:21)],
+       id      = id,
+       dx_cols = dplyr::starts_with("dx"),
+       pc_cols = dplyr::starts_with("pc"),
+       icdv    = 9)
> 
> stopifnot(identical(nrow(df), 1000L))
> 
> # "Correct number of columns (1 per category + Id column + summary column) returned?",
> stopifnot(identical(ncol(df), 14L))
> 
> # None of these should result in an error -------------------------------------
> # "icd 9 data set with all parameters - result should be unchanged."
> expected <- readRDS("icd9_test_result.rds")
> stopifnot(isTRUE(all.equal(df, expected)))
> 
> # "icd 9 data set with missing id parameter"
> stopifnot(
+     all.equal(
+       ccc(pccc_icd9_dataset[, c(1:21)],
+           dx_cols = dplyr::starts_with("dx"),
+           pc_cols = dplyr::starts_with("pc"),
+           icdv    = 9)
+       ,
+      readRDS("icd9_test_result.rds")[, -1]
+   )
+ )
> 
> # "icd 9 data set with missing dx parameter",
> df <- ccc(pccc_icd9_dataset[, c(1:21)],
+           id      = id,
+           pc_cols = dplyr::starts_with("pc"),
+           icdv    = 9)
> 
> # this test will pass in non-interactive mode, the strings are slightly
> # different in interactive mode.  The difference is the quotation marks used.
> # SOLUTION TO THE QUOTE ISSUE: options(useFancyQuotes = FALSE)
> stopifnot(
+   identical(
+     all.equal(df, readRDS("icd9_test_result.rds"))
+     ,
+     c("Component \"neuromusc\": Mean absolute difference: 1",
+       "Component \"cvd\": Mean absolute difference: 1",
+       "Component \"respiratory\": Mean absolute difference: 1",
+       "Component \"renal\": Mean absolute difference: 1",
+       "Component \"gi\": Mean absolute difference: 1",
+       "Component \"hemato_immu\": Mean absolute difference: 1",
+       "Component \"metabolic\": Mean absolute difference: 1",
+       "Component \"congeni_genetic\": Mean absolute difference: 1",
+       "Component \"malignancy\": Mean absolute difference: 1",
+       "Component \"neonatal\": Mean absolute difference: 1",
+       "Component \"tech_dep\": Mean absolute difference: 1",
+       "Component \"transplant\": Mean absolute difference: 1",
+       "Component \"ccc_flag\": Mean absolute difference: 1")
+   )
+ )
> 
> 
> # "icd 9 data set with missing pc parameter"
> out <-
+   all.equal(
+             ccc(pccc_icd9_dataset[, c(1:21)],
+                 id      = id,
+                 pc_cols = dplyr::starts_with("dx"),
+                 icdv    = 9),
+             readRDS("icd9_test_result.rds"))
> 
> stopifnot(
+     grepl("^Component \"neuromusc\": Mean relative difference: 35",      out[1])
+   , grepl("^Component \"cvd\": Mean relative difference: 3",             out[2])
+   , grepl("^Component \"respiratory\": Mean relative difference: 2",     out[3])
+   , grepl("^Component \"renal\": Mean relative difference: 8",           out[4])
+   , grepl("^Component \"gi\": Mean relative difference: 3",              out[5])
+   , grepl("^Component \"hemato_immu\": Mean relative difference: 3",     out[6])
+   , grepl("^Component \"metabolic\": Mean relative difference: 6",       out[7])
+   , grepl("^Component \"congeni_genetic\": Mean absolute difference: 1", out[8])
+   , grepl("^Component \"malignancy\": Mean absolute difference: 1",      out[9])
+   , grepl("^Component \"neonatal\": Mean absolute difference: 1",        out[10])
+   , grepl("^Component \"tech_dep\": Mean relative difference: 4",        out[11])
+   , grepl("^Component \"transplant\": Mean relative difference: 2",      out[12])
+   , grepl("^Component \"ccc_flag\": Mean relative difference: 9",        out[13])
+ )
> 
> # should not be equal, and should have many differences
> # "icd 10 data set with ICD9 parameter"
> stopifnot(
+     typeof(all.equal(
+       ccc(pccc_icd10_dataset[, c(1:21)],
+           id      = id,
+           dx_cols = dplyr::starts_with("dx"),
+           pc_cols = dplyr::starts_with("pc"),
+           icdv    = 9),
+       readRDS("icd10_test_result.rds"))) == "character"
+   )
> 
> # Cases that should result in an error ----------------------------------------
> # "icd 9 data set with only version parameter"
> x <- tryCatch(ccc(pccc_icd9_dataset[, c(1:21)], icdv = 9),
+               error = function(e) e)
> stopifnot(inherits(x, "error"))
> stopifnot(x$message == "dx_cols and pc_cols are both missing.  At least one must not be.")
> 
> # "icd 9 data set with no parameters"
> x <- tryCatch(ccc(pccc_icd9_dataset[, c(1:21)]), error = function(e) e)
> stopifnot(inherits(x, "error"))
> stopifnot(x$message == "dx_cols and pc_cols are both missing.  At least one must not be.")
> 
> # -----------------------------------------------------------------------------
> # "random data set with all parameters ICD9 - result should be unchanged."
> ccc_out <- ccc(data.frame(id = letters[1:3],
+                           dx1 = c('sadcj89sa', '1,2.3.4,5', 'sdf 9'),
+                           pc1 = c('da89v#$%', ' 90v_', 'this is a super long string compared to standard ICD codes and shouldnt break anything - if it does, the world will come to an end... Ok, so maybe not, but that means I need to fix something in this package.'),
+                           other_col = LETTERS[1:3]),
+                id      = id,
+                dx_cols = dplyr::starts_with("dx"),
+                pc_cols = dplyr::starts_with("pc"),
+                icdv    = 9)
> ccc_out$id <- as.factor(ccc_out$id)
> rnd_test <- readRDS("random_data_test_result.rds")
> rnd_test$id <- as.factor(rnd_test$id)
> stopifnot(isTRUE(all.equal(ccc_out, rnd_test)))
> 
> # Need to do some sort of performance test here - don't throw error,
> # but keep track of about how long this takes to run
> # test_that("test to only run locally", {
> #   skip_on_cran()
> #   expect_equal(ccc(), 99)
> # })
> 
> 
> 
> 
> # should not be equal, and should have many differences
> # "icd 9 data set with ICD10 parameter"
> stopifnot(
+     typeof(all.equal(
+       ccc(pccc_icd9_dataset[, c(1:21)],
+           id      = id,
+           dx_cols = dplyr::starts_with("dx"),
+           pc_cols = dplyr::starts_with("pc"),
+           icdv    = 10),
+       readRDS("icd9_test_result.rds"))) == "character"
+   )
> 
> proc.time()
   user  system elapsed 
   0.82    0.07    0.90