simplify columns

ref #4
OuhscBbmc · Dec 23, 2021 · 9ad17eb · 9ad17eb
1 parent 6f1713f
commit 9ad17eb
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Showing 5 changed files with 82 additions and 75 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -19,6 +19,7 @@ Imports:
     readr (>= 2.0),
     rlang (>= 0.4.12),
     tibble (>= 1.4.0),
+    tidyselect,
     yaml
 Suggests:
     covr,

diff --git a/R/execute-checks.R b/R/execute-checks.R
@@ -26,6 +26,7 @@ execute_checks <- function (ds, ds_smell) {
 
 }
 
+#' @importFrom rlang .data
 execute_smells <- function (ds, ds_smell) {
   checkmate::assert_data_frame(ds)
   checkmate::assert_data_frame(ds_smell)
@@ -44,8 +45,8 @@ execute_smells <- function (ds, ds_smell) {
     ds_smell |>
     dplyr::mutate(
       # f             = purrr::invoke_map(function(x) eval(parse(text=x)), .data$equation),
-      smell_value   = NA_real_,
-      smell_pass    = NA
+      value   = NA_real_,
+      pass    = NA
     )
 
   # for( i in 1:14 ) {
@@ -62,16 +63,21 @@ execute_smells <- function (ds, ds_smell) {
     })
 
     tryCatch({
-      ds_smell_result$smell_value[i]   <- f(ds)
+      ds_smell_result$value[i]   <- f(ds)
     }, error = function(e) {
       stop("Problem executing the equation for smell `", ds_smell$check_name[i], "`.\n", e)
     })
 
     # ds_smell_result$smell_value[i]   <- f[[i]](ds)
-    ds_smell_result$smell_pass[i]    <- dplyr::between(ds_smell_result$smell_value[i], left = ds_smell_result$bound_lower[i], right = ds_smell_result$bound_upper[i])
+    ds_smell_result$pass[i]    <- dplyr::between(ds_smell_result$value[i], left = ds_smell_result$bound_lower[i], right = ds_smell_result$bound_upper[i])
   }
 
-  message(nrow(ds_smell_result), " smells have been sniffed  ", sum(!ds_smell_result$smell_pass), " violation(s) were found.\n")
+  message(nrow(ds_smell_result), " smells have been sniffed  ", sum(!ds_smell_result$pass), " violation(s) were found.\n")
 
-  ds_smell_result
+  ds_smell_result |>
+    dplyr::select(
+      .data$check_name,
+      .data$pass,
+      tidyselect::everything()
+    )
 }
diff --git a/R/load-checks.R b/R/load-checks.R
@@ -30,20 +30,20 @@ load_smells <- function (checks) {
     ds_smell <-
       checks$smells |>
       purrr::map_df(tibble::as_tibble) |>
-      dplyr::filter(.data$smell_active) |>
+      dplyr::filter(.data$active) |>
       dplyr::mutate(
         debug         = dplyr::coalesce(.data$debug, FALSE),
       )
 
     ds_smell_inactive <-
       checks$smells |>
       purrr::map_df(tibble::as_tibble) |>
-      dplyr::filter(!.data$smell_active)
+      dplyr::filter(!.data$active)
 
     testit::assert("The count of distinct rule columns (in the yaml checks file) should be 10.", ncol(ds_smell) == 10L)
     testit::assert( # dput(colnames(ds_smell))
       "The smell columns (in the yaml checks file) should be correct.",
-      colnames(ds_smell) == c("check_name", "description", "priority", "smell_active", "debug", "bound_lower", "bound_upper", "bounds_template", "value_template", "equation")
+      colnames(ds_smell) == c("check_name", "description", "priority", "active", "debug", "bound_lower", "bound_upper", "bounds_template", "value_template", "equation")
     )
 
     ds_smell <-
@@ -56,7 +56,7 @@ load_smells <- function (checks) {
     checkmate::assert_character(ds_smell$check_name      , any.missing=F , pattern="^.{4,99}$"  , unique=T)
     checkmate::assert_character(ds_smell$description     , any.missing=F , pattern="^.{4,255}$" , unique=T)
     checkmate::assert_integer(  ds_smell$priority        , any.missing=F , lower=1, upper=5     )
-    checkmate::assert_logical(  ds_smell$smell_active    , any.missing=F                        )
+    checkmate::assert_logical(  ds_smell$active          , any.missing=F                        )
     checkmate::assert_logical(  ds_smell$debug           , any.missing=F                        )
     checkmate::assert_numeric(  ds_smell$bound_lower     , any.missing=F                        )
     checkmate::assert_numeric(  ds_smell$bound_upper     , any.missing=F                        )
@@ -78,20 +78,20 @@ load_rules <- function (checks) {
     checks$rules |>
     purrr::map_df(tibble::as_tibble) |>
     # dplyr::rename(check_name = name) |>
-    dplyr::filter(.data$test_active) |>
+    dplyr::filter(.data$active) |>
     dplyr::mutate(
       debug         = dplyr::coalesce(.data$debug, FALSE),
     )
 
   ds_rule_inactive <-
     checks$rules |>
     purrr::map_df(tibble::as_tibble) |>
-    dplyr::filter(!.data$test_active)
+    dplyr::filter(!.data$active)
 
   #testit::assert("The count of distinct rule columns (in the yaml checks file) should be 7.", ncol(ds_rule) == 10L)
   testit::assert( # dput(colnames(ds_rule))
     "The rule columns (in the yaml checks file) should be correct.",
-    colnames(ds_rule) == c("check_name", "error_message", "priority", "test_active", "debug", "instrument", "passing_test")
+    colnames(ds_rule) == c("check_name", "error_message", "priority", "active", "debug", "instrument", "passing_test")
   )
   # table(ds_rule$check_name)
   # table(ds_rule$error_message)
@@ -101,7 +101,7 @@ load_rules <- function (checks) {
   checkmate::assert_character(ds_rule$check_name    , any.missing=F , pattern="^.{4,99}$"  , unique=T)
   checkmate::assert_character(ds_rule$error_message , any.missing=F , pattern="^.{4,255}$" , unique=T)
   checkmate::assert_integer(  ds_rule$priority      , any.missing=F , lower=1, upper=5      )
-  checkmate::assert_logical(  ds_rule$test_active   , any.missing=F                         )
+  checkmate::assert_logical(  ds_rule$active        , any.missing=F                         )
   checkmate::assert_logical(  ds_rule$debug         , any.missing=F                         )
   checkmate::assert_character(ds_rule$instrument    , any.missing=F , pattern="^.{2,255}$"  )
   checkmate::assert_character(ds_rule$passing_test  , any.missing=F , pattern="^.{5,}$"     , unique=T)

diff --git a/inst/checks/checks-biochemical.yml b/inst/checks/checks-biochemical.yml
@@ -18,7 +18,7 @@ default:
   - check_name           : proportion_female_participants
     description          : Proportion female participants is half the participants till study conclusion
     priority             : 1
-    smell_active         : TRUE
+    active               : TRUE
     debug                : FALSE
     bound_lower          : .5
     bound_upper          : .5
@@ -31,7 +31,7 @@ default:
   - check_name           : proportion_male_participants
     description          : Proportion male participants is half the participants till study conclusion
     priority             : 1
-    smell_active         : TRUE
+    active               : TRUE
     debug                : FALSE
     bound_lower          : .5
     bound_upper          : .5
@@ -44,7 +44,7 @@ default:
   - check_name           : mean_age
     description          : Mean age of participants is between 18 years to 20 years
     priority             : 1
-    smell_active         : TRUE
+    active               : TRUE
     debug                : FALSE
     bound_lower          : 20
     bound_upper          : 80
@@ -57,7 +57,7 @@ default:
   - check_name           : mean_serum_prealbumin_level_at_baseline
     description          : Mean serum pre-albumin levels at baseline are between 31mg/dl and 39mg/dl
     priority             : 1
-    smell_active         : TRUE
+    active               : TRUE
     debug                : FALSE
     bound_lower          : 32
     bound_upper          : 39
@@ -70,7 +70,7 @@ default:
   - check_name           : mean_serum_creatinine_level_at_baseline
     description          : Mean serum creatinine levels at baseline are between 3mg/dl and 15mg/dl
     priority             : 1
-    smell_active         : TRUE
+    active               : TRUE
     debug                : FALSE
     bound_lower          : 3
     bound_upper          : 15
@@ -83,7 +83,7 @@ default:
   - check_name           : average_bmi_at_baseline
     description          : Average BMI is between 18 and 24
     priority             : 1
-    smell_active         : TRUE
+    active               : TRUE
     debug                : FALSE
     bound_lower          : 18
     bound_upper          : 24
@@ -96,7 +96,7 @@ default:
   - check_name           : mean_serum_cholesterol_levels_at_baseline
     description          : Average Cholesterol levels range is between 100mg/dl-140mg/dl at baseline level
     priority             : 1
-    smell_active         : TRUE
+    active               : TRUE
     debug                : FALSE
     bound_lower          : 100
     bound_upper          : 140
@@ -109,7 +109,7 @@ default:
   - check_name           : dialysis_adequacy
     description          : Normal range for Kt/V values are between 1.2 and 5
     priority             : 1
-    smell_active         : TRUE
+    active               : TRUE
     debug                : FALSE
     bound_lower          : 1.2
     bound_upper          : 5
@@ -122,7 +122,7 @@ default:
   - check_name           : average_serum_ferritin_levels_at_baseline
     description          : Mean serum ferritin levels are in the recommended range of > 500ng/dl-1200ng/dl
     priority             : 1
-    smell_active         : TRUE
+    active               : TRUE
     debug                : FALSE
     bound_lower          : 501
     bound_upper          : 1200
@@ -135,7 +135,7 @@ default:
   - check_name           : nutritional_counseling
     description          : Most patients agreed to receiving nutritional counseling
     priority             : 1
-    smell_active         : TRUE
+    active               : TRUE
     debug                : FALSE
     bound_lower          : .85
     bound_upper          : .99
@@ -148,7 +148,7 @@ default:
   - check_name           : definitive_diagnosis
     description          : A 100 percent of study participants were diagnosed with malnutrition associated with Chronic Renal Disease
     priority             : 1
-    smell_active         : TRUE
+    active               : TRUE
     debug                : FALSE
     bound_lower          : 1.0
     bound_upper          : 1.0
@@ -161,7 +161,7 @@ default:
   - check_name           : normalized_protein_catabolic_rate
     description          : Average Normalized Protein Catabolic Rate is < 1.2g/kg/day
     priority             : 1
-    smell_active         : TRUE
+    active               : TRUE
     debug                : FALSE
     bound_lower          : 0
     bound_upper          : 0.12
@@ -175,7 +175,7 @@ default:
   - check_name           : baseline_prealbumin_levels
     error_message        : "Serum pre-albumin level of all enrolled patients do not meet the study criterion"                         # Tranferrin level <100 indicates severe protein-energy malnutrition
     priority             : 1
-    test_active          : TRUE
+    active               : TRUE
     debug                : FALSE
     instrument           : baseline_data                                                                                    # At baseline the study is enrolling malnurished patients or patients with chronic renal failure
     passing_test         : |
@@ -189,7 +189,7 @@ default:
   - check_name           : missing_serum_marker_levels
     error_message        : "Relevant nutritional serum markers are missing"   # All these parameters together, should not be missing
     priority             : 1
-    test_active          : TRUE
+    active               : TRUE
     debug                : FALSE
     instrument           : baseline_data
     passing_test         : |
@@ -203,7 +203,7 @@ default:
   - check_name           : serum_prealbumin_levels_1
     error_message        : "Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit"
     priority             : 1
-    test_active          : TRUE
+    active               : TRUE
     debug                : FALSE
     instrument           : baseline_data, visit_lab_date
     passing_test         : |
@@ -218,7 +218,7 @@ default:
   - check_name           : serum_prealbumin_levels_2
     error_message        : "Baseline prealbumin levels and pre-albumin levels during the 1st visit are not missing however levels in the next reading are missing"
     priority             : 1
-    test_active          : TRUE
+    active               : TRUE
     debug                : FALSE
     instrument           : baseline_data, visit_lab_date, visit_blood_workup
     passing_test         : |
@@ -233,7 +233,7 @@ default:
   - check_name           : serum_prealbumin_levels_completion_data
     error_message        : "Baseline prealbumin levels are not missing however readings are not carefully monitored at completion"
     priority             : 1
-    test_active          : TRUE
+    active               : TRUE
     debug                : FALSE
     instrument           : baseline_data, visit_lab_date, visit_blood_workup, completion_date
     passing_test         : |
@@ -249,7 +249,7 @@ default:
   - check_name           : serum_prealbumin_levels_expectations
     error_message        : "serum prealbumin levels are not missing however subsequent readings did not come as expected"
     priority             : 1
-    test_active          : TRUE
+    active               : TRUE
     debug                : FALSE
     instrument           : baseline_data, visit_lab_date, visit_blood_workup, completion_date
     passing_test         : |
@@ -265,7 +265,7 @@ default:
   - check_name           : pre_albumin_levels
     error_message        : "pre_albumin levels are not improving"
     priority             : 1
-    test_active          : FALSE
+    active               : FALSE
     debug                : FALSE
     instrument           : visit_lab_date
     passing_test         : |
@@ -281,7 +281,7 @@ default:
   - check_name           : baseline_first_visit_lab_parameters
     error_message        : "Serum prealbumin levels are low and protein intake at baseline is less than optimal"
     priority             : 1
-    test_active          : TRUE
+    active               : TRUE
     debug                : FALSE
     instrument           : baseline_data, visit_lab_data
     passing_test         : |
@@ -297,7 +297,7 @@ default:
   - check_name           : daily_first_visit_lab_and_workup_parameters
     error_message        : "In-addition to baseline & visit lab protein parameters, blood work-up npcr levels are also low"
     priority             : 1
-    test_active          : TRUE
+    active               : TRUE
     debug                : FALSE
     instrument           : baseline_data, patient_morale_questionnaire
     passing_test         : |
@@ -314,7 +314,7 @@ default:
   - check_name           : daily_protein_intake
     error_message        : "npcr levels in study have not improved as intended"
     priority             : 1
-    test_active          : TRUE
+    active               : TRUE
     debug                : FALSE
     instrument           : baseline_data, patient_morale_questionnaire
     passing_test         : |
@@ -332,7 +332,7 @@ default:
   - check_name           : hospitalization_reason
     error_message        : "Patient was hospitalized but reason and the date of hospitalization is missing"
     priority             : 1
-    test_active          : TRUE
+    active               : TRUE
     debug                : FALSE
     instrument           : completion_project_questionnaire
     passing_test         : |
@@ -346,7 +346,7 @@ default:
   - check_name           : optimal_daily_protein_intake
     error_message        : "Daily protein intake is optimal but one of the nutritional marker is not within the normal range"
     priority             : 1
-    test_active          : TRUE
+    active               : TRUE
     debug                : FALSE
     instrument           : completion_project_questionnaire, completion_data
     passing_test         : |
@@ -360,7 +360,7 @@ default:
   - check_name           : recommended_npcr_range
     error_message        : "NPCR values are not within the recommended range at completion"
     priority             : 1
-    test_active          : TRUE
+    active               : TRUE
     debug                : FALSE
     instrument           : completion_data                                                              # At baseline the study is enrolling malnurished patients or patients with chronic renal failure
     passing_test         : |
@@ -370,7 +370,7 @@ default:
   - check_name           : npcr
     error_message        : "NPCR at completion is missing"
     priority             : 1
-    test_active          : TRUE
+    active               : TRUE
     debug                : FALSE
     instrument           : completion_data
     passing_test         : |
@@ -385,7 +385,7 @@ default:
   - check_name           : npcr_comparison                                                               # Showing improvement in nutritional status
     error_message        : "NPCR at completion is not greater than npcr at baseline"
     priority             : 1
-    test_active          : TRUE
+    active               : TRUE
     debug                : FALSE
     instrument           : completion_data
     passing_test         : |