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reorder violation_count
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ref #4
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@wibeasley
wibeasley committed Dec 30, 2021
1 parent c2c499e commit 98ee41c
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Showing 2 changed files with 38 additions and 48 deletions.
7 changes: 6 additions & 1 deletion R/execute-checks.R
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Original file line number Diff line number Diff line change
Expand Up @@ -221,7 +221,12 @@ execute_rules <- function (ds, checks) {

checks$rules <-
checks$rules |>
dplyr::left_join(ds_rule_results, by = "check_name")
dplyr::left_join(ds_rule_results, by = "check_name") |>
dplyr::select(
.data$check_name,
.data$violation_count,
tidyselect::everything(),
)

list(
rules = checks$rules,
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79 changes: 32 additions & 47 deletions tests/testthat/_snaps/execute-checks.md
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Original file line number Diff line number Diff line change
Expand Up @@ -105,44 +105,44 @@
result$rules
Output
# A tibble: 14 x 8
check_name error_message priority debug instrument passing_test results
<chr> <chr> <int> <lgl> <chr> <chr> <list>
1 baseline_p~ Serum pre-albu~ 1 FALSE baseline_da~ "function (d~ <tibbl~
2 missing_se~ Relevant nutri~ 1 FALSE baseline_da~ "function (d~ <tibbl~
3 serum_prea~ Baseline preal~ 1 FALSE baseline_da~ "function (d~ <tibbl~
4 serum_prea~ Baseline preal~ 1 FALSE baseline_da~ "function (d~ <NULL>
5 serum_prea~ Baseline preal~ 1 FALSE baseline_da~ "function (d~ <NULL>
6 serum_prea~ serum prealbum~ 1 FALSE baseline_da~ "function (d~ <NULL>
7 baseline_f~ Serum prealbum~ 1 FALSE baseline_da~ "function (d~ <NULL>
8 daily_firs~ In-addition to~ 1 FALSE baseline_da~ "function (d~ <NULL>
9 daily_prot~ npcr levels in~ 1 FALSE baseline_da~ "function (d~ <NULL>
10 hospitaliz~ Patient was ho~ 1 FALSE completion_~ "function (d~ <tibbl~
11 optimal_da~ Daily protein ~ 1 FALSE completion_~ "function (d~ <tibbl~
12 recommende~ NPCR values ar~ 1 FALSE completion_~ "function (d~ <tibbl~
13 npcr NPCR at comple~ 1 FALSE completion_~ "function (d~ <tibbl~
14 npcr_compa~ NPCR at comple~ 1 FALSE completion_~ "function (d~ <tibbl~
# ... with 1 more variable: violation_count <int>
check_name violation_count error_message priority debug instrument
<chr> <int> <chr> <int> <lgl> <chr>
1 baseline_pre~ 10 Serum pre-albumi~ 1 FALSE baseline_data
2 missing_seru~ 3 Relevant nutriti~ 1 FALSE baseline_data
3 serum_prealb~ 15 Baseline prealbu~ 1 FALSE baseline_data~
4 serum_prealb~ NA Baseline prealbu~ 1 FALSE baseline_data~
5 serum_prealb~ NA Baseline prealbu~ 1 FALSE baseline_data~
6 serum_prealb~ NA serum prealbumin~ 1 FALSE baseline_data~
7 baseline_fir~ NA Serum prealbumin~ 1 FALSE baseline_data~
8 daily_first_~ NA In-addition to b~ 1 FALSE baseline_data~
9 daily_protei~ NA npcr levels in s~ 1 FALSE baseline_data~
10 hospitalizat~ 2 Patient was hosp~ 1 FALSE completion_pr~
11 optimal_dail~ 7 Daily protein in~ 1 FALSE completion_pr~
12 recommended_~ 10 NPCR values are ~ 1 FALSE completion_da~
13 npcr 1 NPCR at completi~ 1 FALSE completion_da~
14 npcr_compari~ 2 NPCR at completi~ 1 FALSE completion_da~
# ... with 2 more variables: passing_test <chr>, results <list>

---

Code
as.data.frame(dplyr::select(result$rules, !tidyselect::contains("results")))
Output
check_name
1 baseline_prealbumin_levels
2 missing_serum_marker_levels
3 serum_prealbumin_levels_1
4 serum_prealbumin_levels_2
5 serum_prealbumin_levels_completion_data
6 serum_prealbumin_levels_expectations
7 baseline_first_visit_lab_parameters
8 daily_first_visit_lab_and_workup_parameters
9 daily_protein_intake
10 hospitalization_reason
11 optimal_daily_protein_intake
12 recommended_npcr_range
13 npcr
14 npcr_comparison
check_name violation_count
1 baseline_prealbumin_levels 10
2 missing_serum_marker_levels 3
3 serum_prealbumin_levels_1 15
4 serum_prealbumin_levels_2 NA
5 serum_prealbumin_levels_completion_data NA
6 serum_prealbumin_levels_expectations NA
7 baseline_first_visit_lab_parameters NA
8 daily_first_visit_lab_and_workup_parameters NA
9 daily_protein_intake NA
10 hospitalization_reason 2
11 optimal_daily_protein_intake 7
12 recommended_npcr_range 10
13 npcr 1
14 npcr_comparison 2
error_message
1 Serum pre-albumin level of all enrolled patients do not meet the study criterion
2 Relevant nutritional serum markers are missing
Expand Down Expand Up @@ -203,21 +203,6 @@
12 function (d) {\n dplyr::between(d$completion_data_npcr, 1.2, 1.4)\n}\n
13 function (d) {\n events_to_check <- c("final_visit_arm_1")\n dplyr::if_else(\n d$redcap_event_name %in% events_to_check,\n !is.na(d$completion_data_npcr), # If this row exists in the desired event, then check for nonmissingness.\n TRUE # Otherwise, the test passes for rows associated with all other events.\n )\n}\n
14 function (d) {\n dplyr::if_else(\n !is.na(d$completion_data_npcr),\n (d$npcr_at_baseline < d$completion_data_npcr),\n TRUE\n )\n}
violation_count
1 10
2 3
3 15
4 NA
5 NA
6 NA
7 NA
8 NA
9 NA
10 2
11 7
12 10
13 1
14 2

---

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