R/load-checks.R
load_checks.RdLoad and parse checks in a yaml file, and return a list of useful objects.
load_checks(path_checks, origin)# Step 0: define paths.
# So this package example executes on every machine, temp files are used.
# Replace the two paths for your specific project
path_checks <- system.file("checks/checks-biochemical.yml", package = "trawler")
# Step 1: load the check definitions and the dataset to test
load_checks(path_checks, origin = "REDCap")
#> $github_file_prefix
#> [1] "https://github.com/OuhscBbmc/validator-1/tree/main"
#>
#> $record_id_name
#> [1] "record_id"
#>
#> $record_id_link
#> [1] "<a href=\"https://bbmc.ouhsc.edu/redcap/redcap_v%s/DataEntry/index.php?pid=%s&arm=%s&id=%s&page=%s\" target=\"_blank\">%s</a>"
#>
#> $baseline_date_name
#> [1] "date_enrolled"
#>
#> $redcap_project_id
#> [1] 1612
#>
#> $redcap_version
#> [1] "10.5.1"
#>
#> $redcap_default_arm
#> [1] 1
#>
#> $redcap_codebook
#> [1] "https://bbmc.ouhsc.edu/redcap/redcap_v10.5.1/Design/data_dictionary_codebook.php?pid=1612"
#>
#> $redcap_record_link
#> [1] "<a href=\"https://bbmc.ouhsc.edu/redcap/redcap_v%s/DataEntry/index.php?pid=%s&arm=%s&id=%s&page=%s\" target=\"_blank\">%s</a>"
#>
#> $smells
#> # A tibble: 11 × 10
#> check_name description priority debug bound_lower bound_upper bounds_template
#> <chr> <chr> <int> <lgl> <dbl> <dbl> <chr>
#> 1 females Proportion… 2 FALSE 0.4 0.6 [%.2f, %.2f]
#> 2 males Proportion… 2 FALSE 0.4 0.6 [%.2f, %.2f]
#> 3 age Mean parti… 2 FALSE 20 60 [%.0f, %.0f]
#> 4 serum_pre… Mean serum… 2 FALSE 32 39 [%.0f, %.0f]
#> 5 serum_cre… Mean serum… 2 FALSE 3 15 [%.0f, %.0f]
#> 6 bmi_at_ba… Mean BMI i… 2 FALSE 18 24 [%.0f, %.0f]
#> 7 serum_cho… Mean chole… 1 FALSE 100 140 [%.0f, %.0f]
#> 8 dialysis_… Mean Kt/V … 1 FALSE 1.2 5 [%.1f, %.1f]
#> 9 nutrition… Most patie… 2 FALSE 0.85 0.99 [%.2f, %.2f]
#> 10 definitiv… The propor… 1 FALSE 1 1 [%.1f, %.1f]
#> 11 normalize… Mean Norma… 1 FALSE 0 1.2 [%.1f, %.1f]
#> # ℹ 3 more variables: value_template <chr>, equation <chr>, boundaries <chr>
#>
#> $smells_inactive
#> # A tibble: 1 × 9
#> check_name description priority debug bound_lower bound_upper bounds_template
#> <chr> <chr> <int> <lgl> <dbl> <dbl> <chr>
#> 1 average_se… ??Units co… 1 FALSE 501 1200 [%.0f, %.0f]
#> # ℹ 2 more variables: value_template <chr>, equation <chr>
#>
#> $smell_names_md
#> [1] "11 smells have been defined:\n\n1. females;\n2. males;\n3. age;\n4. serum_prealbumin_level_at_baseline;\n5. serum_creatinine_level_at_baseline;\n6. bmi_at_baseline;\n7. serum_cholesterol_levels_at_baseline;\n8. dialysis_adequacy;\n9. nutritional_counseling;\n10. definitive_diagnosis;\n11. normalized_protein_catabolic_rate;\n"
#>
#> $rules
#> # A tibble: 14 × 6
#> check_name error_message priority debug redcap_instrument passing_test
#> <chr> <chr> <int> <lgl> <chr> <chr>
#> 1 baseline_prealbu… Serum pre-al… 1 FALSE baseline_data "function (…
#> 2 missing_serum_ma… Relevant nut… 1 FALSE baseline_data "function (…
#> 3 serum_prealbumin… Baseline pre… 2 FALSE baseline_data, v… "function (…
#> 4 serum_prealbumin… Baseline pre… 2 FALSE baseline_data, v… "function (…
#> 5 serum_prealbumin… Baseline pre… 2 FALSE baseline_data, v… "function (…
#> 6 serum_prealbumin… serum prealb… 3 FALSE baseline_data, v… "function (…
#> 7 baseline_first_v… Serum prealb… 3 FALSE baseline_data, v… "function (…
#> 8 daily_first_visi… In-addition … 3 FALSE baseline_data, p… "function (…
#> 9 daily_protein_in… npcr levels … 3 FALSE baseline_data, p… "function (…
#> 10 hospitalization_… Patient was … 1 FALSE completion_proje… "function (…
#> 11 optimal_daily_pr… Daily protei… 2 FALSE completion_proje… "function (…
#> 12 recommended_npcr… NPCR values … 2 FALSE completion_data "function (…
#> 13 npcr NPCR at comp… 2 FALSE completion_data "function (…
#> 14 npcr_comparison NPCR at comp… 3 FALSE completion_data "function (…
#>
#> $rules_inactive
#> # A tibble: 1 × 6
#> check_name error_message priority debug redcap_instrument passing_test
#> <chr> <chr> <int> <lgl> <chr> <chr>
#> 1 pre_albumin_levels pre_albumin … 3 FALSE visit_lab_date "function (…
#>
#> attr(,"class")
#> [1] "trawler_checks_definition"