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update snaps
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ref #7
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@wibeasley
wibeasley committed Jul 24, 2023
1 parent 61966c8 commit b4cf836
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88 changes: 44 additions & 44 deletions tests/testthat/_snaps/execute-checks.md
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Expand Up @@ -67,20 +67,20 @@
result$smells
Output
# A tibble: 11 x 12
check_name pass description priority debug bound_lower bound_upper
<chr> <lgl> <chr> <int> <lgl> <dbl> <dbl>
1 females TRUE Proportion of fem~ 2 FALSE 0.4 0.6
2 males TRUE Proportion of mal~ 2 FALSE 0.4 0.6
3 age TRUE Mean participant ~ 2 FALSE 20 60
4 serum_prealb~ FALSE Mean serum pre-al~ 2 FALSE 32 39
5 serum_creati~ FALSE Mean serum creati~ 2 FALSE 3 15
6 bmi_at_basel~ FALSE Mean BMI is betwe~ 2 FALSE 18 24
7 serum_choles~ TRUE Mean cholesterol ~ 1 FALSE 100 140
8 dialysis_ade~ TRUE Mean Kt/V value i~ 1 FALSE 1.2 5
9 nutritional_~ TRUE Most patients agr~ 2 FALSE 0.85 0.99
10 definitive_d~ TRUE The proportion of~ 1 FALSE 1 1
11 normalized_p~ TRUE Mean Normalized P~ 1 FALSE 0 1.2
# ... with 5 more variables: bounds_template <chr>, value_template <chr>,
check_name pass description priority debug bound_lower bound_upper
<chr> <lgl> <chr> <int> <lgl> <dbl> <dbl>
1 females TRUE Proportion~ 2 FALSE 0.4 0.6
2 males TRUE Proportion~ 2 FALSE 0.4 0.6
3 age TRUE Mean parti~ 2 FALSE 20 60
4 serum_prealbumin_le~ FALSE Mean serum~ 2 FALSE 32 39
5 serum_creatinine_le~ FALSE Mean serum~ 2 FALSE 3 15
6 bmi_at_baseline FALSE Mean BMI i~ 2 FALSE 18 24
7 serum_cholesterol_l~ TRUE Mean chole~ 1 FALSE 100 140
8 dialysis_adequacy TRUE Mean Kt/V ~ 1 FALSE 1.2 5
9 nutritional_counsel~ TRUE Most patie~ 2 FALSE 0.85 0.99
10 definitive_diagnosis TRUE The propor~ 1 FALSE 1 1
11 normalized_protein_~ TRUE Mean Norma~ 1 FALSE 0 1.2
# i 5 more variables: bounds_template <chr>, value_template <chr>,
# equation <chr>, boundaries <chr>, value <dbl>

---
Expand Down Expand Up @@ -162,23 +162,23 @@
result$rules
Output
# A tibble: 14 x 8
check_name violation_count error_message priority debug redcap_instrument
<chr> <int> <chr> <int> <lgl> <chr>
1 baseline_pr~ 10 Serum pre-albu~ 1 FALSE baseline_data
2 missing_ser~ 3 Relevant nutri~ 1 FALSE baseline_data
3 serum_preal~ 15 Baseline preal~ 2 FALSE baseline_data, v~
4 serum_preal~ 0 Baseline preal~ 2 FALSE baseline_data, v~
5 serum_preal~ 0 Baseline preal~ 2 FALSE baseline_data, v~
6 serum_preal~ 0 serum prealbum~ 3 FALSE baseline_data, v~
7 baseline_fi~ 0 Serum prealbum~ 3 FALSE baseline_data, v~
8 daily_first~ 0 In-addition to~ 3 FALSE baseline_data, p~
9 daily_prote~ 0 npcr levels in~ 3 FALSE baseline_data, p~
10 hospitaliza~ 2 Patient was ho~ 1 FALSE completion_proje~
11 optimal_dai~ 7 Daily protein ~ 2 FALSE completion_proje~
12 recommended~ 10 NPCR values ar~ 2 FALSE completion_data
13 npcr 1 NPCR at comple~ 2 FALSE completion_data
14 npcr_compar~ 2 NPCR at comple~ 3 FALSE completion_data
# ... with 2 more variables: passing_test <chr>, results <list>
check_name violation_count error_message priority debug redcap_instrument
<chr> <int> <chr> <int> <lgl> <chr>
1 baseline_prea~ 10 Serum pre-al~ 1 FALSE baseline_data
2 missing_serum~ 3 Relevant nut~ 1 FALSE baseline_data
3 serum_prealbu~ 15 Baseline pre~ 2 FALSE baseline_data, v~
4 serum_prealbu~ 0 Baseline pre~ 2 FALSE baseline_data, v~
5 serum_prealbu~ 0 Baseline pre~ 2 FALSE baseline_data, v~
6 serum_prealbu~ 0 serum prealb~ 3 FALSE baseline_data, v~
7 baseline_firs~ 0 Serum prealb~ 3 FALSE baseline_data, v~
8 daily_first_v~ 0 In-addition ~ 3 FALSE baseline_data, p~
9 daily_protein~ 0 npcr levels ~ 3 FALSE baseline_data, p~
10 hospitalizati~ 2 Patient was ~ 1 FALSE completion_proje~
11 optimal_daily~ 7 Daily protei~ 2 FALSE completion_proje~
12 recommended_n~ 10 NPCR values ~ 2 FALSE completion_data
13 npcr 1 NPCR at comp~ 2 FALSE completion_data
14 npcr_comparis~ 2 NPCR at comp~ 3 FALSE completion_data
# i 2 more variables: passing_test <chr>, results <list>

---

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ds_result_unnested
Output
# A tibble: 50 x 5
check_name record_id data_collector baseline_date record_id_linked
<chr> <int> <int> <date> <chr>
1 baseline_pre~ 1 1 2015-01-02 "<a href=\"https://bbmc~
2 baseline_pre~ 2 2 2015-01-02 "<a href=\"https://bbmc~
3 baseline_pre~ 3 3 2015-01-05 "<a href=\"https://bbmc~
4 baseline_pre~ 8 1 2015-02-03 "<a href=\"https://bbmc~
5 baseline_pre~ 9 3 2015-02-08 "<a href=\"https://bbmc~
6 baseline_pre~ 12 3 2015-03-06 "<a href=\"https://bbmc~
7 baseline_pre~ 13 1 2015-03-15 "<a href=\"https://bbmc~
8 baseline_pre~ 14 1 2015-03-10 "<a href=\"https://bbmc~
9 baseline_pre~ 15 3 2015-03-03 "<a href=\"https://bbmc~
10 baseline_pre~ 100 1 2015-04-02 "<a href=\"https://bbmc~
# ... with 40 more rows
check_name record_id data_collector baseline_date record_id_linked
<chr> <int> <int> <date> <chr>
1 baseline_prealbumin_~ 1 1 2015-01-02 "<a href=\"http~
2 baseline_prealbumin_~ 2 2 2015-01-02 "<a href=\"http~
3 baseline_prealbumin_~ 3 3 2015-01-05 "<a href=\"http~
4 baseline_prealbumin_~ 8 1 2015-02-03 "<a href=\"http~
5 baseline_prealbumin_~ 9 3 2015-02-08 "<a href=\"http~
6 baseline_prealbumin_~ 12 3 2015-03-06 "<a href=\"http~
7 baseline_prealbumin_~ 13 1 2015-03-15 "<a href=\"http~
8 baseline_prealbumin_~ 14 1 2015-03-10 "<a href=\"http~
9 baseline_prealbumin_~ 15 3 2015-03-03 "<a href=\"http~
10 baseline_prealbumin_~ 100 1 2015-04-02 "<a href=\"http~
# i 40 more rows

---

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43 changes: 21 additions & 22 deletions tests/testthat/_snaps/load-checks.md
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Expand Up @@ -80,8 +80,7 @@
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]
# ... with 3 more variables: value_template <chr>, equation <chr>,
# boundaries <chr>
# i 3 more variables: value_template <chr>, equation <chr>, boundaries <chr>

---

Expand Down Expand Up @@ -158,7 +157,7 @@
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]
# ... with 2 more variables: value_template <chr>, equation <chr>
# i 2 more variables: value_template <chr>, equation <chr>

---

Expand All @@ -185,22 +184,22 @@
checks$rules
Output
# A tibble: 14 x 6
check_name error_message priority debug redcap_instrument passing_test
<chr> <chr> <int> <lgl> <chr> <chr>
1 baseline_pr~ Serum pre-album~ 1 FALSE baseline_data "function (d)~
2 missing_ser~ Relevant nutrit~ 1 FALSE baseline_data "function (d)~
3 serum_preal~ Baseline prealb~ 2 FALSE baseline_data, v~ "function (d)~
4 serum_preal~ Baseline prealb~ 2 FALSE baseline_data, v~ "function (d)~
5 serum_preal~ Baseline prealb~ 2 FALSE baseline_data, v~ "function (d)~
6 serum_preal~ serum prealbumi~ 3 FALSE baseline_data, v~ "function (d)~
7 baseline_fi~ Serum prealbumi~ 3 FALSE baseline_data, v~ "function (d)~
8 daily_first~ In-addition to ~ 3 FALSE baseline_data, p~ "function (d)~
9 daily_prote~ npcr levels in ~ 3 FALSE baseline_data, p~ "function (d)~
10 hospitaliza~ Patient was hos~ 1 FALSE completion_proje~ "function (d)~
11 optimal_dai~ Daily protein i~ 2 FALSE completion_proje~ "function (d)~
12 recommended~ NPCR values are~ 2 FALSE completion_data "function (d)~
13 npcr NPCR at complet~ 2 FALSE completion_data "function (d)~
14 npcr_compar~ NPCR at complet~ 3 FALSE completion_data "function (d)~
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 (~

---

Expand Down Expand Up @@ -289,7 +288,7 @@
checks$rules_inactive
Output
# A tibble: 1 x 6
check_name error_message priority debug redcap_instrume~ passing_test
<chr> <chr> <int> <lgl> <chr> <chr>
1 pre_albumin_levels pre_albumin l~ 3 FALSE visit_lab_date "function (~
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 (~

1 change: 1 addition & 0 deletions tests/testthat/test-execute-checks.R
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@@ -1,4 +1,5 @@
library(testthat)
# testthat::test_file("tests/testthat/test-execute-checks.R")

test_that("execute-checks-biochemical", {
path_data <- system.file("datasets/pt-event-biochemical.rds", package = "trawler")
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1 change: 1 addition & 0 deletions tests/testthat/test-load-checks.R
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@@ -1,4 +1,5 @@
library(testthat)
# testthat::test_file("tests/testthat/test-load-checks.R")

test_that("load-checks-biochemical", {
path_checks <- system.file("checks/checks-biochemical.yml", package = "trawler")
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