-
Notifications
You must be signed in to change notification settings - Fork 1
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Unit tests for pilot3utils function #13
Merged
Merged
Changes from all commits
Commits
Show all changes
16 commits
Select commit
Hold shift + click to select a range
44eafdd
Initial commit of pilot3utils automated tests using testthat. Continu…
c123e33
Initial commit with systematic testing setup for pilot3utils function.
92c5213
Tidying test-fmt.r
6be0089
Change R program extensions to be compliant with FDA file extension s…
03d6e2d
Updated r-lib lintr removing with_defaults which was deprecated in v3…
1b91b22
Additional unit tests for test-helpers.r
a77407a
Tidying unit test files for pilot3utils.
df6246b
Tidying unit test files for pilot3utils - lintr.
fdf1446
Initial commit using testthat(3e) snapshot feature to unit test the T…
3e42e2a
Tidying commit using testthat(3e) snapshot feature to unit test the T…
4bfeb4c
Tidying commit using testthat(3e) snapshot feature to unit test the f…
3248283
Lintr tidying commit using testthat(3e) snapshot feature to unit test…
2f35244
Tidying commit using testthat(3e) snapshot feature to unit test the e…
d528e2b
Tidying commit using testthat(3e) snapshot feature to unit test the e…
3840a90
Tidying commit using testthat(3e) snapshot feature to unit test the e…
0ac8168
Tidying commit using testthat(3e) snapshot feature to unit test the e…
File filter
Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,2 +1,2 @@ | ||
linters: with_defaults(line_length_linter(150), object_usage_linter=NULL, cyclocomp_linter(complexity_limit = 20)) | ||
linters: linters_with_defaults(line_length_linter(150), object_usage_linter=NULL, cyclocomp_linter(complexity_limit = 20)) | ||
exclusions: list("R/data.R") |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
File renamed without changes.
File renamed without changes.
File renamed without changes.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,24 @@ | ||
#' Retrieve paths to built-in example test files | ||
#' | ||
#' `testthat_examples()` retrieves path to directory of test files, | ||
#' `testthat_example()` retrieves path to a single test file. | ||
#' | ||
#' @keywords internal | ||
#' @param filename Name of test file | ||
#' @export | ||
#' @examples | ||
#' dir(testthat_examples()) | ||
#' testthat_example("success") | ||
testthat_examples <- function() { | ||
system.file("examples", package = "testthat") | ||
} | ||
|
||
#' @export | ||
#' @rdname testthat_examples | ||
testthat_example <- function(filename) { | ||
system.file( | ||
"examples", paste0("test-", filename, ".R"), | ||
package = "testthat", | ||
mustWork = TRUE | ||
) | ||
} |
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,12 @@ | ||
# This file is part of the standard setup for testthat. | ||
# It is recommended that you do not modify it. | ||
# | ||
# Where should you do additional test configuration? | ||
# Learn more about the roles of various files in: | ||
# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview | ||
# * https://testthat.r-lib.org/articles/special-files.html | ||
|
||
library(testthat) | ||
library(pilot3utils) | ||
|
||
test_check("pilot3utils") |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,24 @@ | ||
# nest_rowlabels works | ||
|
||
Code | ||
nest_rowlabels(.data) | ||
Output | ||
# A tibble: 12 x 7 | ||
row_label var1_placebo var1_x~1 var1_~2 ord_l~3 ord_l~4 ord_l~5 | ||
<chr> <chr> <chr> <chr> <dbl> <dbl> <dbl> | ||
1 Baseline "" "" "" 1 0 0 | ||
2 n "79" "74" "81" 1 1 1 | ||
3 Mean (SD) "24.1 (12.19)" "21.3 (~ "24.4 ~ 1 1 2 | ||
4 Median (Range) "21.0 ( 5;61)" "18.0 (~ "21.0 ~ 1 1 3 | ||
5 Week 24 "" "" "" 2 0 0 | ||
6 n "79" "74" "81" 2 1 1 | ||
7 Mean (SD) "26.7 (13.79)" "22.8 (~ "26.4 ~ 2 1 2 | ||
8 Median (Range) "24.0 ( 5;62)" "20.0 (~ "25.0 ~ 2 1 3 | ||
9 Change from Baseline "" "" "" 3 0 0 | ||
10 n "79" "74" "81" 3 1 1 | ||
11 Mean (SD) " 2.5 ( 5.80)" " 1.5 (~ " 2.0 ~ 3 1 2 | ||
12 Median (Range) " 2.0 (-11;16)" " 1.0 (~ " 2.0 ~ 3 1 3 | ||
# ... with abbreviated variable names 1: var1_xanomeline_high_dose, | ||
# 2: var1_xanomeline_low_dose, 3: ord_layer_index, 4: ord_layer_1, | ||
# 5: ord_layer_2 | ||
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,28 @@ | ||
# format_dcsreas works | ||
|
||
Code | ||
format_dcsreas("WITHDRAWAL BY SUBJECT") | ||
Output | ||
[1] "Withdrew Consent" | ||
|
||
# format_eosstt works | ||
|
||
Code | ||
format_eosstt("SCREENING NOT COMPLETED") | ||
Output | ||
[1] "NOT STARTED" | ||
|
||
# format_sitegr1 works | ||
|
||
Code | ||
format_sitegr1("714") | ||
Output | ||
[1] "900" | ||
|
||
# round_sas works | ||
|
||
Code | ||
round_sas(10.56, digits = 0) | ||
Output | ||
[1] 11 | ||
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,54 @@ | ||
# efficacy models works | ||
|
||
Code | ||
efficacy_models(adas, "CHG", 24) | ||
Output | ||
# A tibble: 9 x 3 | ||
row_label `var1_Xanomeline Low Dose` var1_Xanomel~1 | ||
<chr> <chr> <chr> | ||
1 "p-value(Dose Response) [1][2]" <NA> " 0.245 " | ||
2 "" <NA> "" | ||
3 "p-value(Xan - Placebo) [1][3]" " 0.569 " " 0.233 " | ||
4 " Diff of LS Means (SE)" "-0.5 (0.82)" "-1.0 (0.84)" | ||
5 " 95% CI" "(-2.1;1.1)" "(-2.7;0.7)" | ||
6 "" "" "" | ||
7 "p-value(Xan High - Xan Low) [1][3]" <NA> " 0.520 " | ||
8 " Diff of LS Means (SE)" <NA> "-0.5 (0.84)" | ||
9 " 95% CI" <NA> "(-2.2;1.1)" | ||
# ... with abbreviated variable name 1: `var1_Xanomeline High Dose` | ||
|
||
--- | ||
|
||
WAoAAAACAAQCAwACAwAAAAMTAAAAAwAAABAAAAAJAAQACQAAAB1wLXZhbHVlKERvc2UgUmVz | ||
cG9uc2UpIFsxXVsyXQAEAAkAAAAAAAQACQAAAB1wLXZhbHVlKFhhbiAtIFBsYWNlYm8pIFsx | ||
XVszXQAEAAkAAAAXICBEaWZmIG9mIExTIE1lYW5zIChTRSkABAAJAAAACCAgOTUlIENJAAQA | ||
CQAAAAAABAAJAAAAInAtdmFsdWUoWGFuIEhpZ2ggLSBYYW4gTG93KSBbMV1bM10ABAAJAAAA | ||
FyAgRGlmZiBvZiBMUyBNZWFucyAoU0UpAAQACQAAAAggIDk1JSBDSQAAABAAAAAJAAQACQAA | ||
AAJOQQAEAAkAAAACTkEABAAJAAAADCAgIDAuNTY5ICAgIAAEAAkAAAALLTAuNSAoMC44MikA | ||
BAAJAAAACigtMi4xOzEuMSkABAAJAAAAAAAEAAkAAAACTkEABAAJAAAAAk5BAAQACQAAAAJO | ||
QQAAABAAAAAJAAQACQAAAAwgICAwLjI0NSAgICAABAAJAAAAAAAEAAkAAAAMICAgMC4yMzMg | ||
ICAgAAQACQAAAAstMS4wICgwLjg0KQAEAAkAAAAKKC0yLjc7MC43KQAEAAkAAAAAAAQACQAA | ||
AAwgICAwLjUyMCAgICAABAAJAAAACy0wLjUgKDAuODQpAAQACQAAAAooLTIuMjsxLjEpAAAE | ||
AgAAAAEABAAJAAAABWNsYXNzAAAAEAAAAAMABAAJAAAABnRibF9kZgAEAAkAAAADdGJsAAQA | ||
CQAAAApkYXRhLmZyYW1lAAAEAgAAAAEABAAJAAAACXJvdy5uYW1lcwAAAA0AAAACgAAAAP// | ||
//cAAAQCAAAAAQAEAAkAAAAFbmFtZXMAAAAQAAAAAwAEAAkAAAAJcm93X2xhYmVsAAQACQAA | ||
ABl+dmFyMV9YYW5vbWVsaW5lIExvdyBEb3NlAAQACQAAABp+dmFyMV9YYW5vbWVsaW5lIEhp | ||
Z2ggRG9zZQAAAP4= | ||
|
||
--- | ||
|
||
WAoAAAACAAQCAwACAwAAAAMTAAAAAwAAABAAAAAJAAQACQAAAB1wLXZhbHVlKERvc2UgUmVz | ||
cG9uc2UpIFsxXVsyXQAEAAkAAAAAAAQACQAAAB1wLXZhbHVlKFhhbiAtIFBsYWNlYm8pIFsx | ||
XVszXQAEAAkAAAAXICBEaWZmIG9mIExTIE1lYW5zIChTRSkABAAJAAAACCAgOTUlIENJAAQA | ||
CQAAAAAABAAJAAAAInAtdmFsdWUoWGFuIEhpZ2ggLSBYYW4gTG93KSBbMV1bM10ABAAJAAAA | ||
FyAgRGlmZiBvZiBMUyBNZWFucyAoU0UpAAQACQAAAAggIDk1JSBDSQAAABAAAAAJAAAACf// | ||
//8AAAAJ/////wAEAAkAAAAMICAgMC41NjkgICAgAAQACQAAAAstMC41ICgwLjgyKQAEAAkA | ||
AAAKKC0yLjE7MS4xKQAEAAkAAAAAAAAACf////8AAAAJ/////wAAAAn/////AAAAEAAAAAkA | ||
BAAJAAAADCAgIDAuMjQ1ICAgIAAEAAkAAAAAAAQACQAAAAwgICAwLjIzMyAgICAABAAJAAAA | ||
Cy0xLjAgKDAuODQpAAQACQAAAAooLTIuNzswLjcpAAQACQAAAAAABAAJAAAADCAgIDAuNTIw | ||
ICAgIAAEAAkAAAALLTAuNSAoMC44NCkABAAJAAAACigtMi4yOzEuMSkAAAQCAAAAAQAEAAkA | ||
AAAFbmFtZXMAAAAQAAAAAwAEAAkAAAAJcm93X2xhYmVsAAQACQAAABh2YXIxX1hhbm9tZWxp | ||
bmUgTG93IERvc2UABAAJAAAAGXZhcjFfWGFub21lbGluZSBIaWdoIERvc2UAAAQCAAAAAQAE | ||
AAkAAAAJcm93Lm5hbWVzAAAADQAAAAKAAAAA////9wAABAIAAAABAAQACQAAAAVjbGFzcwAA | ||
ABAAAAADAAQACQAAAAZ0YmxfZGYABAAJAAAAA3RibAAEAAkAAAAKZGF0YS5mcmFtZQAAAP4= | ||
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,28 @@ | ||
# fmt_num works | ||
|
||
Code | ||
fmt_num(4.25, digits = 3) | ||
Output | ||
[1] " 4.250" | ||
|
||
# fmt_est works | ||
|
||
Code | ||
fmt_est(1.25, 0.5) | ||
Output | ||
[1] " 1.2 ( 0.50)" | ||
|
||
# fmt_pval works | ||
|
||
Code | ||
fmt_pval(0.52, digits = 3) | ||
Output | ||
[1] " 0.520" | ||
|
||
# fmt_ci works | ||
|
||
Code | ||
fmt_ci(-2.5, -0.09, 2.07) | ||
Output | ||
[1] "-2.50 (-0.09, 2.07)" | ||
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,51 @@ | ||
# pad_row works | ||
|
||
Code | ||
pad_row(.data) | ||
Output | ||
# A tibble: 7 x 5 | ||
STUDYID USUBJID PARAMCD PARAM AVISIT | ||
<chr> <chr> <chr> <chr> <chr> | ||
1 "TEST01" "01-701-1015" "DIABP" "Diastolic Blood Pressure (mmHg)" "BASELINE" | ||
2 "TEST01" "01-701-1015" "DIABP" "Diastolic Blood Pressure (mmHg)" "WEEK 2" | ||
3 "TEST01" "01-701-1015" "SYSBP" "Systolic Blood Pressure (mmHg)" "BASELINE" | ||
4 "TEST01" "01-701-1015" "SYSBP" "Systolic Blood Pressure (mmHg)" "WEEK 2" | ||
5 "TEST01" "01-701-1028" "DIABP" "Diastolic Blood Pressure (mmHg)" "BASELINE" | ||
6 "TEST01" "01-701-1028" "SYSBP" "Systolic Blood Pressure (mmHg)" "BASELINE" | ||
7 "" "" "" "" "" | ||
|
||
# num_fmt works | ||
|
||
Code | ||
num_fmt(5, digits = 0, size = 10, int_len = 3) | ||
Output | ||
[1] " 5 " | ||
|
||
# str_pad works | ||
|
||
Code | ||
str_pad("pilot3", 7, "left") | ||
Output | ||
[1] " pilot3" | ||
|
||
# nrow works | ||
|
||
Code | ||
nrow(matrix(1:12, 3, 4)) | ||
Output | ||
[1] 3 | ||
|
||
# round works | ||
|
||
Code | ||
round(c(0.3, 1.03, 2.67, 5, 8.91), digits = 1) | ||
Output | ||
[1] 0.3 1.0 2.7 5.0 8.9 | ||
|
||
# format works | ||
|
||
Code | ||
format("GFG", width = 8, justify = "l") | ||
Output | ||
[1] "GFG " | ||
|
Binary file not shown.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,41 @@ | ||
test_that("Pilot3 can use the testthat 3e", { | ||
local_edition(3) | ||
expect_true(TRUE) | ||
}) | ||
|
||
test_that("nest_rowlabels works", { | ||
.data <- tibble::tribble( | ||
~row_label1, ~row_label2, ~var1_placebo, ~var1_xanomeline_high_dose, ~var1_xanomeline_low_dose, ~ord_layer_index, ~ord_layer_1, ~ord_layer_2, | ||
"Baseline", "n", "79", "74", "81", 1, 1, 1, | ||
"Baseline", "Mean (SD)", "24.1 (12.19)", "21.3 (11.74)", "24.4 (12.92)", 1, 1, 2, | ||
"Baseline", "Median (Range)", "21.0 ( 5;61)", "18.0 ( 3;57)", "21.0 ( 5;57)", 1, 1, 3, | ||
"Week 24", "n", "79", "74", "81", 2, 1, 1, | ||
"Week 24", "Mean (SD)", "26.7 (13.79)", "22.8 (12.48)", "26.4 (13.18)", 2, 1, 2, | ||
"Week 24", "Median (Range)", "24.0 ( 5;62)", "20.0 ( 3;62)", "25.0 ( 6;62)", 2, 1, 3, | ||
"Change from Baseline", "n", "79", "74", "81", 3, 1, 1, | ||
"Change from Baseline", "Mean (SD)", " 2.5 ( 5.80)", " 1.5 ( 4.26)", " 2.0 ( 5.55)", 3, 1, 2, | ||
"Change from Baseline", "Median (Range)", " 2.0 (-11;16)", " 1.0 ( -7;13)", " 2.0 (-11;17)", 3, 1, 3 | ||
) | ||
.nest_rowlabels <- tibble::tribble( | ||
~row_label, ~var1_placebo, ~var1_xanomeline_high_dose, ~var1_xanomeline_low_dose, ~ord_layer_index, ~ord_layer_1, ~ord_layer_2, | ||
"Baseline", "", "", "", 1, 0, 0, | ||
"n", "79", "74", "81", 1, 1, 1, | ||
"Mean (SD)", "24.1 (12.19)", "21.3 (11.74)", "24.4 (12.92)", 1, 1, 2, | ||
"Median (Range)", "21.0 ( 5;61)", "18.0 ( 3;57)", "21.0 ( 5;57)", 1, 1, 3, | ||
"Week 24", "", "", "", 2, 0, 0, | ||
"n", "79", "74", "81", 2, 1, 1, | ||
"Mean (SD)", "26.7 (13.79)", "22.8 (12.48)", "26.4 (13.18)", 2, 1, 2, | ||
"Median (Range)", "24.0 ( 5;62)", "20.0 ( 3;62)", "25.0 ( 6;62)", 2, 1, 3, | ||
"Change from Baseline", "", "", "", 3, 0, 0, | ||
"n", "79", "74", "81", 3, 1, 1, | ||
"Mean (SD)", " 2.5 ( 5.80)", " 1.5 ( 4.26)", " 2.0 ( 5.55)", 3, 1, 2, | ||
"Median (Range)", " 2.0 (-11;16)", " 1.0 ( -7;13)", " 2.0 (-11;17)", 3, 1, 3 | ||
) | ||
expect_equal(nrow(.data), 9) | ||
expect_equal(nrow(.nest_rowlabels), 12) | ||
expect_equal(nrow(nest_rowlabels(.data)), 12) | ||
expect_s3_class(nest_rowlabels(.data), "tbl_df") | ||
expect_snapshot(nest_rowlabels(.data), dplyr::select(.nest_rowlabels)) | ||
expect_length(nrow(.data), 1) | ||
expect_length(nrow(.nest_rowlabels), 1) | ||
}) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,67 @@ | ||
test_that("Pilot3 can use the testthat 3e", { | ||
local_edition(3) | ||
expect_true(TRUE) | ||
}) | ||
|
||
test_that("format_dcsreas works", { | ||
.data_format_dcsreas <- tibble::tribble( | ||
~OUTPUT, | ||
"Withdrew Consent" | ||
) | ||
expect_equal(format_dcsreas("ADVERSE EVENT"), "Adverse Event") | ||
expect_equal(format_dcsreas("STUDY TERMINATED BY SPONSOR"), "Sponsor Decision") | ||
expect_equal(format_dcsreas("DEATH"), "Death") | ||
expect_equal(format_dcsreas("WITHDRAWAL BY SUBJECT"), "Withdrew Consent") | ||
expect_snapshot(format_dcsreas("WITHDRAWAL BY SUBJECT"), dplyr::select(.data_format_dcsreas)) | ||
expect_equal(format_dcsreas("PHYSICIAN DECISION"), "Physician Decision") | ||
expect_equal(format_dcsreas("LACK OF EFFICACY"), "Lack of Efficacy") | ||
expect_equal(format_dcsreas("PROTOCOL VIOLATION"), "Protocol Violation") | ||
expect_equal(format_dcsreas("LOST TO FOLLOW-UP"), "Lost to Follow-up") | ||
expect_length(format_dcsreas("ADVERSE"), 1) | ||
expect_length(format_dcsreas("ADVERSE EVENT"), 1) | ||
expect_length(format_dcsreas(NA), 1) | ||
}) | ||
|
||
test_that("format_eosstt works", { | ||
.data_format_eosstt <- tibble::tribble( | ||
~OUTPUT, | ||
"NOT STARTED" | ||
) | ||
expect_equal(format_eosstt("SCREEN FAILURE"), "NOT STARTED") | ||
expect_equal(format_eosstt("SCREENING FAILURE"), "DISCONTINUED") | ||
expect_equal(format_eosstt("COMPLETED"), "COMPLETED") | ||
expect_equal(format_eosstt("SCREENING NOT COMPLETED"), "NOT STARTED") | ||
expect_snapshot(format_eosstt("SCREENING NOT COMPLETED"), dplyr::select(.data_format_eosstt)) | ||
expect_equal(format_eosstt(""), "DISCONTINUED") | ||
expect_equal(format_eosstt(NA), "ONGOING") | ||
expect_length(format_eosstt("SCREEN FAILURE"), 1) | ||
expect_length(format_eosstt(NA), 1) | ||
}) | ||
|
||
test_that("format_sitegr1 works", { | ||
.data_format_sitegr1 <- tibble::tribble( | ||
~OUTPUT, | ||
"900" | ||
) | ||
expect_equal(format_sitegr1("702"), "900") | ||
expect_equal(format_sitegr1("706"), "900") | ||
expect_equal(format_sitegr1("707"), "900") | ||
expect_equal(format_sitegr1("711"), "900") | ||
expect_equal(format_sitegr1("714"), "900") | ||
expect_snapshot(format_sitegr1("714"), dplyr::select(.data_format_sitegr1)) | ||
expect_equal(format_sitegr1("715"), "900") | ||
expect_equal(format_sitegr1("717"), "900") | ||
expect_length(format_sitegr1("717"), 1) | ||
}) | ||
|
||
test_that("round_sas works", { | ||
.data_round_sas <- tibble::tribble( | ||
~OUTPUT, | ||
11 | ||
) | ||
expect_equal(round_sas(10.56, digits = 0), 11) | ||
expect_snapshot(round_sas(10.56, digits = 0), dplyr::select(.data_round_sas)) | ||
expect_equal(round_sas(9.06, digits = 0), 9) | ||
expect_equal(round_sas(-5.6, digits = 0), -6) | ||
expect_length(round_sas(10.56, digits = 0), 1) | ||
}) |
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Those four lines are not testing the efficacy models? @SHAESEN2 - yes, preparing to commit the unit test for the efficacy_models function. thx. |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,36 @@ | ||
test_that("Pilot3 can use the testthat 3e", { | ||
local_edition(3) | ||
expect_true(TRUE) | ||
}) | ||
test_that("efficacy models works", { | ||
#use DESCRIPTION file imports/suggests packages for pilot3utils environment | ||
adas <- haven::read_xpt("./adadas.xpt") | ||
adas <- adas %>% | ||
filter( | ||
EFFFL == "Y", | ||
ITTFL == "Y", | ||
PARAMCD == "ACTOT", | ||
ANL01FL == "Y" | ||
) | ||
model_portion <- efficacy_models(adas, "CHG", 24) | ||
.data_model_portion <- tibble::tribble( | ||
~row_label, ~`~var1_Xanomeline Low Dose`, ~`~var1_Xanomeline High Dose`, | ||
"p-value(Dose Response) [1][2]", "NA", " 0.245 ", | ||
"", "NA", "", | ||
"p-value(Xan - Placebo) [1][3]", " 0.569 ", " 0.233 ", | ||
" Diff of LS Means (SE)", "-0.5 (0.82)", "-1.0 (0.84)", | ||
" 95% CI", "(-2.1;1.1)", "(-2.7;0.7)", | ||
"", "", "", | ||
"p-value(Xan High - Xan Low) [1][3]", "NA", " 0.520 ", | ||
" Diff of LS Means (SE)", "NA", "-0.5 (0.84)", | ||
" 95% CI", "NA", "(-2.2;1.1)" | ||
) | ||
expect_equal(efficacy_models(adas, "CHG", 24), model_portion) | ||
expect_snapshot(efficacy_models(adas, "CHG", 24), dplyr::select(model_portion)) | ||
expect_length(efficacy_models(adas, "CHG", 24), 3) | ||
expect_s3_class(model_portion, "tbl_df") | ||
expect_s3_class(.data_model_portion, "tbl_df") | ||
expect_snapshot_value(.data_model_portion, "serialize") | ||
expect_snapshot_value(model_portion, "serialize") | ||
expect_length(.data_model_portion, 3) | ||
}) |
Oops, something went wrong.
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
I wonder if we need to rename the files to make it traceable eg in this file it seems you are testing adam format functions, rather than just functions
@SHAESEN2 - yes, the filenames are autogenerated and can be changed to make traceable to a requirements traceability matrix (RTM) for pilot3utils.
The admiral package has excellent test coverage already for the functions used in pilot3. The focus in this issue has been to unit test the functions defined in the pilot3utils package source. thx.
The unit test file names can be whatever pilot3 team wishes. With test_dir( ) every source file in the
specified directory gets tested with a "dot" output representing a function 'PASS' (see below). The _snaps
directory can be used for snapshotting test results for comparison. The testthat package creates test files in the
pilot3utils package using '.R' not '.r' extension - easy enough to change extension to match the regulatory specification. The traceability aspect to match the unit test to a specific pilot3 requirement is an excellent
point. One limitation (of using snapshots) is that snapshots are not aware if an output is correct - so an expect strategy comparing unit test output against 'correct' (point of truth) is necessary. thx.
The snapshots appear in the _snaps directory when the expect_snapshot unit test is run. Even a slight difference in expected outcome and previous test snapshot results in an error getting issued. An example using the pilot3utils nest_rowlabels function appears below using expect_snapshot and other testthat expect suggests.
It is pretty cool but the traceability matrix is a great idea then Pilot3 can link requirement to unit test PASS and store the snapshot in the repository.