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update roxygen header of 3 r files with examples #38

Merged
merged 18 commits into from
Sep 1, 2023
Merged

update roxygen header of 3 r files with examples #38

merged 18 commits into from
Sep 1, 2023

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hoppanda
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@hoppanda hoppanda linked an issue Aug 18, 2023 that may be closed by this pull request
add examples to functions #29
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github-actions bot commented Aug 18, 2023 •
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Code Coverage Summary

Filename                   Stmts    Miss  Cover    Missing
-----------------------  -------  ------  -------  --------------------
R/bucher.R                    22       9  59.09%   37, 63-72
R/data_generation.R           20      20  0.00%    36-73
R/maic_unanchored_tte.R       85      85  0.00%    25-164
R/matching.R                 203     181  10.84%   35-102, 121, 163-419
R/process_data.R             101     101  0.00%    39-275
R/survival-helper.R          140     140  0.00%    14-255
TOTAL                        571     536  6.13%

Diff against main

Filename               Stmts    Miss  Cover
-------------------  -------  ------  --------
R/matching.R              +8     -10  +8.79%
R/survival-helper.R       +1      +1  +100.00%
TOTAL                     +9      -9  +3.10%

Results for commit: ad2979c

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

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github-actions bot commented Aug 18, 2023 •
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Unit Tests Summary

3 tests   3 ✔️  0s ⏱️
2 suites  0 💤
1 files    0 ❌

Results for commit 45c8412.

♻️ This comment has been updated with latest results.

gravesti
gravesti reviewed Aug 21, 2023
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R/matching.R Outdated
@@ -294,62 +311,18 @@ plot.maicplus_estimate_weights <- function(x, ggplot = FALSE,
#' @param processed_agd a data frame, object returned after using \code{\link{process_agd}} or
#' aggregated data following the same naming convention
#'
#' @examples
#' load(system.file("extdata", "agd.rda", package = "maicplus", mustWork = TRUE))
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@MikeJSeo Do you have the code to generate agd.rda? Could you add the code in data-raw/agd.R

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I think I just stored this data.frame manually:
agd <- data.frame(
STUDY = "Lung study",
ARM = "Total",
N = 300,
AGE_MEAN = 51,
AGE_MEDIAN = 49,
AGE_SD = 3.25,
SEX_MALE_PROP = 147/300,
ECOG0_PROP = 0.40,
ECOG0_COUNT = 40,
SMOKE_PROP = 58/(300-5),
N_PR_THER_MEDIAN = 2
)

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Do we even need agd.rda? Let's just do this?
target_pop <- read.csv(system.file("extdata","aggregate_data_example_1.csv", package = "maicplus", mustWork =
agd <- process_agd(target_pop)

MikeJSeo
MikeJSeo reviewed Sep 1, 2023
View reviewed changes
R/survival-helper.R Outdated Show resolved Hide resolved
R/matching.R Outdated
@@ -294,62 +311,18 @@ plot.maicplus_estimate_weights <- function(x, ggplot = FALSE,
#' @param processed_agd a data frame, object returned after using \code{\link{process_agd}} or
#' aggregated data following the same naming convention
#'
#' @examples
#' load(system.file("extdata", "agd.rda", package = "maicplus", mustWork = TRUE))
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I think I just stored this data.frame manually:
agd <- data.frame(
STUDY = "Lung study",
ARM = "Total",
N = 300,
AGE_MEAN = 51,
AGE_MEDIAN = 49,
AGE_SD = 3.25,
SEX_MALE_PROP = 147/300,
ECOG0_PROP = 0.40,
ECOG0_COUNT = 40,
SMOKE_PROP = 58/(300-5),
N_PR_THER_MEDIAN = 2
)

R/matching.R Outdated
@@ -294,62 +311,18 @@ plot.maicplus_estimate_weights <- function(x, ggplot = FALSE,
#' @param processed_agd a data frame, object returned after using \code{\link{process_agd}} or
#' aggregated data following the same naming convention
#'
#' @examples
#' load(system.file("extdata", "agd.rda", package = "maicplus", mustWork = TRUE))
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Do we even need agd.rda? Let's just do this?
target_pop <- read.csv(system.file("extdata","aggregate_data_example_1.csv", package = "maicplus", mustWork =
agd <- process_agd(target_pop)

@gravesti gravesti merged commit 7aabd6c into main Sep 1, 2023
20 of 22 checks passed
@gravesti gravesti deleted the 29-add-examples-to-functions branch September 1, 2023 12:14
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@MikeJSeo MikeJSeo MikeJSeo left review comments

@gravesti gravesti gravesti approved these changes

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add examples to functions
3 participants
@hoppanda @MikeJSeo @gravesti