18 EXT01 #41
Merged
18 EXT01 #41
Conversation
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
added 6 commits
September 9, 2021 17:37
(transformation as factor: maybe needed later)
waddella
approved these changes
Sep 23, 2021
| if(prune_0) tbl <- tbl %>% prune_table() | ||
| if (prune_0) | ||
| tbl <- prune_table(tbl) | ||
| else |
R/ext01.R
Outdated
| @@ -0,0 +1,227 @@ | |||
| #' Exposure Summary Table | |||
| #' | |||
| #'The EXT01 table provides an overview of the of the exposure of the patients in terms of Total dose administered or | |||
R/ext01.R
Outdated
| )) { | ||
|
|
||
| # provide a clearer error message in the case of missing variable | ||
| missing_var = setdiff(summaryvars, colnames(adex)) |
There was a problem hiding this comment.
please create a utility function error_if_missing_vars
R/ext01.R
Outdated
|
|
||
| # provide a clearer error message in the case of missing variable | ||
| missing_var = setdiff(summaryvars, colnames(adex)) | ||
| if(length(missing_var) > 0) { |
There was a problem hiding this comment.
please add space before (, use the lintr plugin to lint your package
R/ext01.R
Outdated
| if(prune_0) tbl <- tbl %>% prune_table() | ||
|
|
||
| #TDOD: sort | ||
| tbl_sorted <- tbl |
R/ext01.R
Outdated
| #' @param group `(nested list)` providing for each parameter value that should be analyzed in a categorical way: the | ||
| #' name of the parameter `(string)`, a series of breakpoints `(vector)` where the first breakpoints is typically `-Inf` | ||
| #' and the last `Inf`, and a series of name which will describe each category `(vector)`. | ||
| #'@param paramvar `(vector)` providing the name of the parameters whose statistical summary should be presented. To |
R/ext01.R
Outdated
| c("<5000", "5000-7000", "7000-9000", ">9000") | ||
| ) | ||
| ), | ||
| paramvar = c(""), |
There was a problem hiding this comment.
- when can you change the paramvar? isn't it always
PARAM? i.e. remove the argument - if argument needed, then empty string is probably not allowed.
- does this go into the study object and should be called
paramvar_adex?.
R/ext01.R
Outdated
| ) | ||
| } | ||
|
|
||
| adex$AVAL_gp <- NA #NA |
There was a problem hiding this comment.
why are we deriving this and why is it not in AVALC?
R/ext01.R
Outdated
| if(paramvar != "ALL") { | ||
|
|
||
| adex <- adex %>% | ||
| mutate(AVAL = ifelse(PARAM %in% paramvar, AVAL, NA)) |
There was a problem hiding this comment.
why is this not already in the adam dataset?
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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.
close insightsengineering/chevron-tasks#14
Create ext01 table which could serve as template for tables that require summary statistics and binning of continuous variables in the same table. End result is slightly different from the one presented in the TLG catalog for the supplementary table.
Thank you for the review .