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Remove dynamic domain determination #193

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merged 21 commits into from
Jan 16, 2024
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1 change: 1 addition & 0 deletions NAMESPACE
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@ export(type_log)
export(var_names_log)
export(var_ord_msg)
export(xportr_df_label)
export(xportr_domain_name)
export(xportr_format)
export(xportr_label)
export(xportr_length)
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7 changes: 3 additions & 4 deletions R/df_label.R
Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@
#' label = c("Subject-Level Analysis", "Adverse Events Analysis")
#' )
#'
#' adsl <- xportr_df_label(adsl, metadata)
#' adsl <- xportr_df_label(adsl, metadata, domain = "adsl")
xportr_df_label <- function(.df,
metadata = NULL,
domain = NULL,
Expand All @@ -54,10 +54,9 @@ xportr_df_label <- function(.df,
domain_name <- getOption("xportr.df_domain_name")
label_name <- getOption("xportr.df_label")

## Common section to detect domain from argument or pipes
## Common section to detect domain from argument or attribute
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df_arg <- tryCatch(as_name(enexpr(.df)), error = function(err) NULL)
domain <- get_domain(.df, df_arg, domain)
domain <- get_domain(.df, domain)
if (!is.null(domain)) attr(.df, "_xportr.df_arg_") <- domain

## End of common section
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7 changes: 3 additions & 4 deletions R/format.R
Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@
#' format = c(NA, "DATE9.")
#' )
#'
#' adsl <- xportr_format(adsl, metadata)
#' adsl <- xportr_format(adsl, metadata, domain = "adsl")
xportr_format <- function(.df,
metadata = NULL,
domain = NULL,
Expand All @@ -57,10 +57,9 @@ xportr_format <- function(.df,
format_name <- getOption("xportr.format_name")
variable_name <- getOption("xportr.variable_name")

## Common section to detect domain from argument or pipes
## Common section to detect domain from argument or attribute

df_arg <- tryCatch(as_name(enexpr(.df)), error = function(err) NULL)
domain <- get_domain(.df, df_arg, domain)
domain <- get_domain(.df, domain)
if (!is.null(domain)) attr(.df, "_xportr.df_arg_") <- domain

## End of common section
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7 changes: 3 additions & 4 deletions R/label.R
Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,7 @@
#' label = c("Unique Subject Identifier", "Study Site Identifier", "Age", "Sex")
#' )
#'
#' adsl <- xportr_label(adsl, metadata)
#' adsl <- xportr_label(adsl, metadata, domain = "adsl")
xportr_label <- function(.df,
metadata = NULL,
domain = NULL,
Expand All @@ -73,10 +73,9 @@ xportr_label <- function(.df,
variable_name <- getOption("xportr.variable_name")
variable_label <- getOption("xportr.label")

## Common section to detect domain from argument or pipes
## Common section to detect domain from argument or attribute

df_arg <- tryCatch(as_name(enexpr(.df)), error = function(err) NULL)
domain <- get_domain(.df, df_arg, domain)
domain <- get_domain(.df, domain)
if (!is.null(domain)) attr(.df, "_xportr.df_arg_") <- domain

## End of common section
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7 changes: 3 additions & 4 deletions R/length.R
Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,7 @@
#' length = c(10, 8)
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#' )
#'
#' adsl <- xportr_length(adsl, metadata)
#' adsl <- xportr_length(adsl, metadata, domain = "adsl")
xportr_length <- function(.df,
metadata = NULL,
domain = NULL,
Expand All @@ -80,10 +80,9 @@ xportr_length <- function(.df,
variable_length <- getOption("xportr.length")
variable_name <- getOption("xportr.variable_name")

## Common section to detect domain from argument or pipes
## Common section to detect domain from argument or attribute

df_arg <- tryCatch(as_name(enexpr(.df)), error = function(err) NULL)
domain <- get_domain(.df, df_arg, domain)
domain <- get_domain(.df, domain)
if (!is.null(domain)) attr(.df, "_xportr.df_arg_") <- domain

## End of common section
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25 changes: 22 additions & 3 deletions R/metadata.R
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,8 @@
#' @return `.df` dataset with metadata and domain attributes set
#' @export
#'
#' @rdname metadata
#'
#' @examples
#'
#' metadata <- data.frame(
Expand All @@ -33,18 +35,35 @@
#' library(magrittr)
#'
#' adlb %>%
#' xportr_domain_name("adlb") %>%
#' xportr_metadata(metadata, "test") %>%
#' xportr_type() %>%
#' xportr_order()
#' }
xportr_metadata <- function(.df, metadata, domain = NULL) {
## Common section to detect domain from argument or pipes
## Common section to detect domain from argument or attribute

df_arg <- tryCatch(as_name(enexpr(.df)), error = function(err) NULL)
domain <- get_domain(.df, df_arg, domain)
domain <- get_domain(.df, domain)
if (!is.null(domain)) attr(.df, "_xportr.df_arg_") <- domain

## End of common section

structure(.df, `_xportr.df_metadata_` = metadata)
}


#' Update Metadata Domain Name
#'
#' Similar to `xportr_metadata`, but just added the domain and not the metadata.
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#'
#' @inheritParams xportr_length
#'
#' @return `.df` dataset with domain argument set
#' @export
#'
#' @rdname metadata
xportr_domain_name <- function(.df, domain) {
attr(.df, "_xportr.df_arg_") <- domain

.df
}
7 changes: 3 additions & 4 deletions R/order.R
Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@
#' order = 1:4
#' )
#'
#' adsl <- xportr_order(adsl, metadata)
#' adsl <- xportr_order(adsl, metadata, domain = "adsl")
xportr_order <- function(.df,
metadata = NULL,
domain = NULL,
Expand All @@ -76,10 +76,9 @@ xportr_order <- function(.df,
order_name <- getOption("xportr.order_name")
variable_name <- getOption("xportr.variable_name")

## Common section to detect domain from argument or pipes
## Common section to detect domain from argument or attribute

df_arg <- tryCatch(as_name(enexpr(.df)), error = function(err) NULL)
domain <- get_domain(.df, df_arg, domain)
domain <- get_domain(.df, domain)
if (!is.null(domain)) attr(.df, "_xportr.df_arg_") <- domain

## End of common section
Expand Down
1 change: 1 addition & 0 deletions R/support-test.R
Original file line number Diff line number Diff line change
Expand Up @@ -180,6 +180,7 @@ multiple_vars_in_spec_helper2 <- function(FUN) {
local_cli_theme()

adsl %>%
xportr_domain_name("adsl") %>%
FUN(metadata) %>%
testthat::expect_no_message(message = "There are multiple specs for the same variable name")
}
5 changes: 2 additions & 3 deletions R/type.R
Original file line number Diff line number Diff line change
Expand Up @@ -97,10 +97,9 @@ xportr_type <- function(.df,
numericTypes <- c(getOption("xportr.numeric_types"), "_numeric")
format_name <- getOption("xportr.format_name")

## Common section to detect domain from argument or pipes
## Common section to detect domain from argument or attribute

df_arg <- tryCatch(as_name(enexpr(.df)), error = function(err) NULL)
domain <- get_domain(.df, df_arg, domain)
domain <- get_domain(.df, domain)
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if (!is.null(domain)) attr(.df, "_xportr.df_arg_") <- domain

## End of common section
Expand Down
9 changes: 3 additions & 6 deletions R/utils-xportr.R
Original file line number Diff line number Diff line change
Expand Up @@ -305,21 +305,18 @@ xpt_validate <- function(data) {
return(err_cnd)
}

#' Get the domain from argument or from magrittr's pipe (`%>%`)
#' Get the domain from argument or from the existing domain attr
#'
#' @return A string representing the domain
#' @noRd
get_domain <- function(.df, df_arg, domain) {
get_domain <- function(.df, domain) {
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if (!is.null(domain) && !is.character(domain)) {
abort(c("`domain` must be a vector with type <character>.",
x = glue("Instead, it has type <{typeof(domain)}>.")
))
}

if (identical(df_arg, ".")) {
df_arg <- get_pipe_call()
}
result <- domain %||% attr(.df, "_xportr.df_arg_") %||% df_arg
result <- domain %||% attr(.df, "_xportr.df_arg_")
result
}

Expand Down
11 changes: 6 additions & 5 deletions README.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -127,11 +127,12 @@ Each `xportr_` function has been written in a way to take in a part of the speci

```{r, warning = FALSE, message=FALSE, eval=TRUE}
adsl %>%
xportr_type(var_spec, "ADSL", verbose = "warn") %>%
xportr_length(var_spec, "ADSL", verbose = "warn") %>%
xportr_label(var_spec, "ADSL", verbose = "warn") %>%
xportr_order(var_spec, "ADSL", verbose = "warn") %>%
xportr_format(var_spec, "ADSL") %>%
xportr_domain_name("ADSL") %>%
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xportr_type(var_spec, verbose = "warn") %>%
xportr_length(var_spec, verbose = "warn") %>%
xportr_label(var_spec, verbose = "warn") %>%
xportr_order(var_spec, verbose = "warn") %>%
xportr_format(var_spec) %>%
xportr_write("adsl.xpt", label = "Subject-Level Analysis Dataset")
```

Expand Down
12 changes: 6 additions & 6 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,6 @@

<!-- badges: start -->

[<img src="https://img.shields.io/badge/Slack-RValidationHub-blue?style=flat&logo=slack">](https://RValidationHub.slack.com)
[![R build
status](https://github.com/atorus-research/xportr/workflows/R-CMD-check/badge.svg)](https://github.com/atorus-research/xportr/actions?workflow=R-CMD-check)
[<img src="https://img.shields.io/codecov/c/gh/atorus-research/xportr">](https://app.codecov.io/gh/atorus-research/xportr)
Expand Down Expand Up @@ -135,11 +134,12 @@ We have suppressed the warning for the sake of brevity.

``` r
adsl %>%
xportr_type(var_spec, "ADSL", verbose = "warn") %>%
xportr_length(var_spec, "ADSL", verbose = "warn") %>%
xportr_label(var_spec, "ADSL", verbose = "warn") %>%
xportr_order(var_spec, "ADSL", verbose = "warn") %>%
xportr_format(var_spec, "ADSL") %>%
xportr_domain_name("ADSL") %>%
xportr_type(var_spec, verbose = "warn") %>%
xportr_length(var_spec, verbose = "warn") %>%
xportr_label(var_spec, verbose = "warn") %>%
xportr_order(var_spec, verbose = "warn") %>%
xportr_format(var_spec) %>%
xportr_write("adsl.xpt", label = "Subject-Level Analysis Dataset")
```

Expand Down
8 changes: 8 additions & 0 deletions man/xportr_metadata.Rd → man/metadata.Rd

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2 changes: 1 addition & 1 deletion man/xportr_df_label.Rd

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2 changes: 1 addition & 1 deletion man/xportr_format.Rd

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2 changes: 1 addition & 1 deletion man/xportr_label.Rd

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2 changes: 1 addition & 1 deletion man/xportr_length.Rd

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2 changes: 1 addition & 1 deletion man/xportr_order.Rd

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