diff --git a/R/table-nih-enrollment.R b/R/table-nih-enrollment.R index 3d48032..2fdb2aa 100644 --- a/R/table-nih-enrollment.R +++ b/R/table-nih-enrollment.R @@ -21,6 +21,7 @@ #' @author Will Beasley, Peter Higgins, Andrew Peters, Sreeharsha Mandem #' #' @examples +#' library(magrittr) #' ds_1 <- tibble::tribble( #' ~subject_id, ~gender , ~race , ~ethnicity , #' 1L, "Male" , "Black or African American", "Not Hispanic or Latino" , @@ -36,7 +37,6 @@ #' table_nih_enrollment(ds_1) #' table_nih_enrollment_pretty(ds_1) #' -#' \dontrun{ #' table_nih_enrollment(ds_1) %>% #' tidyr::spread(key=gender, value=n) #' @@ -46,7 +46,6 @@ #' ) %>% #' dplyr::select(-gender, -ethnicity) %>% #' tidyr::spread(key=gender_ethnicity, value=n) -#' } #' #' ds_2 <- tibble::tribble( #' ~subject_id, ~gender , ~race , ~ethnicity , @@ -70,7 +69,6 @@ #' table_nih_enrollment_pretty(ds_2, d_lu_ethnicity=ds_lu_ethnicity) #' #' ## Read a 500-patient fake dataset -#' library(magrittr) #' path <- system.file("misc/example-data-1.csv", package="codified") #' ds_3 <- readr::read_csv(path) %>% #' dplyr::mutate( @@ -109,15 +107,13 @@ #' d_lu_ethnicity = ds_lu_ethnicity #' ) #' -#' #' table_nih_enrollment_pretty( #' d = ds_3, #' d_lu_gender = ds_lu_gender, #' d_lu_race = ds_lu_race, #' d_lu_ethnicity = ds_lu_ethnicity #' ) -#' -#' + #' @export table_nih_enrollment <- function( d, d_lu_gender=NULL, d_lu_race=NULL, d_lu_ethnicity=NULL ) { @@ -151,12 +147,7 @@ table_nih_enrollment <- function( d, d_lu_gender=NULL, d_lu_race=NULL, d_lu_ethn gender = levels_gender, race = levels_race, ethnicity = levels_ethnicity - ) #%>% - # dplyr::transmute( - # gender_ethnicity = paste0(.data$gender, " by ", .data$ethnicity) - # ) %>% - # dplyr::pull(gender_ethnicity) %>% - # dput() + ) if( !is.null(d_lu_gender) ) { d <- d %>% @@ -186,7 +177,7 @@ table_nih_enrollment <- function( d, d_lu_gender=NULL, d_lu_race=NULL, d_lu_ethn gender = factor(.data$gender , levels=levels_gender ), race = factor(.data$race , levels=levels_race ), ethnicity = factor(.data$ethnicity, levels=levels_ethnicity ), - n = dplyr::coalesce(.data$n, 0L) + n = dplyr::coalesce(.data$n, 0L) ) %>% dplyr::select(.data$gender, .data$race, .data$ethnicity, .data$n) %>% dplyr::arrange(.data$gender, .data$race, .data$ethnicity) @@ -212,31 +203,16 @@ table_nih_enrollment_pretty <- function(d, d_lu_gender=NULL, d_lu_race=NULL, d_l table_nih_enrollment(d, d_lu_gender, d_lu_race, d_lu_ethnicity) %>% dplyr::mutate( - # n = scales::comma(n), - # n = n + 1000, # This line is just to test the commas gender_ethnicity = paste0(.data$gender, " by ", .data$ethnicity) ) %>% dplyr::select(-.data$gender, -.data$ethnicity) %>% tidyr::spread(key=.data$gender_ethnicity, value=.data$n) %>% dplyr::select(!!column_order) %>% - # dplyr::select( - # `Racial\nCategories` = `race`, - # `Female` = `Female by Not Hispanic or Latino`, - # `Male` = `Male by Not Hispanic or Latino`, - # `Unknown/ Not Reported` = `Unknown/Not Reported by Not Hispanic or Latino`, - # `Female` = `Female by Hispanic or Latino`, - # `Male` = `Male by Hispanic or Latino`, - # `Unknown/ Not Reported` = `Unknown/Not Reported by Hispanic or Latino`, - # `Female` = `Female by Unknown/Not Reported Ethnicity`, - # `Male` = `Male by Unknown/Not Reported Ethnicity`, - # `Unknown/ Not Reported` = `Unknown/Not Reported by Unknown/Not Reported Ethnicity`, - # ) %>% knitr::kable( - format = "html", - # align = "lrrrrrrrrr", + format = "html", format.args = list(big.mark=","), escape = FALSE, - col.names = c( + col.names = c( "Racial\nCategories", "Female", "Male", @@ -262,4 +238,3 @@ table_nih_enrollment_pretty <- function(d, d_lu_gender=NULL, d_lu_race=NULL, d_l )) %>% kableExtra::add_header_above(c(" " = 1L, "Ethnic Categories" = 9L)) } - diff --git a/inst/doc/nih-enrollment-html.R b/inst/doc/nih-enrollment-html.R index 8016f62..6a0cae0 100644 --- a/inst/doc/nih-enrollment-html.R +++ b/inst/doc/nih-enrollment-html.R @@ -32,21 +32,21 @@ ds %>% knitr::kable(caption = "Observed Dataset (first ten rows)") ds_lu_gender <- tibble::tribble( - ~input, ~displayed , - "0" , "Female", - "1" , "Male", + ~input, ~displayed , + "0" , "Female" , + "1" , "Male" , "U" , "Unknown/Not Reported" ) knitr::kable(ds_lu_gender, caption = "Gender Mapping") ds_lu_race <- tibble::tribble( - ~input , ~displayed , - "1" , "American Indian/Alaska Native", - "2" , "Asian", - "3" , "Native Hawaiian or Other Pacific Islander", - "4" , "Black or African American", - "5" , "White", - "M" , "More than One Race", + ~input , ~displayed , + "1" , "American Indian/Alaska Native" , + "2" , "Asian" , + "3" , "Native Hawaiian or Other Pacific Islander" , + "4" , "Black or African American" , + "5" , "White" , + "M" , "More than One Race" , "6" , "Unknown or Not Reported" ) knitr::kable(ds_lu_race, caption = "Race Mapping") diff --git a/inst/doc/nih-enrollment-html.Rmd b/inst/doc/nih-enrollment-html.Rmd index b875294..7470fc9 100644 --- a/inst/doc/nih-enrollment-html.Rmd +++ b/inst/doc/nih-enrollment-html.Rmd @@ -65,21 +65,21 @@ ds %>% knitr::kable(caption = "Observed Dataset (first ten rows)") ds_lu_gender <- tibble::tribble( - ~input, ~displayed , - "0" , "Female", - "1" , "Male", + ~input, ~displayed , + "0" , "Female" , + "1" , "Male" , "U" , "Unknown/Not Reported" ) knitr::kable(ds_lu_gender, caption = "Gender Mapping") ds_lu_race <- tibble::tribble( - ~input , ~displayed , - "1" , "American Indian/Alaska Native", - "2" , "Asian", - "3" , "Native Hawaiian or Other Pacific Islander", - "4" , "Black or African American", - "5" , "White", - "M" , "More than One Race", + ~input , ~displayed , + "1" , "American Indian/Alaska Native" , + "2" , "Asian" , + "3" , "Native Hawaiian or Other Pacific Islander" , + "4" , "Black or African American" , + "5" , "White" , + "M" , "More than One Race" , "6" , "Unknown or Not Reported" ) knitr::kable(ds_lu_race, caption = "Race Mapping") @@ -122,15 +122,12 @@ codified::table_nih_enrollment_pretty( REDCap Data Source ===================================================== - A hosted (fake) clinical trial dataset demonstrates how to extract demographic data from [REDCap](https://projectredcap.org/) and then present the demographic data in the NIH Inclusion Enrollment Report format. ## Establish Datasets - First, install the `REDCapR` package if necessary, and then [load it into memory](http://r-pkgs.had.co.nz/package.html#package). - ```{r install-redcapr} if( !requireNamespace("REDCapR", quietly=T) ) devtools::install_github("OuhscBbmc/REDCapR") diff --git a/inst/doc/nih-enrollment-html.html b/inst/doc/nih-enrollment-html.html index 9ca3abc..ea71978 100644 --- a/inst/doc/nih-enrollment-html.html +++ b/inst/doc/nih-enrollment-html.html @@ -1530,177 +1530,363 @@

2.1 Establish Datasets

head(10) %>% knitr::kable(caption = "Observed Dataset (first ten rows)") - + - - - - - - - + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Observed Dataset (first ten rows) +Observed Dataset (first ten rows) +
record_idname_lastdobethnicityracegender
+record_id + +name_last + +dob + +ethnicity + +race + +gender +
1Cornel1991-05-13140
2Wojdyla1931-10-14140
3Stunkard1964-09-15131
4Cimochowski1969-05-03141
5Woodland1969-11-22140
6Pistoia1943-08-26141
7Ahlquist1944-01-22140
8Ashlin1931-04-14141
9Djokovic1962-07-07111
10Mosses1978-06-20130
+1 + +Cornel + +1991-05-13 + +1 + +4 + +0 +
+2 + +Wojdyla + +1931-10-14 + +1 + +4 + +0 +
+3 + +Stunkard + +1964-09-15 + +1 + +3 + +1 +
+4 + +Cimochowski + +1969-05-03 + +1 + +4 + +1 +
+5 + +Woodland + +1969-11-22 + +1 + +4 + +0 +
+6 + +Pistoia + +1943-08-26 + +1 + +4 + +1 +
+7 + +Ahlquist + +1944-01-22 + +1 + +4 + +0 +
+8 + +Ashlin + +1931-04-14 + +1 + +4 + +1 +
+9 + +Djokovic + +1962-07-07 + +1 + +1 + +1 +
+10 + +Mosses + +1978-06-20 + +1 + +3 + +0 + 
ds_lu_gender <- tibble::tribble(
-  ~input,   ~displayed                      ,
-  "0"   ,  "Female",
-  "1"   ,  "Male",
+  ~input,   ~displayed            ,
+  "0"   ,  "Female"               , 
+  "1"   ,  "Male"                 ,
   "U"   ,  "Unknown/Not Reported"
 )
 knitr::kable(ds_lu_gender, caption = "Gender Mapping")
- + - - - + + + - - - + + + - - - + + + - - - + + +
Gender Mapping +Gender Mapping +
inputdisplayed
+input + +displayed +
0Female
+0 + +Female +
1Male
+1 + +Male +
UUnknown/Not Reported
+U + +Unknown/Not Reported + 
ds_lu_race <- tibble::tribble(
-  ~input ,   ~displayed                      ,
-  "1"    , "American Indian/Alaska Native",
-  "2"    , "Asian",
-  "3"    , "Native Hawaiian or Other Pacific Islander",
-  "4"    , "Black or African American",
-  "5"    , "White",
-  "M"    , "More than One Race",
+  ~input , ~displayed                                   ,
+  "1"    , "American Indian/Alaska Native"              ,
+  "2"    , "Asian"                                      ,
+  "3"    , "Native Hawaiian or Other Pacific Islander"  ,
+  "4"    , "Black or African American"                  ,
+  "5"    , "White"                                      ,
+  "M"    , "More than One Race"                         ,
   "6"    , "Unknown or Not Reported"
 )
 knitr::kable(ds_lu_race, caption = "Race Mapping")
- + - - - + + + - - - + + + - - - + + + - - - + + + - - - + + + - - - + + + - - - + + + - - - + + +
Race Mapping +Race Mapping +
inputdisplayed
+input + +displayed +
1American Indian/Alaska Native
+1 + +American Indian/Alaska Native +
2Asian
+2 + +Asian +
3Native Hawaiian or Other Pacific Islander
+3 + +Native Hawaiian or Other Pacific Islander +
4Black or African American
+4 + +Black or African American +
5White
+5 + +White +
MMore than One Race
+M + +More than One Race +
6Unknown or Not Reported
+6 + +Unknown or Not Reported +
@@ -1712,25 +1898,43 @@

2.1 Establish Datasets

) knitr::kable(ds_lu_ethnicity, caption = "Ethnicity Mapping") - + - - - + + + - - - + + + - - - + + + - - - + + +
Ethnicity Mapping +Ethnicity Mapping +
inputdisplayed
+input + +displayed +
2Not Hispanic or Latino
+2 + +Not Hispanic or Latino +
1Hispanic or Latino
+1 + +Hispanic or Latino +
0Unknown/Not Reported Ethnicity
+0 + +Unknown/Not Reported Ethnicity +
@@ -1746,393 +1950,907 @@

2.2 Apply Map to Observed Dataset knitr::kable(ds_summary_long, caption = "Counts of Each Subgroup") - + - - - - - + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Counts of Each Subgroup +Counts of Each Subgroup +
genderraceethnicityn
+gender + +race + +ethnicity + +n +
FemaleAmerican Indian/Alaska NativeNot Hispanic or Latino1
FemaleAmerican Indian/Alaska NativeHispanic or Latino8
FemaleAmerican Indian/Alaska NativeUnknown/Not Reported Ethnicity0
FemaleAsianNot Hispanic or Latino0
FemaleAsianHispanic or Latino0
FemaleAsianUnknown/Not Reported Ethnicity0
FemaleNative Hawaiian or Other Pacific IslanderNot Hispanic or Latino1
FemaleNative Hawaiian or Other Pacific IslanderHispanic or Latino28
FemaleNative Hawaiian or Other Pacific IslanderUnknown/Not Reported Ethnicity3
FemaleBlack or African AmericanNot Hispanic or Latino1
FemaleBlack or African AmericanHispanic or Latino172
FemaleBlack or African AmericanUnknown/Not Reported Ethnicity14
FemaleWhiteNot Hispanic or Latino1
FemaleWhiteHispanic or Latino22
FemaleWhiteUnknown/Not Reported Ethnicity2
FemaleMore than One RaceNot Hispanic or Latino0
FemaleMore than One RaceHispanic or Latino0
FemaleMore than One RaceUnknown/Not Reported Ethnicity0
FemaleUnknown or Not ReportedNot Hispanic or Latino0
FemaleUnknown or Not ReportedHispanic or Latino7
FemaleUnknown or Not ReportedUnknown/Not Reported Ethnicity0
MaleAmerican Indian/Alaska NativeNot Hispanic or Latino0
MaleAmerican Indian/Alaska NativeHispanic or Latino10
MaleAmerican Indian/Alaska NativeUnknown/Not Reported Ethnicity0
MaleAsianNot Hispanic or Latino0
MaleAsianHispanic or Latino0
MaleAsianUnknown/Not Reported Ethnicity0
MaleNative Hawaiian or Other Pacific IslanderNot Hispanic or Latino1
MaleNative Hawaiian or Other Pacific IslanderHispanic or Latino22
MaleNative Hawaiian or Other Pacific IslanderUnknown/Not Reported Ethnicity1
MaleBlack or African AmericanNot Hispanic or Latino5
MaleBlack or African AmericanHispanic or Latino154
MaleBlack or African AmericanUnknown/Not Reported Ethnicity6
MaleWhiteNot Hispanic or Latino0
MaleWhiteHispanic or Latino33
MaleWhiteUnknown/Not Reported Ethnicity1
MaleMore than One RaceNot Hispanic or Latino0
MaleMore than One RaceHispanic or Latino0
MaleMore than One RaceUnknown/Not Reported Ethnicity0
MaleUnknown or Not ReportedNot Hispanic or Latino0
MaleUnknown or Not ReportedHispanic or Latino7
MaleUnknown or Not ReportedUnknown/Not Reported Ethnicity0
Unknown/Not ReportedAmerican Indian/Alaska NativeNot Hispanic or Latino0
Unknown/Not ReportedAmerican Indian/Alaska NativeHispanic or Latino0
Unknown/Not ReportedAmerican Indian/Alaska NativeUnknown/Not Reported Ethnicity0
Unknown/Not ReportedAsianNot Hispanic or Latino0
Unknown/Not ReportedAsianHispanic or Latino0
Unknown/Not ReportedAsianUnknown/Not Reported Ethnicity0
Unknown/Not ReportedNative Hawaiian or Other Pacific IslanderNot Hispanic or Latino0
Unknown/Not ReportedNative Hawaiian or Other Pacific IslanderHispanic or Latino0
Unknown/Not ReportedNative Hawaiian or Other Pacific IslanderUnknown/Not Reported Ethnicity0
Unknown/Not ReportedBlack or African AmericanNot Hispanic or Latino0
Unknown/Not ReportedBlack or African AmericanHispanic or Latino0
Unknown/Not ReportedBlack or African AmericanUnknown/Not Reported Ethnicity0
Unknown/Not ReportedWhiteNot Hispanic or Latino0
Unknown/Not ReportedWhiteHispanic or Latino0
Unknown/Not ReportedWhiteUnknown/Not Reported Ethnicity0
Unknown/Not ReportedMore than One RaceNot Hispanic or Latino0
Unknown/Not ReportedMore than One RaceHispanic or Latino0
Unknown/Not ReportedMore than One RaceUnknown/Not Reported Ethnicity0
Unknown/Not ReportedUnknown or Not ReportedNot Hispanic or Latino0
Unknown/Not ReportedUnknown or Not ReportedHispanic or Latino0
Unknown/Not ReportedUnknown or Not ReportedUnknown/Not Reported Ethnicity0
+Female + +American Indian/Alaska Native + +Not Hispanic or Latino + +1 +
+Female + +American Indian/Alaska Native + +Hispanic or Latino + +8 +
+Female + +American Indian/Alaska Native + +Unknown/Not Reported Ethnicity + +0 +
+Female + +Asian + +Not Hispanic or Latino + +0 +
+Female + +Asian + +Hispanic or Latino + +0 +
+Female + +Asian + +Unknown/Not Reported Ethnicity + +0 +
+Female + +Native Hawaiian or Other Pacific Islander + +Not Hispanic or Latino + +1 +
+Female + +Native Hawaiian or Other Pacific Islander + +Hispanic or Latino + +28 +
+Female + +Native Hawaiian or Other Pacific Islander + +Unknown/Not Reported Ethnicity + +3 +
+Female + +Black or African American + +Not Hispanic or Latino + +1 +
+Female + +Black or African American + +Hispanic or Latino + +172 +
+Female + +Black or African American + +Unknown/Not Reported Ethnicity + +14 +
+Female + +White + +Not Hispanic or Latino + +1 +
+Female + +White + +Hispanic or Latino + +22 +
+Female + +White + +Unknown/Not Reported Ethnicity + +2 +
+Female + +More than One Race + +Not Hispanic or Latino + +0 +
+Female + +More than One Race + +Hispanic or Latino + +0 +
+Female + +More than One Race + +Unknown/Not Reported Ethnicity + +0 +
+Female + +Unknown or Not Reported + +Not Hispanic or Latino + +0 +
+Female + +Unknown or Not Reported + +Hispanic or Latino + +7 +
+Female + +Unknown or Not Reported + +Unknown/Not Reported Ethnicity + +0 +
+Male + +American Indian/Alaska Native + +Not Hispanic or Latino + +0 +
+Male + +American Indian/Alaska Native + +Hispanic or Latino + +10 +
+Male + +American Indian/Alaska Native + +Unknown/Not Reported Ethnicity + +0 +
+Male + +Asian + +Not Hispanic or Latino + +0 +
+Male + +Asian + +Hispanic or Latino + +0 +
+Male + +Asian + +Unknown/Not Reported Ethnicity + +0 +
+Male + +Native Hawaiian or Other Pacific Islander + +Not Hispanic or Latino + +1 +
+Male + +Native Hawaiian or Other Pacific Islander + +Hispanic or Latino + +22 +
+Male + +Native Hawaiian or Other Pacific Islander + +Unknown/Not Reported Ethnicity + +1 +
+Male + +Black or African American + +Not Hispanic or Latino + +5 +
+Male + +Black or African American + +Hispanic or Latino + +154 +
+Male + +Black or African American + +Unknown/Not Reported Ethnicity + +6 +
+Male + +White + +Not Hispanic or Latino + +0 +
+Male + +White + +Hispanic or Latino + +33 +
+Male + +White + +Unknown/Not Reported Ethnicity + +1 +
+Male + +More than One Race + +Not Hispanic or Latino + +0 +
+Male + +More than One Race + +Hispanic or Latino + +0 +
+Male + +More than One Race + +Unknown/Not Reported Ethnicity + +0 +
+Male + +Unknown or Not Reported + +Not Hispanic or Latino + +0 +
+Male + +Unknown or Not Reported + +Hispanic or Latino + +7 +
+Male + +Unknown or Not Reported + +Unknown/Not Reported Ethnicity + +0 +
+Unknown/Not Reported + +American Indian/Alaska Native + +Not Hispanic or Latino + +0 +
+Unknown/Not Reported + +American Indian/Alaska Native + +Hispanic or Latino + +0 +
+Unknown/Not Reported + +American Indian/Alaska Native + +Unknown/Not Reported Ethnicity + +0 +
+Unknown/Not Reported + +Asian + +Not Hispanic or Latino + +0 +
+Unknown/Not Reported + +Asian + +Hispanic or Latino + +0 +
+Unknown/Not Reported + +Asian + +Unknown/Not Reported Ethnicity + +0 +
+Unknown/Not Reported + +Native Hawaiian or Other Pacific Islander + +Not Hispanic or Latino + +0 +
+Unknown/Not Reported + +Native Hawaiian or Other Pacific Islander + +Hispanic or Latino + +0 +
+Unknown/Not Reported + +Native Hawaiian or Other Pacific Islander + +Unknown/Not Reported Ethnicity + +0 +
+Unknown/Not Reported + +Black or African American + +Not Hispanic or Latino + +0 +
+Unknown/Not Reported + +Black or African American + +Hispanic or Latino + +0 +
+Unknown/Not Reported + +Black or African American + +Unknown/Not Reported Ethnicity + +0 +
+Unknown/Not Reported + +White + +Not Hispanic or Latino + +0 +
+Unknown/Not Reported + +White + +Hispanic or Latino + +0 +
+Unknown/Not Reported + +White + +Unknown/Not Reported Ethnicity + +0 +
+Unknown/Not Reported + +More than One Race + +Not Hispanic or Latino + +0 +
+Unknown/Not Reported + +More than One Race + +Hispanic or Latino + +0 +
+Unknown/Not Reported + +More than One Race + +Unknown/Not Reported Ethnicity + +0 +
+Unknown/Not Reported + +Unknown or Not Reported + +Not Hispanic or Latino + +0 +
+Unknown/Not Reported + +Unknown or Not Reported + +Hispanic or Latino + +0 +
+Unknown/Not Reported + +Unknown or Not Reported + +Unknown/Not Reported Ethnicity + +0 +
@@ -2453,7 +3171,7 @@

3.1 Establish Datasets

token = "F304DEC3793FECC3B6DEEFF66302CAD3", # User-speciifc token/password. guess_type = FALSE # Keep all variables as strings/characters. )$data -
## 500 records and 13 columns were read from REDCap in 3.8 seconds.  The http status code was 200.
+
## 500 records and 13 columns were read from REDCap in 0.7 seconds.  The http status code was 200.

3.2 Conform to NIH Cosmetics

diff --git a/man/table_nih_enrollment.Rd b/man/table_nih_enrollment.Rd index 17b2af6..035d03c 100644 --- a/man/table_nih_enrollment.Rd +++ b/man/table_nih_enrollment.Rd @@ -27,6 +27,7 @@ Produce an NIH enrollment table, leveraging metadata to adapt to the observed \l https://grants.nih.gov/grants/how-to-apply-application-guide/forms-d/general/g.500-phs-inclusion-enrollment-report.htm } \examples{ +library(magrittr) ds_1 <- tibble::tribble( ~subject_id, ~gender , ~race , ~ethnicity , 1L, "Male" , "Black or African American", "Not Hispanic or Latino" , @@ -42,7 +43,6 @@ ds_1 <- tibble::tribble( table_nih_enrollment(ds_1) table_nih_enrollment_pretty(ds_1) -\dontrun{ table_nih_enrollment(ds_1) \%>\% tidyr::spread(key=gender, value=n) @@ -52,7 +52,6 @@ table_nih_enrollment(ds_1) \%>\% ) \%>\% dplyr::select(-gender, -ethnicity) \%>\% tidyr::spread(key=gender_ethnicity, value=n) -} ds_2 <- tibble::tribble( ~subject_id, ~gender , ~race , ~ethnicity , @@ -76,7 +75,6 @@ table_nih_enrollment(ds_2, d_lu_ethnicity=ds_lu_ethnicity) table_nih_enrollment_pretty(ds_2, d_lu_ethnicity=ds_lu_ethnicity) ## Read a 500-patient fake dataset -library(magrittr) path <- system.file("misc/example-data-1.csv", package="codified") ds_3 <- readr::read_csv(path) \%>\% dplyr::mutate( @@ -115,15 +113,12 @@ table_nih_enrollment( d_lu_ethnicity = ds_lu_ethnicity ) - table_nih_enrollment_pretty( d = ds_3, d_lu_gender = ds_lu_gender, d_lu_race = ds_lu_race, d_lu_ethnicity = ds_lu_ethnicity ) - - } \author{ Will Beasley, Peter Higgins, Andrew Peters, Sreeharsha Mandem diff --git a/vignettes/nih-enrollment-html.Rmd b/vignettes/nih-enrollment-html.Rmd index b875294..7470fc9 100644 --- a/vignettes/nih-enrollment-html.Rmd +++ b/vignettes/nih-enrollment-html.Rmd @@ -65,21 +65,21 @@ ds %>% knitr::kable(caption = "Observed Dataset (first ten rows)") ds_lu_gender <- tibble::tribble( - ~input, ~displayed , - "0" , "Female", - "1" , "Male", + ~input, ~displayed , + "0" , "Female" , + "1" , "Male" , "U" , "Unknown/Not Reported" ) knitr::kable(ds_lu_gender, caption = "Gender Mapping") ds_lu_race <- tibble::tribble( - ~input , ~displayed , - "1" , "American Indian/Alaska Native", - "2" , "Asian", - "3" , "Native Hawaiian or Other Pacific Islander", - "4" , "Black or African American", - "5" , "White", - "M" , "More than One Race", + ~input , ~displayed , + "1" , "American Indian/Alaska Native" , + "2" , "Asian" , + "3" , "Native Hawaiian or Other Pacific Islander" , + "4" , "Black or African American" , + "5" , "White" , + "M" , "More than One Race" , "6" , "Unknown or Not Reported" ) knitr::kable(ds_lu_race, caption = "Race Mapping") @@ -122,15 +122,12 @@ codified::table_nih_enrollment_pretty( REDCap Data Source ===================================================== - A hosted (fake) clinical trial dataset demonstrates how to extract demographic data from [REDCap](https://projectredcap.org/) and then present the demographic data in the NIH Inclusion Enrollment Report format. ## Establish Datasets - First, install the `REDCapR` package if necessary, and then [load it into memory](http://r-pkgs.had.co.nz/package.html#package). - ```{r install-redcapr} if( !requireNamespace("REDCapR", quietly=T) ) devtools::install_github("OuhscBbmc/REDCapR")