diff --git a/R/tableone.R b/R/tableone.R index 925dd6ae..d1f0885e 100644 --- a/R/tableone.R +++ b/R/tableone.R @@ -17,6 +17,23 @@ #' Pre-implemented functions are summarize_long and summarize_short #' @param ... Pass options to render_table #' +#' @section Example Output: +#' \if{html}{tableone(engine = "gt")} +#' +#' \if{html}{\figure{tableone_gt_ex.png}{options: width=65\%}} +#' +#' \if{html}{tableone(engine = "DT")} +#' +#' \if{html}{\figure{tableone_DT_ex.png}{options: width=65\%}} +#' +#' \if{html}{tableone(engine = "kable")} +#' +#' \if{html}{\figure{tableone_kable_html_ex.png}{options: width=65\%}} +#' +#' \if{html}{tableone(engine = "kable", output_format = "latex")} +#' +#' \if{html}{\figure{tableone_kable_latex_ex.png}{options: width=65\%}} +#' #' @examples #' #' # metadata for table @@ -25,8 +42,23 @@ #' t1_fn <- "My table one footnote" #' #' +#' ## table by treatment - without overall and render with GT +#' tbl_gt <- +#' adtte %>% +#' dplyr::filter(SAFFL == "Y") %>% +#' dplyr::select(AGE, AGEGR1, SEX, EVNTDESC, TRTA) %>% +#' visR::tableone( +#' strata = "TRTA", +#' overall = FALSE, +#' title = t1_title, +#' datasource = t1_ds, +#' footnote = t1_fn, +#' engine = "gt" +#' ) +#' #' ## table by treatment - without overall and render with DT -#' adtte %>% +#' tbl_DT <- +#' adtte %>% #' dplyr::filter(SAFFL == "Y") %>% #' dplyr::select(AGE, AGEGR1, SEX, EVNTDESC, TRTA) %>% #' visR::tableone( @@ -38,21 +70,9 @@ #' engine = "DT" #' ) #' -#' ## table by treatment - without overall and render with GT -#' adtte %>% -#' dplyr::filter(SAFFL == "Y") %>% -#' dplyr::select(AGE, AGEGR1, SEX, EVNTDESC, TRTA) %>% -#' visR::tableone( -#' strata = "TRTA", -#' overall = FALSE, -#' title = t1_title, -#' datasource = t1_ds, -#' footnote = t1_fn, -#' engine = "gt" -#' ) -#' #' ## table by treatment - without overall and render with kable -#' adtte %>% +#' tbl_kable_html <- +#' adtte %>% #' dplyr::filter(SAFFL == "Y") %>% #' dplyr::select(AGE, AGEGR1, SEX, EVNTDESC, TRTA) %>% #' visR::tableone( @@ -66,7 +86,8 @@ #' #' ## table by treatment - without overall and render with kable as #' ## a latex table format rather than html -#' adtte %>% +#' tbl_kable_latex <- +#' adtte %>% #' dplyr::filter(SAFFL == "Y") %>% #' dplyr::select(AGE, AGEGR1, SEX, EVNTDESC, TRTA) %>% #' visR::tableone( diff --git a/README.md b/README.md index 97d1167a..07402648 100644 --- a/README.md +++ b/README.md @@ -43,7 +43,7 @@ current focus on developing a stable API. | [![R-CMD-check](https://github.com/openpharma/visR/actions/workflows/check-standard.yaml/badge.svg?branch=main)](https://github.com/openpharma/visR/actions/workflows/check-standard.yaml) | `main` branch | | [![pkgdown](https://github.com/openpharma/visR/actions/workflows/makedocs.yml/badge.svg)](https://github.com/openpharma/visR/actions/workflows/makedocs.yml) | Documentation building to [Github pages](https://openpharma.github.io/visR/) | | [![CRAN status](https://www.r-pkg.org/badges/version/visR)](https://CRAN.R-project.org/package=visR) | Latest CRAN release | -| | `riskmetric` score | +| | `riskmetric` score | @@ -117,7 +117,8 @@ covr::package_coverage( code = "tools::testInstalledPackage(pkg = 'visR', types = c('tests'))", quiet = FALSE ) -#> visR Coverage: 99.88% +#> visR Coverage: 99.64% +#> R/estimate_cuminc.R: 85.71% #> R/visr.R: 99.12% #> R/add_annotation.R: 100.00% #> R/add_CI.R: 100.00% @@ -127,7 +128,6 @@ covr::package_coverage( #> R/add_risktable.R: 100.00% #> R/apply_attrition.R: 100.00% #> R/apply_theme.R: 100.00% -#> R/estimate_cuminc.R: 100.00% #> R/estimate_KM.R: 100.00% #> R/get_attrition.R: 100.00% #> R/get_COX_HR.R: 100.00% diff --git a/man/figures/tableone_DT_ex.png b/man/figures/tableone_DT_ex.png new file mode 100644 index 00000000..89eacee3 Binary files /dev/null and b/man/figures/tableone_DT_ex.png differ diff --git a/man/figures/tableone_gt_ex.png b/man/figures/tableone_gt_ex.png new file mode 100644 index 00000000..ac2f84f3 Binary files /dev/null and b/man/figures/tableone_gt_ex.png differ diff --git a/man/figures/tableone_kable_html_ex.png b/man/figures/tableone_kable_html_ex.png new file mode 100644 index 00000000..bba6d628 Binary files /dev/null and b/man/figures/tableone_kable_html_ex.png differ diff --git a/man/figures/tableone_kable_latex_ex.png b/man/figures/tableone_kable_latex_ex.png new file mode 100644 index 00000000..0c73b1cb Binary files /dev/null and b/man/figures/tableone_kable_latex_ex.png differ diff --git a/man/tableone.Rd b/man/tableone.Rd index cff6c21d..d509fbbb 100644 --- a/man/tableone.Rd +++ b/man/tableone.Rd @@ -44,6 +44,25 @@ A typical example of a summary table are "table one", the first table in an appl Calculate summary statistics and present them in a formatted table } +\section{Example Output}{ + +\if{html}{tableone(engine = "gt")} + +\if{html}{\figure{tableone_gt_ex.png}{options: width=65\%}} + +\if{html}{tableone(engine = "DT")} + +\if{html}{\figure{tableone_DT_ex.png}{options: width=65\%}} + +\if{html}{tableone(engine = "kable")} + +\if{html}{\figure{tableone_kable_html_ex.png}{options: width=65\%}} + +\if{html}{tableone(engine = "kable", output_format = "latex")} + +\if{html}{\figure{tableone_kable_latex_ex.png}{options: width=65\%}} +} + \examples{ # metadata for table @@ -52,8 +71,23 @@ t1_ds <- "ADaM Interim Dataset for Time-to-Event Analysis" t1_fn <- "My table one footnote" +## table by treatment - without overall and render with GT +tbl_gt <- + adtte \%>\% + dplyr::filter(SAFFL == "Y") \%>\% + dplyr::select(AGE, AGEGR1, SEX, EVNTDESC, TRTA) \%>\% + visR::tableone( + strata = "TRTA", + overall = FALSE, + title = t1_title, + datasource = t1_ds, + footnote = t1_fn, + engine = "gt" + ) + ## table by treatment - without overall and render with DT -adtte \%>\% +tbl_DT <- + adtte \%>\% dplyr::filter(SAFFL == "Y") \%>\% dplyr::select(AGE, AGEGR1, SEX, EVNTDESC, TRTA) \%>\% visR::tableone( @@ -65,21 +99,9 @@ adtte \%>\% engine = "DT" ) -## table by treatment - without overall and render with GT -adtte \%>\% - dplyr::filter(SAFFL == "Y") \%>\% - dplyr::select(AGE, AGEGR1, SEX, EVNTDESC, TRTA) \%>\% - visR::tableone( - strata = "TRTA", - overall = FALSE, - title = t1_title, - datasource = t1_ds, - footnote = t1_fn, - engine = "gt" - ) - ## table by treatment - without overall and render with kable -adtte \%>\% +tbl_kable_html <- + adtte \%>\% dplyr::filter(SAFFL == "Y") \%>\% dplyr::select(AGE, AGEGR1, SEX, EVNTDESC, TRTA) \%>\% visR::tableone( @@ -93,7 +115,8 @@ adtte \%>\% ## table by treatment - without overall and render with kable as ## a latex table format rather than html -adtte \%>\% +tbl_kable_latex <- + adtte \%>\% dplyr::filter(SAFFL == "Y") \%>\% dplyr::select(AGE, AGEGR1, SEX, EVNTDESC, TRTA) \%>\% visR::tableone(