From e9422a418b05f560a113896504215d6e04833791 Mon Sep 17 00:00:00 2001
From: Andreas Gammelgaard Damsbo <andreas@gdamsbo.dk>
Date: Mon, 24 Mar 2025 14:43:50 +0100
Subject: [PATCH] docs

---
 NAMESPACE                |  8 +++++++-
 R/plot_box.R             |  2 +-
 R/regression_plot.R      |  2 +-
 man/append_list.Rd       |  6 +++---
 man/clean_common_axis.Rd | 19 +++++++++++++++++++
 man/create_baseline.Rd   | 28 ++++++++++++++++++++++++++++
 man/create_log_tics.Rd   | 20 ++++++++++++++++++++
 man/data-plots.Rd        | 23 +++++++++++++++++++++--
 man/data_description.Rd  | 23 +++++++++++++++++++++++
 man/data_type.Rd         | 27 +++++++++++++++++++++++++++
 man/limit_log.Rd         |  8 ++++----
 man/missing_fraction.Rd  |  2 +-
 man/outcome_type.Rd      | 22 ----------------------
 man/regression_model.Rd  | 19 +++++++++++--------
 man/remove_empty_cols.Rd |  2 +-
 man/remove_na_attr.Rd    |  6 ++++--
 man/subset_types.Rd      |  4 ++--
 17 files changed, 173 insertions(+), 48 deletions(-)
 create mode 100644 man/clean_common_axis.Rd
 create mode 100644 man/create_baseline.Rd
 create mode 100644 man/create_log_tics.Rd
 create mode 100644 man/data_description.Rd
 create mode 100644 man/data_type.Rd
 delete mode 100644 man/outcome_type.Rd

diff --git a/NAMESPACE b/NAMESPACE
index aa34d84..9480d52 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -9,10 +9,13 @@ export(allign_axes)
 export(append_list)
 export(argsstring2list)
 export(baseline_table)
+export(clean_common_axis)
 export(clean_date)
 export(clean_sep)
 export(columnSelectInput)
 export(contrast_text)
+export(create_baseline)
+export(create_log_tics)
 export(create_overview_datagrid)
 export(create_plot)
 export(custom_theme)
@@ -20,8 +23,10 @@ export(cut_variable_server)
 export(cut_variable_ui)
 export(data_correlations_server)
 export(data_correlations_ui)
+export(data_description)
 export(data_summary_server)
 export(data_summary_ui)
+export(data_type)
 export(data_visuals_server)
 export(data_visuals_ui)
 export(default_format_arguments)
@@ -61,8 +66,9 @@ export(missing_fraction)
 export(modal_cut_variable)
 export(modal_update_factor)
 export(modify_qmd)
-export(outcome_type)
 export(overview_vars)
+export(plot_box)
+export(plot_box_single)
 export(plot_euler)
 export(plot_euler_single)
 export(plot_hbars)
diff --git a/R/plot_box.R b/R/plot_box.R
index 97f88f7..09ab6c8 100644
--- a/R/plot_box.R
+++ b/R/plot_box.R
@@ -36,7 +36,7 @@ plot_box <- function(data, x, y, z = NULL) {
 #'
 #' @name data-plots
 #'
-#' @returns
+#' @returns ggplot object
 #' @export
 #'
 #' @examples
diff --git a/R/regression_plot.R b/R/regression_plot.R
index 252e1ec..a21a4bf 100644
--- a/R/regression_plot.R
+++ b/R/regression_plot.R
@@ -123,7 +123,7 @@ limit_log <- function(data, fun, ...) {
 #'
 #' @param data numeric vector
 #'
-#' @returns
+#' @returns numeric vector
 #' @export
 #'
 #' @examples
diff --git a/man/append_list.Rd b/man/append_list.Rd
index 990f3a6..880daa0 100644
--- a/man/append_list.Rd
+++ b/man/append_list.Rd
@@ -20,8 +20,8 @@ list
 Append list with named index
 }
 \examples{
-ls_d <- list(test=c(1:20))
+ls_d <- list(test = c(1:20))
 ls_d <- list()
-data.frame(letters[1:20],1:20) |> append_list(ls_d,"letters")
-letters[1:20]|> append_list(ls_d,"letters")
+data.frame(letters[1:20], 1:20) |> append_list(ls_d, "letters")
+letters[1:20] |> append_list(ls_d, "letters")
 }
diff --git a/man/clean_common_axis.Rd b/man/clean_common_axis.Rd
new file mode 100644
index 0000000..175053c
--- /dev/null
+++ b/man/clean_common_axis.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data_plots.R
+\name{clean_common_axis}
+\alias{clean_common_axis}
+\title{Extract and clean axis ranges}
+\usage{
+clean_common_axis(p, axis)
+}
+\arguments{
+\item{p}{plot}
+
+\item{axis}{axis. x or y.}
+}
+\value{
+vector
+}
+\description{
+Extract and clean axis ranges
+}
diff --git a/man/create_baseline.Rd b/man/create_baseline.Rd
new file mode 100644
index 0000000..82e6fe1
--- /dev/null
+++ b/man/create_baseline.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/baseline_table.R
+\name{create_baseline}
+\alias{create_baseline}
+\title{Create a baseline table}
+\usage{
+create_baseline(data, ..., by.var, add.p = FALSE, add.overall = FALSE)
+}
+\arguments{
+\item{data}{data}
+
+\item{...}{passed as fun.arg to baseline_table()}
+
+\item{add.p}{add comparison/p-value}
+
+\item{add.overall}{add overall column}
+
+\item{strat.var}{grouping/strat variable}
+}
+\value{
+gtsummary table list object
+}
+\description{
+Create a baseline table
+}
+\examples{
+mtcars |> create_baseline(by.var = "gear", add.p="yes"=="yes")
+}
diff --git a/man/create_log_tics.Rd b/man/create_log_tics.Rd
new file mode 100644
index 0000000..9baf394
--- /dev/null
+++ b/man/create_log_tics.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/regression_plot.R
+\name{create_log_tics}
+\alias{create_log_tics}
+\title{Create summetric log ticks}
+\usage{
+create_log_tics(data)
+}
+\arguments{
+\item{data}{numeric vector}
+}
+\value{
+numeric vector
+}
+\description{
+Create summetric log ticks
+}
+\examples{
+c(sample(seq(.1, 1, .1), 3), sample(1:10, 3)) |> create_log_tics()
+}
diff --git a/man/data-plots.Rd b/man/data-plots.Rd
index 539381f..f580b0e 100644
--- a/man/data-plots.Rd
+++ b/man/data-plots.Rd
@@ -1,11 +1,13 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data_plots.R, R/plot_hbar.R, R/plot_ridge.R,
-%   R/plot_sankey.R, R/plot_scatter.R, R/plot_violin.R
+% Please edit documentation in R/data_plots.R, R/plot_box.R, R/plot_hbar.R,
+%   R/plot_ridge.R, R/plot_sankey.R, R/plot_scatter.R, R/plot_violin.R
 \name{data-plots}
 \alias{data-plots}
 \alias{data_visuals_ui}
 \alias{data_visuals_server}
 \alias{create_plot}
+\alias{plot_box}
+\alias{plot_box_single}
 \alias{plot_hbars}
 \alias{plot_ridge}
 \alias{sankey_ready}
@@ -20,6 +22,10 @@ data_visuals_server(id, data, ...)
 
 create_plot(data, type, x, y, z = NULL, ...)
 
+plot_box(data, x, y, z = NULL)
+
+plot_box_single(data, x, y = NULL, seed = 2103)
+
 plot_hbars(data, x, y, z = NULL)
 
 plot_ridge(data, x, y, z = NULL, ...)
@@ -56,6 +62,10 @@ ggplot2 object
 
 ggplot2 object
 
+ggplot object
+
+ggplot2 object
+
 ggplot2 object
 
 data.frame
@@ -71,6 +81,10 @@ Data correlations evaluation module
 
 Wrapper to create plot based on provided type
 
+Beautiful box plot(s)
+
+Create nice box-plots
+
 Nice horizontal stacked bars (Grotta bars)
 
 Plot nice ridge plot
@@ -85,6 +99,11 @@ Beatiful violin plot
 }
 \examples{
 create_plot(mtcars, "plot_violin", "mpg", "cyl")
+mtcars |> plot_box(x = "mpg", y = "cyl", z = "gear")
+mtcars |>
+  default_parsing() |>
+  plot_box(x = "mpg", y = "cyl", z = "gear")
+mtcars |> plot_box_single("mpg","cyl")
 mtcars |> plot_hbars(x = "carb", y = "cyl")
 mtcars |> plot_hbars(x = "carb", y = NULL)
 mtcars |>
diff --git a/man/data_description.Rd b/man/data_description.Rd
new file mode 100644
index 0000000..97a0b0d
--- /dev/null
+++ b/man/data_description.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/helpers.R
+\name{data_description}
+\alias{data_description}
+\title{Ultra short data dascription}
+\usage{
+data_description(data)
+}
+\arguments{
+\item{data}{}
+}
+\value{
+character vector
+}
+\description{
+Ultra short data dascription
+}
+\examples{
+data.frame(
+  sample(1:8, 20, TRUE),
+  sample(c(1:8, NA), 20, TRUE)
+) |> data_description()
+}
diff --git a/man/data_type.Rd b/man/data_type.Rd
new file mode 100644
index 0000000..af3716a
--- /dev/null
+++ b/man/data_type.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/regression_model.R
+\name{data_type}
+\alias{data_type}
+\title{Data type assessment}
+\usage{
+data_type(data)
+}
+\arguments{
+\item{data}{data}
+}
+\value{
+outcome type
+}
+\description{
+Data type assessment
+}
+\examples{
+mtcars |>
+  default_parsing() |>
+  lapply(data_type)
+c(1, 2) |> data_type()
+1 |> data_type()
+c(rep(NA, 10)) |> data_type()
+sample(1:100, 50) |> data_type()
+factor(letters[1:20]) |> data_type()
+}
diff --git a/man/limit_log.Rd b/man/limit_log.Rd
index 55bcf3c..9504060 100644
--- a/man/limit_log.Rd
+++ b/man/limit_log.Rd
@@ -20,8 +20,8 @@ numeric vector
 Easily round log scale limits for nice plots
 }
 \examples{
-limit_log(-.1,floor)
-limit_log(.1,ceiling)
-limit_log(-2.1,ceiling)
-limit_log(2.1,ceiling)
+limit_log(-.1, floor)
+limit_log(.1, ceiling)
+limit_log(-2.1, ceiling)
+limit_log(2.1, ceiling)
 }
diff --git a/man/missing_fraction.Rd b/man/missing_fraction.Rd
index 6182c2a..b3acab9 100644
--- a/man/missing_fraction.Rd
+++ b/man/missing_fraction.Rd
@@ -16,5 +16,5 @@ numeric vector
 Get missingsness fraction
 }
 \examples{
-c(NA,1:10,rep(NA,3)) |> missing_fraction()
+c(NA, 1:10, rep(NA, 3)) |> missing_fraction()
 }
diff --git a/man/outcome_type.Rd b/man/outcome_type.Rd
deleted file mode 100644
index 6a674da..0000000
--- a/man/outcome_type.Rd
+++ /dev/null
@@ -1,22 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/regression_model.R
-\name{outcome_type}
-\alias{outcome_type}
-\title{Outcome data type assessment}
-\usage{
-outcome_type(data)
-}
-\arguments{
-\item{data}{data}
-}
-\value{
-outcome type
-}
-\description{
-Outcome data type assessment
-}
-\examples{
-mtcars |>
-  default_parsing() |>
-  lapply(outcome_type)
-}
diff --git a/man/regression_model.Rd b/man/regression_model.Rd
index 049e24d..d86453b 100644
--- a/man/regression_model.Rd
+++ b/man/regression_model.Rd
@@ -111,7 +111,7 @@ m <- mtcars |>
     args.list = NULL,
     vars = c("mpg", "cyl")
   )
-  broom::tidy(m)
+broom::tidy(m)
 \dontrun{
 gtsummary::trial |>
   regression_model_uv(outcome.str = "age")
@@ -126,7 +126,7 @@ m <- gtsummary::trial |> regression_model_uv(
   fun = "stats::glm",
   args.list = list(family = stats::binomial(link = "logit"))
 )
-lapply(m,broom::tidy) |> dplyr::bind_rows()
+lapply(m, broom::tidy) |> dplyr::bind_rows()
 }
 \dontrun{
 gtsummary::trial |>
@@ -154,12 +154,15 @@ broom::tidy(ls$model)
 broom::tidy(m)
 }
 \dontrun{
-gtsummary::trial |> regression_model_uv(
-  outcome.str = "trt",
-  fun = "stats::glm",
-  args.list = list(family = stats::binomial(link = "logit"))
-) |> lapply(broom::tidy) |> dplyr::bind_rows()
+gtsummary::trial |>
+  regression_model_uv(
+    outcome.str = "trt",
+    fun = "stats::glm",
+    args.list = list(family = stats::binomial(link = "logit"))
+  ) |>
+  lapply(broom::tidy) |>
+  dplyr::bind_rows()
 ms <- regression_model_uv_list(data = default_parsing(mtcars), outcome.str = "mpg", fun.descr = "Linear regression model")
-lapply(ms$model,broom::tidy) |> dplyr::bind_rows()
+lapply(ms$model, broom::tidy) |> dplyr::bind_rows()
 }
 }
diff --git a/man/remove_empty_cols.Rd b/man/remove_empty_cols.Rd
index 690a7c9..48f9699 100644
--- a/man/remove_empty_cols.Rd
+++ b/man/remove_empty_cols.Rd
@@ -18,5 +18,5 @@ data frame
 Removes columns with completenes below cutoff
 }
 \examples{
-data.frame(a=1:10,b=NA, c=c(2,NA)) |> remove_empty_cols(cutoff=.5)
+data.frame(a = 1:10, b = NA, c = c(2, NA)) |> remove_empty_cols(cutoff = .5)
 }
diff --git a/man/remove_na_attr.Rd b/man/remove_na_attr.Rd
index e5e01f8..41bb4ee 100644
--- a/man/remove_na_attr.Rd
+++ b/man/remove_na_attr.Rd
@@ -16,6 +16,8 @@ data.frame
 Remove NA labels
 }
 \examples{
-ds <- mtcars |> lapply(\(.x) REDCapCAST::set_attr(.x,label=NA,attr = "label"))
-ds |> remove_na_attr() |> str()
+ds <- mtcars |> lapply(\(.x) REDCapCAST::set_attr(.x, label = NA, attr = "label"))
+ds |>
+  remove_na_attr() |>
+  str()
 }
diff --git a/man/subset_types.Rd b/man/subset_types.Rd
index bd01efe..7b3f366 100644
--- a/man/subset_types.Rd
+++ b/man/subset_types.Rd
@@ -4,7 +4,7 @@
 \alias{subset_types}
 \title{Easily subset by data type function}
 \usage{
-subset_types(data, types, type.fun = outcome_type)
+subset_types(data, types, type.fun = data_type)
 }
 \arguments{
 \item{data}{data}
@@ -21,6 +21,6 @@ Easily subset by data type function
 }
 \examples{
 default_parsing(mtcars) |> subset_types("ordinal")
-default_parsing(mtcars) |> subset_types(c("dichotomous", "ordinal"))
+default_parsing(mtcars) |> subset_types(c("dichotomous", "ordinal" ,"categorical"))
 #' default_parsing(mtcars) |> subset_types("factor",class)
 }