too much..

man/all_but.Rd

@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data_plots.R
+\name{all_but}
+\alias{all_but}
+\title{Select all from vector but}
+\usage{
+all_but(data, ...)
+}
+\arguments{
+\item{data}{vector}
+
+\item{...}{exclude}
+}
+\value{
+vector
+}
+\description{
+Select all from vector but
+}
+\examples{
+all_but(1:10, c(2, 3), 11, 5)
+}

man/append_list.Rd

@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/helpers.R
+\name{append_list}
+\alias{append_list}
+\title{Append list with named index}
+\usage{
+append_list(data, list, index)
+}
+\arguments{
+\item{data}{data to add to list}
+
+\item{list}{list}
+
+\item{index}{index name}
+}
+\value{
+list
+}
+\description{
+Append list with named index
+}
+\examples{
+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")
+}

man/columnSelectInput.Rd

@@ -0,0 +1,45 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/columnSelectInput.R
+\name{columnSelectInput}
+\alias{columnSelectInput}
+\title{A selectizeInput customized for data frames with column labels}
+\usage{
+columnSelectInput(
+  inputId,
+  label,
+  data,
+  selected = "",
+  ...,
+  col_subset = NULL,
+  placeholder = "",
+  onInitialize,
+  none_label = "No variable selected"
+)
+}
+\arguments{
+\item{inputId}{passed to \code{\link[shiny]{selectizeInput}}}
+
+\item{label}{passed to \code{\link[shiny]{selectizeInput}}}
+
+\item{data}{\code{data.frame} object from which fields should be populated}
+
+\item{selected}{default selection}
+
+\item{...}{passed to \code{\link[shiny]{selectizeInput}}}
+
+\item{col_subset}{a \code{vector} containing the list of allowable columns to select}
+
+\item{placeholder}{passed to \code{\link[shiny]{selectizeInput}} options}
+
+\item{onInitialize}{passed to \code{\link[shiny]{selectizeInput}} options}
+
+\item{none_label}{label for "none" item}
+}
+\value{
+a \code{\link[shiny]{selectizeInput}} dropdown element
+}
+\description{
+Copied and modified from the IDEAFilter package
+Adds the option to select "none" which is handled later
+}
+\keyword{internal}

man/contrast_text.Rd

@@ -0,0 +1,52 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/contrast_text.R
+\name{contrast_text}
+\alias{contrast_text}
+\title{Contrast Text Color}
+\usage{
+contrast_text(
+  background,
+  light_text = "white",
+  dark_text = "black",
+  threshold = 0.5,
+  method = "perceived_2",
+  ...
+)
+}
+\arguments{
+\item{background}{A hex/named color value that represents the background.}
+
+\item{light_text}{A hex/named color value that represents the light text
+color.}
+
+\item{dark_text}{A hex/named color value that represents the dark text color.}
+
+\item{threshold}{A numeric value between 0 and 1 that is used to determine
+the luminance threshold of the background color for text color.}
+
+\item{method}{A character string that specifies the method for calculating
+the luminance. Three different methods are available:
+c("relative","perceived","perceived_2")}
+
+\item{...}{parameter overflow. Ignored.}
+}
+\value{
+A character string that contains the best contrast text color.
+}
+\description{
+Calculates the best contrast text color for a given
+background color.
+}
+\details{
+This function aids in deciding the font color to print on a given background.
+The function is based on the example provided by teppo:
+https://stackoverflow.com/a/66669838/21019325.
+The different methods provided are based on the methods outlined in the
+StackOverflow thread:
+https://stackoverflow.com/questions/596216/formula-to-determine-perceived-brightness-of-rgb-color
+}
+\examples{
+contrast_text(c("#F2F2F2", "blue"))
+
+contrast_text(c("#F2F2F2", "blue"), method="relative")
+}

man/data-correlations.Rd

@@ -1,19 +1,25 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/correlations-module.R
+% Please edit documentation in R/correlations-module.R, R/data_plots.R
 \name{data-correlations}
 \alias{data-correlations}
 \alias{data_correlations_ui}
 \alias{data_correlations_server}
+\alias{data_visuals_ui}
+\alias{data_visuals_server}
 \title{Data correlations evaluation module}
 \usage{
 data_correlations_ui(id, ...)
 
 data_correlations_server(id, data, include.class = NULL, cutoff = 0.7, ...)
+
+data_visuals_ui(id, tab_title = "Plots", ...)
+
+data_visuals_server(id, data, ...)
 }
 \arguments{
 \item{id}{Module id. (Use 'ns("id")')}
 
-\item{...}{arguments passed to toastui::datagrid}
+\item{...}{ignored}
 
 \item{data}{data}
 
@@ -24,8 +30,14 @@ data_correlations_server(id, data, include.class = NULL, cutoff = 0.7, ...)
 \value{
 Shiny ui module
 
+shiny server module
+
+Shiny ui module
+
 shiny server module
 }
 \description{
+Data correlations evaluation module
+
 Data correlations evaluation module
 }

man/data-plots.Rd

@@ -0,0 +1,70 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data_plots.R
+\name{data-plots}
+\alias{data-plots}
+\alias{plot_ridge}
+\alias{create_plot}
+\alias{plot_hbars}
+\alias{plot_violin}
+\alias{plot_scatter}
+\alias{plot_sankey}
+\title{Title}
+\usage{
+plot_ridge(data, x, y, z = NULL, ...)
+
+create_plot(data, type, x, y, z = NULL, ...)
+
+plot_hbars(data, x, y, z = NULL)
+
+plot_violin(data, x, y, z = NULL)
+
+plot_scatter(data, x, y, z = NULL)
+
+plot_sankey(data, x, y, z = NULL, color.group = "x", colors = NULL)
+}
+\arguments{
+\item{...}{ignored for now}
+
+\item{type}{plot type (derived from possible_plots() and matches custom function)}
+}
+\value{
+ggplot2 object
+
+ggplot2 object
+
+ggplot2 object
+
+ggplot2 object
+
+ggplot2 object
+
+ggplot2 object
+}
+\description{
+Title
+
+Wrapper to create plot based on provided type
+
+Nice horizontal stacked bars (Grotta bars)
+
+Beatiful violin plot
+
+Beautiful violin plot
+
+Beautiful sankey plot with option to split by a tertiary group
+}
+\examples{
+mtcars |>
+  default_parsing() |>
+  plot_ridge(x = "mpg", y = "cyl")
+mtcars |> plot_ridge(x = "mpg", y = "cyl", z = "gear")
+create_plot(mtcars, "plot_violin", "mpg", "cyl")
+mtcars |> plot_hbars(x = "carb", y = "cyl")
+mtcars |> plot_hbars(x = "carb", y = NULL)
+mtcars |> plot_violin(x = "mpg", y = "cyl", z = "gear")
+mtcars |> plot_scatter(x = "mpg", y = "wt")
+ds <- data.frame(g = sample(LETTERS[1:2], 100, TRUE), first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), last = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)))
+ds |> plot_sankey("first", "last")
+ds |> plot_sankey("first", "last", color.group = "y")
+ds |> plot_sankey("first", "last", z = "g", color.group = "y")
+}

man/get_label.Rd

@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data_plots.R
+\name{get_label}
+\alias{get_label}
+\title{Print label, and if missing print variable name}
+\usage{
+get_label(data, var = NULL)
+}
+\arguments{
+\item{data}{vector or data frame}
+}
+\value{
+character string
+}
+\description{
+Print label, and if missing print variable name
+}
+\examples{
+mtcars |> get_label(var = "mpg")
+mtcars |> get_label()
+mtcars$mpg |> get_label()
+gtsummary::trial |> get_label(var = "trt")
+1:10 |> get_label()
+}

man/get_plot_options.Rd

@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data_plots.R
+\name{get_plot_options}
+\alias{get_plot_options}
+\title{Get the function options based on the selected function description}
+\usage{
+get_plot_options(data)
+}
+\arguments{
+\item{data}{vector}
+}
+\value{
+list
+}
+\description{
+Get the function options based on the selected function description
+}
+\examples{
+ls <- mtcars |>
+  default_parsing() |>
+  dplyr::pull(mpg) |>
+  possible_plots() |>
+  (\(.x){
+    .x[[1]]
+  })() |>
+  get_plot_options()
+}

man/is_valid_redcap_url.Rd

@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/redcap_read_shiny_module.R
+\name{is_valid_redcap_url}
+\alias{is_valid_redcap_url}
+\title{Title}
+\usage{
+is_valid_redcap_url(url)
+}
+\arguments{
+\item{url}{}
+}
+\description{
+Title
+}
+\examples{
+url <- c(
+  "www.example.com",
+  "http://example.com",
+  "https://redcap.your.inst/api/"
+)
+is_valid_redcap_url(url)
+}

man/is_valid_token.Rd

@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/redcap_read_shiny_module.R
+\name{is_valid_token}
+\alias{is_valid_token}
+\title{Validate REDCap token}
+\usage{
+is_valid_token(token, pattern_env = NULL, nchar = 32)
+}
+\arguments{
+\item{token}{token}
+
+\item{pattern_env}{pattern}
+}
+\description{
+Validate REDCap token
+}
+\examples{
+token <- paste(sample(c(1:9, LETTERS[1:6]), 32, TRUE), collapse = "")
+is_valid_token(token)
+}

man/launch_freesearcheR.Rd

@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/shiny_freesearcheR.R
-\name{launch}
-\alias{launch}
+\name{launch_freesearcheR}
+\alias{launch_freesearcheR}
 \title{Easily launch the freesearcheR app}
 \usage{
-launch(...)
+launch_freesearcheR(...)
 }
 \arguments{
 \item{...}{passed on to \code{shiny::runApp()}}

man/line_break.Rd

@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data_plots.R
+\name{line_break}
+\alias{line_break}
+\title{Line breaking at given number of characters for nicely plotting labels}
+\usage{
+line_break(data, lineLength = 20)
+}
+\arguments{
+\item{lineLength}{}
+}
+\description{
+Line breaking at given number of characters for nicely plotting labels
+}

man/plot_sankey_single.Rd

@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data_plots.R
+\name{plot_sankey_single}
+\alias{plot_sankey_single}
+\title{Beautiful sankey plot}
+\usage{
+plot_sankey_single(data, x, y, color.group = "x", colors = NULL)
+}
+\arguments{
+\item{colors}{}
+}
+\value{
+ggplot2 object
+}
+\description{
+Beautiful sankey plot
+}
+\examples{
+ds <- data.frame(g = sample(LETTERS[1:2], 100, TRUE), first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), last = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)))
+ds |> plot_sankey_single("first", "last")
+ds |> plot_sankey_single("first", "last", color.group = "y")
+}

man/possible_plots.Rd

@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data_plots.R
+\name{possible_plots}
+\alias{possible_plots}
+\title{Get possible regression models}
+\usage{
+possible_plots(data)
+}
+\arguments{
+\item{data}{data}
+}
+\value{
+character vector
+}
+\description{
+Get possible regression models
+}
+\examples{
+mtcars |>
+  default_parsing() |>
+  dplyr::pull("cyl") |>
+  possible_plots()
+
+mtcars |>
+  default_parsing() |>
+  dplyr::select("mpg") |>
+  possible_plots()
+}

man/redcap_read_shiny_module.Rd

@@ -1,30 +1,21 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/redcap_read_shiny_module.R
-\docType{data}
 \name{m_redcap_readUI}
 \alias{m_redcap_readUI}
 \alias{m_redcap_readServer}
-\alias{tdm_redcap_read}
-\alias{redcap_app}
+\alias{redcap_demo_app}
 \title{Shiny module to browser and export REDCap data}
-\format{
-An object of class \code{teal_data_module} of length 2.
-}
 \usage{
 m_redcap_readUI(id, include_title = TRUE)
 
-m_redcap_readServer(id, output.format = c("df", "teal", "list"))
+m_redcap_readServer(id)
 
-tdm_redcap_read
-
-redcap_app()
+redcap_demo_app()
 }
 \arguments{
 \item{id}{Namespace id}
 
 \item{include_title}{logical to include title}
-
-\item{output.format}{data.frame ("df") or teal data object ("teal")}
 }
 \value{
 shiny ui element
@@ -34,13 +25,10 @@ shiny server module
 \description{
 Shiny module to browser and export REDCap data
 
-REDCap import teal data module
-
 Test app for the redcap_read_shiny_module
 }
 \examples{
 \dontrun{
-redcap_app()
+redcap_demo_app()
 }
 }
-\keyword{datasets}

man/sankey_ready.Rd

@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data_plots.R
+\name{sankey_ready}
+\alias{sankey_ready}
+\title{Readying data for sankey plot}
+\usage{
+sankey_ready(data, x, y, z = NULL, numbers = "count")
+}
+\arguments{
+\item{z}{}
+}
+\description{
+Readying data for sankey plot
+}
+\examples{
+ds <- data.frame(g = sample(LETTERS[1:2], 100, TRUE), first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), last = sample(c(letters[1:4], NA), 100, TRUE, prob = c(rep(.23, 4), .08)))
+ds |> sankey_ready("first", "last")
+ds |> sankey_ready("first", "last", numbers = "percentage")
+}

man/subset_types.Rd

@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data_plots.R
+\name{subset_types}
+\alias{subset_types}
+\title{Easily subset by data type function}
+\usage{
+subset_types(data, types, type.fun = outcome_type)
+}
+\arguments{
+\item{data}{data}
+
+\item{types}{desired types}
+
+\item{type.fun}{function to get type. Default is outcome_type}
+}
+\value{
+vector
+}
+\description{
+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("factor",class)
+}

man/supported_plots.Rd

@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data_plots.R
+\name{supported_plots}
+\alias{supported_plots}
+\title{Implemented functions}
+\usage{
+supported_plots()
+}
+\value{
+list
+}
+\description{
+Library of supported functions. The list name and "descr" element should be
+unique for each element on list.
+\itemize{
+\item descr: Plot description
+\item primary.type: Primary variable data type (continuous, dichotomous or ordinal)
+\item secondary.type: Secondary variable data type (continuous, dichotomous or ordinal)
+\item secondary.extra: "none" or NULL to have option to choose none.
+\item tertiary.type: Tertiary variable data type (continuous, dichotomous or ordinal)
+}
+}
+\examples{
+supported_plots() |> str()
+}

man/update-factor.Rd

@@ -0,0 +1,48 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/update-factor-ext.R
+\name{update-factor}
+\alias{update-factor}
+\alias{update_factor_ui}
+\alias{update_factor_server}
+\alias{modal_update_factor}
+\title{Module to Reorder the Levels of a Factor Variable}
+\usage{
+update_factor_ui(id)
+
+update_factor_server(id, data_r = reactive(NULL))
+
+modal_update_factor(
+  id,
+  title = i18n("Update levels of a factor"),
+  easyClose = TRUE,
+  size = "l",
+  footer = NULL
+)
+}
+\arguments{
+\item{id}{Module ID.}
+
+\item{data_r}{A \code{\link[shiny:reactive]{shiny::reactive()}} function returning a \code{data.frame}.}
+
+\item{title}{An optional title for the dialog.}
+
+\item{easyClose}{If \code{TRUE}, the modal dialog can be dismissed by
+clicking outside the dialog box, or be pressing the Escape key. If
+\code{FALSE} (the default), the modal dialog can't be dismissed in those
+ways; instead it must be dismissed by clicking on a \code{modalButton()}, or
+from a call to \code{\link[shiny:removeModal]{removeModal()}} on the server.}
+
+\item{size}{One of \code{"s"} for small, \code{"m"} (the default) for medium,
+\code{"l"} for large, or \code{"xl"} for extra large. Note that \code{"xl"} only
+works with Bootstrap 4 and above (to opt-in to Bootstrap 4+,
+pass \code{\link[bslib:bs_theme]{bslib::bs_theme()}} to the \code{theme} argument of a page container
+like \code{\link[shiny:fluidPage]{fluidPage()}}).}
+
+\item{footer}{UI for footer. Use \code{NULL} for no footer.}
+}
+\value{
+A \code{\link[shiny:reactive]{shiny::reactive()}} function returning the data.
+}
+\description{
+This module contain an interface to reorder the levels of a factor variable.
+}

man/vertical_stacked_bars.Rd

@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data_plots.R
+\name{vertical_stacked_bars}
+\alias{vertical_stacked_bars}
+\title{Vertical stacked bar plot wrapper}
+\usage{
+vertical_stacked_bars(
+  data,
+  score = "full_score",
+  group = "pase_0_q",
+  strata = NULL,
+  t.size = 10,
+  l.color = "black",
+  l.size = 0.5,
+  draw.lines = TRUE
+)
+}
+\arguments{
+\item{t.size}{}
+}
+\description{
+Vertical stacked bar plot wrapper
+}