updated docs

NAMESPACE

@@ -1,14 +1,19 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(cut,hms)
+S3method(plot,tbl_regression)
 export(add_class_icon)
 export(add_sparkline)
 export(argsstring2list)
 export(baseline_table)
+export(clean_date)
+export(clean_sep)
 export(create_overview_datagrid)
 export(custom_theme)
 export(cut_variable_server)
 export(cut_variable_ui)
+export(data_correlations_server)
+export(data_correlations_ui)
 export(data_summary_server)
 export(data_summary_ui)
 export(default_format_arguments)
@@ -16,24 +21,35 @@ export(default_parsing)
 export(factorize)
 export(file_export)
 export(format_writer)
+export(get_fun_options)
 export(getfun)
+export(gg_theme_export)
+export(gg_theme_shiny)
 export(index_embed)
 export(is_any_class)
 export(is_consecutive)
 export(is_datetime)
+export(launch)
 export(m_datafileUI)
 export(m_redcap_readServer)
 export(m_redcap_readUI)
+export(merge_long)
 export(modal_cut_variable)
 export(modify_qmd)
+export(outcome_type)
 export(overview_vars)
+export(possible_functions)
 export(read_input)
 export(regression_model)
+export(regression_model_list)
 export(regression_model_uv)
+export(regression_model_uv_list)
 export(regression_table)
+export(remove_empty_cols)
 export(remove_na_attr)
 export(shiny_freesearcheR)
 export(specify_qmd_format)
+export(supported_functions)
 export(tbl_merge)
 export(update_variables_server)
 export(update_variables_ui)

R/correlations-module.R

@@ -6,7 +6,7 @@
 #' @returns Shiny ui module
 #' @export
 data_correlations_ui <- function(id, ...) {
-  ns <- NS(id)
+  ns <- shiny::NS(id)
 
   shiny::tagList(
     shiny::textOutput(outputId = ns("suggest")),

R/regression_model.R

@@ -13,6 +13,7 @@
 #'
 #' @return object of standard class for fun
 #' @export
+#' @rdname regression_model
 #'
 #' @examples
 #' gtsummary::trial |>
@@ -149,6 +150,7 @@ regression_model <- function(data,
 #' @param ... ignored for now
 #'
 #' @importFrom stats as.formula
+#' @rdname regression_model
 #'
 #' @return object of standard class for fun
 #' @export
@@ -323,7 +325,7 @@ supported_functions <- function() {
 #'
 #' @param data data
 #'
-#' @returns
+#' @returns character vector
 #' @export
 #'
 #' @examples
@@ -412,8 +414,9 @@ get_fun_options <- function(data) {
 #' argsstring2list() or list of arguments. Default is NULL.
 #' @param ... ignored
 #'
-#' @returns
+#' @returns list
 #' @export
+#' @rdname regression_model
 #'
 #' @examples
 #' \dontrun{
@@ -528,19 +531,9 @@ list2str <- function(data) {
 }
 
 
-#' Title
-#'
-#' @param data
-#' @param outcome.str
-#' @param fun.descr
-#' @param fun
-#' @param formula.str
-#' @param args.list
-#' @param vars
-#' @param ...
-#'
 #' @returns list
 #' @export
+#' @rdname regression_model
 #'
 #' @examples
 #' \dontrun{

R/shiny_freesearcheR.R

@@ -23,3 +23,15 @@ shiny_freesearcheR <- function(...) {
   a <- shiny::runApp(appDir = paste0(appDir,"/app.R"), ...)
   return(invisible(a))
 }
+
+
+#' Easily launch the freesearcheR app
+#'
+#' @param ... passed on to `shiny::runApp()`
+#'
+#' @returns shiny app
+#' @export
+#'
+launch <- function(...){
+  shiny_freesearcheR(...)
+}

man/clean_date.Rd

@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/update-variables-ext.R
+\name{clean_date}
+\alias{clean_date}
+\title{Attempts at applying uniform date format}
+\usage{
+clean_date(data)
+}
+\arguments{
+\item{data}{character string vector of possible dates}
+}
+\value{
+character string
+}
+\description{
+Attempts at applying uniform date format
+}

man/clean_sep.Rd

@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/update-variables-ext.R
+\name{clean_sep}
+\alias{clean_sep}
+\title{gsub wrapper for piping with default values for separator substituting}
+\usage{
+clean_sep(data, old.sep = "[-.,/]", new.sep = "-")
+}
+\arguments{
+\item{data}{character vector}
+
+\item{old.sep}{old separator}
+
+\item{new.sep}{new separator}
+}
+\value{
+character vector
+}
+\description{
+gsub wrapper for piping with default values for separator substituting
+}

man/data-correlations.Rd

@@ -0,0 +1,31 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/correlations-module.R
+\name{data-correlations}
+\alias{data-correlations}
+\alias{data_correlations_ui}
+\alias{data_correlations_server}
+\title{Data correlations evaluation module}
+\usage{
+data_correlations_ui(id, ...)
+
+data_correlations_server(id, data, include.class = NULL, cutoff = 0.7, ...)
+}
+\arguments{
+\item{id}{Module id. (Use 'ns("id")')}
+
+\item{...}{arguments passed to toastui::datagrid}
+
+\item{data}{data}
+
+\item{color.main}{main color}
+
+\item{color.sec}{secondary color}
+}
+\value{
+Shiny ui module
+
+shiny server module
+}
+\description{
+Data correlations evaluation module
+}

man/data-summary.Rd

@@ -8,16 +8,18 @@
 \usage{
 data_summary_ui(id)
 
-data_summary_server(id, data, color.main, color.sec)
+data_summary_server(id, data, color.main, color.sec, ...)
 }
 \arguments{
-\item{id}{id}
+\item{id}{Module id. (Use 'ns("id")')}
 
 \item{data}{data}
 
 \item{color.main}{main color}
 
 \item{color.sec}{secondary color}
+
+\item{...}{arguments passed to toastui::datagrid}
 }
 \value{
 Shiny ui module

man/get_fun_options.Rd

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

man/gg_theme_export.Rd

@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/theme.R
+\name{gg_theme_export}
+\alias{gg_theme_export}
+\title{GGplot default theme for plotting export objects}
+\usage{
+gg_theme_export()
+}
+\arguments{
+\item{data}{ggplot object}
+}
+\value{
+ggplot object
+}
+\description{
+GGplot default theme for plotting export objects
+}

man/gg_theme_shiny.Rd

@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/theme.R
+\name{gg_theme_shiny}
+\alias{gg_theme_shiny}
+\title{GGplot default theme for plotting in Shiny}
+\usage{
+gg_theme_shiny()
+}
+\arguments{
+\item{data}{ggplot object}
+}
+\value{
+ggplot object
+}
+\description{
+GGplot default theme for plotting in Shiny
+}

man/launch.Rd

@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/shiny_freesearcheR.R
+\name{launch}
+\alias{launch}
+\title{Easily launch the freesearcheR app}
+\usage{
+launch(...)
+}
+\arguments{
+\item{...}{passed on to \code{shiny::runApp()}}
+}
+\value{
+shiny app
+}
+\description{
+Easily launch the freesearcheR app
+}

man/merge_long.Rd

@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/regression_plot.R
+\name{merge_long}
+\alias{merge_long}
+\title{Wrapper to pivot gtsummary table data to long for plotting}
+\usage{
+merge_long(list, model.names)
+}
+\arguments{
+\item{list}{a custom regression models list}
+
+\item{model.names}{names of models to include}
+}
+\value{
+list
+}
+\description{
+Wrapper to pivot gtsummary table data to long for plotting
+}

man/outcome_type.Rd

@@ -0,0 +1,22 @@
+% 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)
+}

man/plot.tbl_regression.Rd

@@ -0,0 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/regression_plot.R
+\name{plot.tbl_regression}
+\alias{plot.tbl_regression}
+\title{Regression coef plot from gtsummary. Slightly modified to pass on arguments}
+\usage{
+\method{plot}{tbl_regression}(x, ...)
+}
+\arguments{
+\item{x}{(\code{tbl_regression}, \code{tbl_uvregression})\cr
+A 'tbl_regression' or 'tbl_uvregression' object}
+
+\item{...}{arguments passed to \code{ggstats::ggcoef_plot(...)}}
+}
+\value{
+ggplot object
+}
+\description{
+Regression coef plot from gtsummary. Slightly modified to pass on arguments
+}
+\examples{
+\dontrun{
+mod <- lm(mpg ~ ., mtcars)
+p <- mod |>
+  gtsummary::tbl_regression() |>
+  plot(colour = "variable")
+}
+
+}

man/possible_functions.Rd

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

man/regression_model.Rd

@@ -2,41 +2,85 @@
 % Please edit documentation in R/regression_model.R
 \name{regression_model}
 \alias{regression_model}
+\alias{regression_model_uv}
+\alias{regression_model_list}
+\alias{regression_model_uv_list}
 \title{Create a regression model programatically}
 \usage{
 regression_model(
   data,
   outcome.str,
-  auto.mode = TRUE,
+  auto.mode = FALSE,
   formula.str = NULL,
   args.list = NULL,
   fun = NULL,
   vars = NULL,
   ...
 )
+
+regression_model_uv(
+  data,
+  outcome.str,
+  args.list = NULL,
+  fun = NULL,
+  vars = NULL,
+  ...
+)
+
+regression_model_list(
+  data,
+  outcome.str,
+  fun.descr,
+  fun = NULL,
+  formula.str = NULL,
+  args.list = NULL,
+  vars = NULL,
+  ...
+)
+
+regression_model_uv_list(
+  data,
+  outcome.str,
+  fun.descr,
+  fun = NULL,
+  formula.str = NULL,
+  args.list = NULL,
+  vars = NULL,
+  ...
+)
 }
 \arguments{
-\item{data}{data set}
+\item{data}{data}
 
-\item{outcome.str}{Name of outcome variable. Character vector.}
+\item{outcome.str}{name of outcome variable}
 
 \item{auto.mode}{Make assumptions on function dependent on outcome data format. Overwrites other arguments.}
 
-\item{formula.str}{Formula as string. Passed through 'glue::glue'. If given, 'outcome.str' and 'vars' are ignored. Optional.}
+\item{formula.str}{custom formula glue string. Default is NULL.}
 
-\item{args.list}{List of arguments passed to 'fun' with 'do.call'.}
+\item{args.list}{custom character string to be converted using
+argsstring2list() or list of arguments. Default is NULL.}
 
-\item{fun}{Name of function as character vector or function to use for model creation.}
+\item{fun}{name of custom function. Default is NULL.}
 
 \item{vars}{character vector of variables to include}
 
-\item{...}{ignored for now}
+\item{...}{ignored}
+
+\item{fun.descr}{Description of chosen function matching description in
+"supported_functions()"}
 }
 \value{
 object of standard class for fun
+
+object of standard class for fun
+
+list
+
+list
 }
 \description{
-Create a regression model programatically
+Output is a concatenated list of model information and model
 }
 \examples{
 gtsummary::trial |>
@@ -49,10 +93,73 @@ gtsummary::trial |>
     formula.str = "{outcome.str}~.",
     args.list = NULL
   )
-gtsummary::trial |> regression_model(
+gtsummary::trial |>
+  default_parsing() |>
+  regression_model(
+    outcome.str = "trt",
+    auto.mode = FALSE,
+    fun = "stats::glm",
+    args.list = list(family = binomial(link = "logit"))
+  )
+m <- mtcars |>
+  default_parsing() |>
+  regression_model(
+    outcome.str = "mpg",
+    auto.mode = FALSE,
+    fun = "stats::lm",
+    formula.str = "{outcome.str}~{paste(vars,collapse='+')}",
+    args.list = NULL,
+    vars = c("mpg", "cyl")
+  )
+  broom::tidy(m)
+\dontrun{
+gtsummary::trial |>
+  regression_model_uv(outcome.str = "age")
+gtsummary::trial |>
+  regression_model_uv(
+    outcome.str = "age",
+    fun = "stats::lm",
+    args.list = NULL
+  )
+m <- gtsummary::trial |> regression_model_uv(
   outcome.str = "trt",
-  auto.mode = FALSE,
   fun = "stats::glm",
-  args.list = list(family = binomial(link = "logit"))
+  args.list = list(family = stats::binomial(link = "logit"))
 )
+lapply(m,broom::tidy) |> dplyr::bind_rows()
+}
+\dontrun{
+gtsummary::trial |>
+  regression_model(
+    outcome.str = "age",
+    fun = "stats::lm",
+    formula.str = "{outcome.str}~.",
+    args.list = NULL
+  )
+ls <- regression_model_list(data = default_parsing(mtcars), outcome.str = "cyl", fun.descr = "Ordinal logistic regression model")
+summary(ls$model)
+
+ls <- regression_model_list(data = default_parsing(gtsummary::trial), outcome.str = "trt", fun.descr = "Logistic regression model")
+tbl <- gtsummary::tbl_regression(ls$model, exponentiate = TRUE)
+m <- gtsummary::trial |>
+  default_parsing() |>
+  regression_model(
+    outcome.str = "trt",
+    fun = "stats::glm",
+    formula.str = "{outcome.str}~.",
+    args.list = list(family = stats::binomial(link = "logit"))
+  )
+tbl2 <- gtsummary::tbl_regression(m, exponentiate = TRUE)
+broom::tidy(ls$model)
+broom::tidy(m)
+}
+\dontrun{
+gtsummary::trial |> regression_model_uv(
+  outcome.str = "trt",
+  fun = "stats::glm",
+  args.list = list(family = stats::binomial(link = "logit"))
+) |> lapply(broom::tidy) |> dplyr::bind_rows()
+ms <- regression_model_uv_list(data = default_parsing(mtcars), outcome.str = "mpg", fun.descr = "Linear regression model")
+lapply(ms$model,broom::tidy) |> dplyr::bind_rows()
+}
 }

man/regression_model_uv.Rd

@@ -1,51 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/regression_model.R
-\name{regression_model_uv}
-\alias{regression_model_uv}
-\title{Create a regression model programatically}
-\usage{
-regression_model_uv(
-  data,
-  outcome.str,
-  args.list = NULL,
-  fun = NULL,
-  vars = NULL,
-  ...
-)
-}
-\arguments{
-\item{data}{data set}
-
-\item{outcome.str}{Name of outcome variable. Character vector.}
-
-\item{args.list}{List of arguments passed to 'fun' with 'do.call'.}
-
-\item{fun}{Name of function as character vector or function to use for model creation.}
-
-\item{vars}{character vector of variables to include}
-
-\item{...}{ignored for now}
-}
-\value{
-object of standard class for fun
-}
-\description{
-Create a regression model programatically
-}
-\examples{
-\dontrun{
-gtsummary::trial |>
-  regression_model_uv(outcome.str = "age")
-gtsummary::trial |>
-  regression_model_uv(
-    outcome.str = "age",
-    fun = "stats::lm",
-    args.list = NULL
-  )
-gtsummary::trial |> regression_model_uv(
-  outcome.str = "trt",
-  fun = "stats::glm",
-  args.list = list(family = stats::binomial(link = "logit"))
-)
-}
-}

man/regression_table.Rd

@@ -23,7 +23,7 @@ Create table of regression model
 }
 \examples{
 \dontrun{
-gtsummary::trial |>
+tbl <- gtsummary::trial |>
   regression_model(
     outcome.str = "stage",
     fun = "MASS::polr"
@@ -36,7 +36,7 @@ gtsummary::trial |>
     formula.str = "{outcome.str}~.",
     args.list = NULL
   ) |>
-  regression_table()
+  regression_table() |> plot()
 gtsummary::trial |>
   regression_model(
     outcome.str = "trt",

man/remove_empty_cols.Rd

@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/helpers.R
+\name{remove_empty_cols}
+\alias{remove_empty_cols}
+\title{Removes columns with completenes below cutoff}
+\usage{
+remove_empty_cols(data, cutoff = 0.7)
+}
+\arguments{
+\item{data}{data frame}
+
+\item{cutoff}{numeric}
+}
+\value{
+data frame
+}
+\description{
+Removes columns with completenes below cutoff
+}
+\examples{
+data.frame(a=1:10,b=NA, c=c(2,NA)) |> remove_empty_cols(cutoff=.5)
+}

man/supported_functions.Rd

@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/regression_model.R
+\name{supported_functions}
+\alias{supported_functions}
+\title{Implemented functions}
+\usage{
+supported_functions()
+}
+\value{
+list
+}
+\description{
+Library of supported functions. The list name and "descr" element should be
+unique for each element on list.
+}
+\examples{
+supported_functions()
+}