Initial commit

man/baseline_table.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/baseline_table.R
+\name{baseline_table}
+\alias{baseline_table}
+\title{Print a flexible baseline characteristics table}
+\usage{
+baseline_table(
+  data,
+  fun.args = NULL,
+  fun = gtsummary::tbl_summary,
+  vars = NULL
+)
+}
+\arguments{
+\item{data}{data set}
+
+\item{fun.args}{list of arguments passed to}
+
+\item{fun}{function to}
+
+\item{vars}{character vector of variables to include}
+}
+\value{
+object of standard class for fun
+}
+\description{
+Print a flexible baseline characteristics table
+}
+\examples{
+mtcars |> baseline_table()
+mtcars |> baseline_table(fun.args = list(by = "gear"))
+}

man/file_extension.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/helpers.R
+\name{file_extension}
+\alias{file_extension}
+\title{Helper to import files correctly}
+\usage{
+file_extension(filenames)
+}
+\arguments{
+\item{filenames}{file names}
+}
+\value{
+character vector
+}
+\description{
+Helper to import files correctly
+}
+\examples{
+file_extension(list.files(here::here(""))[[2]])[[1]]
+file_extension(c("file.cd..ks", "file"))
+}

man/getfun.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/helpers.R
+\name{getfun}
+\alias{getfun}
+\title{Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()'}
+\usage{
+getfun(x)
+}
+\arguments{
+\item{x}{function or function name}
+}
+\value{
+function or character vector
+}
+\description{
+This function follows the idea from this comment: https://stackoverflow.com/questions/38983179/do-call-a-function-in-r-without-loading-the-package
+}
+\examples{
+getfun("stats::lm")
+}

man/read_input.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/helpers.R
+\name{read_input}
+\alias{read_input}
+\title{Flexible file import based on extension}
+\usage{
+read_input(file, consider.na = c("NA", "\\"\\"", ""))
+}
+\arguments{
+\item{file}{file name}
+
+\item{consider.na}{character vector of strings to consider as NAs}
+}
+\value{
+tibble
+}
+\description{
+Flexible file import based on extension
+}
+\examples{
+read_input("https://raw.githubusercontent.com/agdamsbo/cognitive.index.lookup/main/data/sample.csv")
+}

man/regression_model.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/regression_model.R
+\name{regression_model}
+\alias{regression_model}
+\title{Print a flexible baseline characteristics table}
+\usage{
+regression_model(
+  data,
+  outcome.str = "gear",
+  outcome.factor = TRUE,
+  formula.str = NULL,
+  args.list = list(Hess = TRUE, method = "logistic"),
+  fun = "MASS::polr",
+  vars = NULL
+)
+}
+\arguments{
+\item{data}{data set}
+
+\item{outcome.str}{Name of outcome variable. Character vector.}
+
+\item{outcome.factor}{Factorize outcome variable. Logical.}
+
+\item{formula.str}{Formula as string. Passed through 'glue::glue'. If given, 'outcome.str' and 'vars' are ignored. Optional.}
+
+\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}
+}
+\value{
+object of standard class for fun
+}
+\description{
+Print a flexible baseline characteristics table
+}
+\examples{
+gtsummary::trial |>
+  regression_model(outcome.str = "stage", fun = "MASS::polr")
+gtsummary::trial |>
+  regression_model(
+    outcome.str = "age",
+    outcome.factor = FALSE,
+    fun = "stats::lm",
+    formula.str = "{outcome.str}~.",
+    args.list = NULL
+  )
+gtsummary::trial |> regression_model(
+  outcome.str = "trt",
+  fun = "stats::glm",
+  args.list = list(family = binomial(link = "logit"))
+)
+}

man/regression_table.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/regression_table.R
+\name{regression_table}
+\alias{regression_table}
+\title{Create table of regression model}
+\usage{
+regression_table(data, args.list = NULL, fun = "gtsummary::tbl_regression")
+}
+\arguments{
+\item{data}{regression model}
+
+\item{args.list}{list of arguments passed to 'fun'.}
+
+\item{fun}{function to use for table creation. Default is "gtsummary::tbl_regression".}
+}
+\value{
+object of standard class for fun
+}
+\description{
+Create table of regression model
+}
+\examples{
+gtsummary::trial |>
+  regression_model(
+    outcome.str = "stage",
+    fun = "MASS::polr"
+  ) |>
+  regression_table(args.list = list(exponentiate = TRUE))
+gtsummary::trial |>
+  regression_model(
+    outcome.str = "age",
+    outcome.factor = FALSE,
+    fun = "stats::lm",
+    formula.str = "{outcome.str}~.",
+    args.list = NULL
+  ) |>
+  regression_table()
+gtsummary::trial |>
+  regression_model(
+    outcome.str = "trt",
+    fun = "stats::glm",
+    args.list = list(family = binomial(link = "logit"))
+  ) |>
+  regression_table(args.list = list(exponentiate = TRUE))
+}

man/write_quarto.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/helpers.R
+\name{write_quarto}
+\alias{write_quarto}
+\title{Wrapper to save data in RDS, load into specified qmd and render}
+\usage{
+write_quarto(
+  data,
+  fileformat,
+  qmd.file = here::here("analyses.qmd"),
+  file = NULL,
+  ...
+)
+}
+\arguments{
+\item{data}{list to pass to qmd}
+
+\item{fileformat}{output format. Ignored if file!=NULL}
+
+\item{qmd.file}{qmd file to render. Default is 'here::here("analyses.qmd")'}
+
+\item{file}{exact filename (Optional)}
+
+\item{...}{Ignored for now}
+}
+\value{
+none
+}
+\description{
+Wrapper to save data in RDS, load into specified qmd and render
+}