updated data import

man/columnSelectInput.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/columnSelectInput.R
+% Please edit documentation in R/custom_SelectInput.R
 \name{columnSelectInput}
 \alias{columnSelectInput}
 \title{A selectizeInput customized for data frames with column labels}
@@ -42,4 +42,3 @@ a \code{\link[shiny]{selectizeInput}} dropdown element
 Copied and modified from the IDEAFilter package
 Adds the option to select "none" which is handled later
 }
-\keyword{internal}

man/data-plots.Rd

@@ -7,6 +7,7 @@
 \alias{plot_hbars}
 \alias{plot_violin}
 \alias{plot_scatter}
+\alias{sankey_ready}
 \alias{plot_sankey}
 \title{Title}
 \usage{
@@ -20,9 +21,19 @@ plot_violin(data, x, y, z = NULL)
 
 plot_scatter(data, x, y, z = NULL)
 
+sankey_ready(data, x, y, z = NULL, numbers = "count")
+
 plot_sankey(data, x, y, z = NULL, color.group = "x", colors = NULL)
 }
 \arguments{
+\item{data}{data.frame}
+
+\item{x}{primary variable}
+
+\item{y}{secondary variable}
+
+\item{z}{tertiary variable}
+
 \item{...}{ignored for now}
 
 \item{type}{plot type (derived from possible_plots() and matches custom function)}
@@ -38,6 +49,8 @@ ggplot2 object
 
 ggplot2 object
 
+data.frame
+
 ggplot2 object
 }
 \description{
@@ -51,6 +64,8 @@ Beatiful violin plot
 
 Beautiful violin plot
 
+Readying data for sankey plot
+
 Beautiful sankey plot with option to split by a tertiary group
 }
 \examples{
@@ -63,6 +78,9 @@ 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 = 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")
 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")

man/drop_empty_event.Rd

@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/redcap_read_shiny_module.R
+\name{drop_empty_event}
+\alias{drop_empty_event}
+\title{Drop empty events from REDCap export}
+\usage{
+drop_empty_event(data, event = "redcap_event_name")
+}
+\arguments{
+\item{data}{data}
+
+\item{event}{"redcap_event_name", "redcap_repeat_instrument" or
+"redcap_repeat_instance"}
+}
+\value{
+data.frame
+}
+\description{
+Drop empty events from REDCap export
+}

man/get_label.Rd

@@ -8,6 +8,8 @@ get_label(data, var = NULL)
 }
 \arguments{
 \item{data}{vector or data frame}
+
+\item{var}{variable name. Optional.}
 }
 \value{
 character string

man/grepl_fix.Rd

@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/wide2long.R
+\name{grepl_fix}
+\alias{grepl_fix}
+\title{Matches pattern to vector based on match type}
+\usage{
+grepl_fix(data, pattern, type = c("prefix", "infix", "suffix"))
+}
+\arguments{
+\item{data}{vector}
+
+\item{pattern}{pattern(s) to match. Character vector of length 1 or more.}
+
+\item{type}{type of match. can be one of "prefix","infix" or "suffix".}
+}
+\value{
+logical vector
+}
+\description{
+Matches pattern to vector based on match type
+}
+\examples{
+c("id", "age", "weight_0", "weight_1") |> grepl_fix(pattern = c("_0", "_1"), type = "suffix")
+}

man/import-file.Rd

@@ -0,0 +1,52 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/import-file-ext.R
+\name{import-file}
+\alias{import-file}
+\alias{import_file_ui}
+\alias{import_file_server}
+\title{Import data from a file}
+\usage{
+import_file_ui(
+  id,
+  title = TRUE,
+  preview_data = TRUE,
+  file_extensions = c(".csv", ".txt", ".xls", ".xlsx", ".rds", ".fst", ".sas7bdat",
+    ".sav"),
+  layout_params = c("dropdown", "inline")
+)
+
+import_file_server(
+  id,
+  btn_show_data = TRUE,
+  show_data_in = c("popup", "modal"),
+  trigger_return = c("button", "change"),
+  return_class = c("data.frame", "data.table", "tbl_df", "raw"),
+  reset = reactive(NULL),
+  read_fns = list()
+)
+}
+\arguments{
+\item{preview_data}{Show or not a preview of the data under the file input.}
+
+\item{file_extensions}{File extensions accepted by \code{\link[shiny:fileInput]{shiny::fileInput()}}, can also be MIME type.}
+
+\item{layout_params}{How to display import parameters : in a dropdown button or inline below file input.}
+
+\item{read_fns}{Named list with custom function(s) to read data:
+\itemize{
+\item the name must be the extension of the files to which the function will be applied
+\item the value must be a function that can have 5 arguments (you can ignore some of them, but you have to use the same names),
+passed by user through the interface:
+\itemize{
+\item \code{file}: path to the file
+\item \code{sheet}: for Excel files, sheet to read
+\item \code{skip}: number of row to skip
+\item \code{dec}: decimal separator
+\item \code{encoding}: file encoding
+\item \code{na.strings}: character(s) to interpret as missing values.
+}
+}}
+}
+\description{
+Let user upload a file and import data
+}

man/import_delim.Rd

@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/import-file-ext.R
+\name{import_delim}
+\alias{import_delim}
+\title{Wrapper of data.table::fread to import delim files with few presets}
+\usage{
+import_delim(file, skip, encoding, na.strings)
+}
+\arguments{
+\item{file}{file}
+
+\item{encoding}{encoding}
+
+\item{na.strings}{na.strings}
+}
+\value{
+data.frame
+}
+\description{
+Wrapper of data.table::fread to import delim files with few presets
+}

man/is_valid_redcap_url.Rd

@@ -2,21 +2,26 @@
 % Please edit documentation in R/redcap_read_shiny_module.R
 \name{is_valid_redcap_url}
 \alias{is_valid_redcap_url}
-\title{Title}
+\title{Test if url is valid format for REDCap API}
 \usage{
 is_valid_redcap_url(url)
 }
 \arguments{
-\item{url}{}
+\item{url}{url}
+}
+\value{
+logical
 }
 \description{
-Title
+Test if url is valid format for REDCap API
 }
 \examples{
 url <- c(
   "www.example.com",
-  "http://example.com",
-  "https://redcap.your.inst/api/"
+  "redcap.your.inst/api/",
+  "https://redcap.your.inst/api/",
+  "https://your.inst/redcap/api/",
+  "https://www.your.inst/redcap/api/"
 )
 is_valid_redcap_url(url)
 }

man/is_valid_token.Rd

@@ -11,6 +11,9 @@ is_valid_token(token, pattern_env = NULL, nchar = 32)
 
 \item{pattern_env}{pattern}
 }
+\value{
+logical
+}
 \description{
 Validate REDCap token
 }

man/line_break.Rd

@@ -4,11 +4,23 @@
 \alias{line_break}
 \title{Line breaking at given number of characters for nicely plotting labels}
 \usage{
-line_break(data, lineLength = 20)
+line_break(data, lineLength = 20, fixed = FALSE)
 }
 \arguments{
-\item{lineLength}{}
+\item{data}{string}
+
+\item{lineLength}{maximum line length}
+
+\item{fixed}{flag to force split at exactly the value given in lineLength.
+Default is FALSE, only splitting at spaces.}
+}
+\value{
+character string
 }
 \description{
 Line breaking at given number of characters for nicely plotting labels
 }
+\examples{
+"Lorem ipsum... you know the routine" |> line_break()
+paste(sample(letters[1:10], 100, TRUE), collapse = "") |> line_break(fixed=TRUE)
+}

man/plot_sankey_single.Rd

@@ -4,10 +4,15 @@
 \alias{plot_sankey_single}
 \title{Beautiful sankey plot}
 \usage{
-plot_sankey_single(data, x, y, color.group = "x", colors = NULL)
+plot_sankey_single(data, x, y, color.group = c("x", "y"), colors = NULL, ...)
 }
 \arguments{
-\item{colors}{}
+\item{color.group}{set group to colour by. "x" or "y".}
+
+\item{colors}{optinally specify colors. Give NA color, color for each level
+in primary group and color for each level in secondary group.}
+
+\item{...}{passed to sankey_ready()}
 }
 \value{
 ggplot2 object

man/repeated_instruments.Rd

@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/redcap_read_shiny_module.R
+\name{repeated_instruments}
+\alias{repeated_instruments}
+\title{Get names of repeated instruments}
+\usage{
+repeated_instruments(uri, token)
+}
+\arguments{
+\item{uri}{REDCap database uri}
+
+\item{token}{database token}
+}
+\value{
+vector
+}
+\description{
+Get names of repeated instruments
+}

man/sankey_ready.Rd

@@ -1,19 +0,0 @@
-% 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/selectInputIcon.Rd

@@ -0,0 +1,53 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/import-file-ext.R
+\name{selectInputIcon}
+\alias{selectInputIcon}
+\title{Create a select input control with icon(s)}
+\usage{
+selectInputIcon(
+  inputId,
+  label,
+  choices,
+  selected = NULL,
+  multiple = FALSE,
+  selectize = TRUE,
+  size = NULL,
+  width = NULL,
+  icon = NULL
+)
+}
+\arguments{
+\item{inputId}{The \code{input} slot that will be used to access the value.}
+
+\item{label}{Display label for the control, or \code{NULL} for no label.}
+
+\item{choices}{List of values to select from. If elements of the list are
+named, then that name --- rather than the value --- is displayed to the
+user. It's also possible to group related inputs by providing a named list
+whose elements are (either named or unnamed) lists, vectors, or factors. In
+this case, the outermost names will be used as the group labels (leveraging
+the \verb{<optgroup>} HTML tag) for the elements in the respective sublist. See
+the example section for a small demo of this feature.}
+
+\item{selected}{The initially selected value (or multiple values if \code{multiple = TRUE}). If not specified then defaults to the first value for
+single-select lists and no values for multiple select lists.}
+
+\item{multiple}{Is selection of multiple items allowed?}
+
+\item{selectize}{Whether to use \pkg{selectize.js} or not.}
+
+\item{size}{Number of items to show in the selection box; a larger number
+will result in a taller box. Not compatible with \code{selectize=TRUE}.
+Normally, when \code{multiple=FALSE}, a select input will be a drop-down list,
+but when \code{size} is set, it will be a box instead.}
+
+\item{width}{The width of the input, e.g. \code{'400px'}, or \code{'100\%'};
+see \code{\link[shiny:validateCssUnit]{validateCssUnit()}}.}
+}
+\value{
+A numeric input control that can be added to a UI definition.
+}
+\description{
+Extend form controls by adding text or icons before,
+after, or on both sides of a classic \code{selectInput}.
+}

man/vectorSelectInput.Rd

@@ -0,0 +1,66 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/custom_SelectInput.R
+\name{vectorSelectInput}
+\alias{vectorSelectInput}
+\title{A selectizeInput customized for named vectors}
+\usage{
+vectorSelectInput(
+  inputId,
+  label,
+  choices,
+  selected = "",
+  ...,
+  placeholder = "",
+  onInitialize
+)
+}
+\arguments{
+\item{inputId}{passed to \code{\link[shiny]{selectizeInput}}}
+
+\item{label}{passed to \code{\link[shiny]{selectizeInput}}}
+
+\item{choices}{A named \code{vector} from which fields should be populated}
+
+\item{selected}{default selection}
+
+\item{...}{passed to \code{\link[shiny]{selectizeInput}}}
+
+\item{placeholder}{passed to \code{\link[shiny]{selectizeInput}} options}
+
+\item{onInitialize}{passed to \code{\link[shiny]{selectizeInput}} options}
+}
+\value{
+a \code{\link[shiny]{selectizeInput}} dropdown element
+}
+\description{
+A selectizeInput customized for named vectors
+}
+\examples{
+if (shiny::interactive()) {
+shinyApp(
+  ui = fluidPage(
+    shiny::uiOutput("select"),
+    tableOutput("data")
+  ),
+  server = function(input, output) {
+    output$select <- shiny::renderUI({
+      vectorSelectInput(
+        inputId = "variable", label = "Variable:",
+        data = c(
+          "Cylinders" = "cyl",
+          "Transmission" = "am",
+          "Gears" = "gear"
+        )
+      )
+    })
+
+    output$data <- renderTable(
+      {
+        mtcars[, c("mpg", input$variable), drop = FALSE]
+      },
+      rownames = TRUE
+    )
+  }
+)
+}
+}

man/vertical_stacked_bars.Rd

@@ -16,7 +16,18 @@ vertical_stacked_bars(
 )
 }
 \arguments{
-\item{t.size}{}
+\item{data}{data.frame}
+
+\item{score}{outcome variable}
+
+\item{group}{grouping variable}
+
+\item{strata}{stratifying variable}
+
+\item{t.size}{text size}
+}
+\value{
+ggplot2 object
 }
 \description{
 Vertical stacked bar plot wrapper

man/wide2long.Rd

@@ -0,0 +1,63 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/wide2long.R
+\name{wide2long}
+\alias{wide2long}
+\title{Alternative pivoting method for easily pivoting based on name pattern}
+\usage{
+wide2long(
+  data,
+  pattern,
+  type = c("prefix", "infix", "suffix"),
+  id.col = 1,
+  instance.name = "instance"
+)
+}
+\arguments{
+\item{data}{data}
+
+\item{pattern}{pattern(s) to match. Character vector of length 1 or more.}
+
+\item{type}{type of match. can be one of "prefix","infix" or "suffix".}
+
+\item{id.col}{ID column. Will fill ID for all. Column name or numeric index.
+Default is "1", first column.}
+
+\item{instance.name}{}
+}
+\value{
+data.frame
+}
+\description{
+This function requires and assumes a systematic naming of variables.
+For now only supports one level pivoting. Adding more levels would require
+an added "ignore" string pattern or similarly. Example 2.
+}
+\examples{
+data.frame(
+  1:20, sample(70:80, 20, TRUE),
+  sample(70:100, 20, TRUE),
+  sample(70:100, 20, TRUE),
+  sample(170:200, 20, TRUE)
+) |>
+  setNames(c("id", "age", "weight_0", "weight_1", "height_1")) |>
+  wide2long(pattern = c("_0", "_1"), type = "suffix")
+data.frame(
+  1:20, sample(70:80, 20, TRUE),
+  sample(70:100, 20, TRUE),
+  sample(70:100, 20, TRUE),
+  sample(170:200, 20, TRUE)
+) |>
+  setNames(c("id", "age", "weight_0", "weight_a_1", "height_b_1")) |>
+  wide2long(pattern = c("_0", "_1"), type = "suffix")
+# Optional filling of missing values by last observation carried forward
+# Needed for mmrm analyses
+long_missings |>
+  # Fills record ID assuming none are missing
+  tidyr::fill(record_id) |>
+  # Grouping by ID for the last step
+  dplyr::group_by(record_id) |>
+  # Filling missing data by ID
+  tidyr::fill(names(long_missings)[!names(long_missings) \%in\% new_names]) |>
+  # Remove grouping
+  dplyr::ungroup()
+}