R/darleq3_shiny.R

In nsj3/darleq3: Diatom-based water quality indices

##
## Copyright (c) 2019, Steve Juggins
##
## License GPL-2
##
## Permission is hereby granted to use, copy, modify and distribute the software in accordance with
## the GPL-2 license and subject to the following condition:
##
## The above copyright notice and this permission notice shall be
## included in all copies or substantial portions of the Software.
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## THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
## EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
## MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
## NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
## LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
## OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
## WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
##


#' Run DARLEQ3 as an interactive shiny app
#'
#' @param browser Logical to indicate if the app should open in an external browser (the default) or in R/RStudio's default shiny app window.
#'
#' @details
#' \code{runDARLEQ} runs darleq3 as an interactive shiny app. When running the function will open a web browser displaying the shiny app:
#'
#' \if{html}{\figure{darleq3shiny.png}{options: width="60\%" alt=""}}
#' \if{latex}{\figure{darleq3shiny.png}{options: width=9cm}}
#'
#' To use the app follow these simple steps:
#' * 1: Click the Browse... button to select and upload a DARLEQ diatom file (see function \code{\link{read_DARLEQ}} for guidelines on how to format this file).
#' * 2: Once uploaded, select a sheet and click import.  A summary (number of samples & taxa) will be displayed in the Data summary box when upload is complete.
#' * 3: Select the metric type. "TDI3 & 4 for LM" will calculate TDI3 and TDI4 for river samples according to the DARLEQ 2 taxon list,  TDI5LM will calculate TDI5 for river LM diatom data, TDI for NGS will calculate TDI5NGS for river NGS diatom data, "LTDI for LM" will calculate LTDI1 and LTDI2 for lake LM data, and "DAM for LM" will calculate the diatom acidification metric for river LM data.  A summary of results will appear in the Results summary box when the calculations are complete.
#' * 4: Click Download Results to save the results in an Excel file.  The default name for this file will be the "DARLEQ3_Results_" concatenated with the original data filename, worksheet name, and date.
#'
#' To quit the app simple close the browser and or hit Escape in the RStudio Console window.
#'
#' @examples
#' \dontrun{
#' library(darleq3)
#' runDARLEQ()
#' }
#'
#' @export runDARLEQ
#'
#' @importFrom shinydashboard dashboardPage dashboardHeader dashboardSidebar
#' @importFrom shinyjs disable enable

runDARLEQ <- function(browser=TRUE) {
  fn <- system.file("shiny_app/app.R", package="darleq3")
  if (browser)
     shiny::shinyAppFile(fn, options=list(launch.browser=TRUE))
  else
     shiny::shinyAppFile(fn)
}