Download

Although the app is free to run on the RShiny server, we recommend that regular users download it and run it locally on their machine. This is to avoid the risk of becoming disconnected from the server before the results have been saved.

To run the app locally, you need to download R and RStudio (both are free to download and use). If you already have R and RStudio installed, make sure you are running the latest version of R (a quick way to update R from within RStudio is to type the following, only available for Windows )

install.packages("installr"); library(installr) # install+load installr

updateR() # updating R.

Unfortunately macOS users must download and install the latest version of R directly.  The latest version can be found on this link macOS latest version.

To download R, click on the link that applies to your machine.

Download R (Windows) and follow the detailed instructions for the installation.

Download R (MAC) and follow the detailed instructions for the installation, based on the characteristics of your device.

To download RStudio, click on the link that applies to your machine.

Download RStudio (Windows)

Download RStudio (MAC)

More information for the RStudio installation can be found on this link RStudio, .

To run the app:

If your personal device is macOS , then after RStudio has been downloaded and before any kind of package installation please implement the next step

      1. install XQuartz, installation instructions
      2. install Xcode go through the installation instructions 
      3. install the developments tools and libraries
      4. restart RStudio

If your personal device is Windows before installing any kind of package download RTools

  1.  For Windows 64-bit follow the installation instructions,
  2.  For Windows 32-bit follow the installation instructions

Now for both users of Windows and macOS

  • Install devtools, if not already installed, by using install.packages(“devtools”)
  • Load devtools using library(devtools)
  • Install and run the app using
install_github(“alexdiana1992/eDNAShinyApp”, ref = “master”)
library(eDNAShinyApp)
runeDNAShinyApp()

Note: If you are asked to update any packages select to update them all. If any error messages appear that mention that the wrong version is loaded for any package then please install the package by using install.packages(”  “) where the same of the package related to the error should be inside the quotation marks.

Note: If you get an error message such as Error: unexpected input in “ it may be because R does not recognize the quotation marks that have been copied and pasted from the webpage; simply delete these and type them in to replace them.

Note: When installing the package from github, you may get error messages for some of the  packages that it relies on, similar to

In file.copy(savedcopy, lib, recursive = TRUE) :
problem copying C:\Users\….\Documents\R\win-library\4.0\00LOCK\glue\libs\x64\glue.dll to C:\Users\…\Documents\R\win-library\4.0\glue\libs\x64\glue.dll: Permission denied.

This could be because some of the packages are already installed and running, in which case, you should still be able to load and use the app by running the last two lines of the above code. If not, then you should run the command options(“install.lock”=FALSE), and then try installing the package again.

Note: Occasionally, R may crash for no apparent reason…if the MCMC was running and you got a message that you have to abort the process, then please reload the app and try again. If it happens again, then it may be that the data have not been loaded correctly or there are missing values or equivalent, in which case do feel free to email e.matechou@kent.ac.uk for advice.

Before first usage of the RShiny app it is highly recommended to go through the ,Diana, A., Matechou, E., Griffin, J. E., E. Buxton, A. S. and Griffiths, R. A., (2021) An RShiny app for modelling environmental DNA data: accounting for false positive and false negative observation error, Ecography (Software notes)