The functionality for using the dmdScheme is available either via the online app (which can also be housed at an inhouse shiny server), the local running app, or via the R command line. The simplest method is using the online app, as no additional software needs to be installed locally. To be able to use the dmdScheme functionality locally, either via the app or via the R command line, it is necessary to install R [@RCoreTeam2019] and the
dmdScheme package [@Krug2019a] in R.
In the following section, I will go through the different stages of using the
dmdScheme via the web app, a local app or the R prompt. The detailed commands which have to be used can be found in Figure 1.
The app (Figure 2) can be accessed either via the internet as a web app at https://rmkrug.shinyapps.io/dmd_app/, or locally. To run it locally, you need R and the
dmdScheme package installed. After loading the
dmdScheme package, you can start the app locally by running
run_app() at the R prompt. After these steps, the usage of the two apps is identical.
When using the
dmdScheme from the command line, the initial setup is the same as running the app locally, only that it is not necessary to start the app.
dmdScheme does not come with a specific scheme, and installs upon loading a generic dmdScheme from the dmdScheme scheme repository at https://github.com/Exp-Micro-Ecol-Hub/dmdSchemeRepository. In nearly all circumstances, a specific scheme needs to be installed, together with the accompanying R package. In the app, this is done via selecting a theme in the section “Available dmdSchemes”. This list is populated automatically upon starting of the app from the schemes available in the scheme repository. The selection of the scheme will download the scheme definition package, install any accompanying R package as specified in the scheme definition package, load the accompanying R package, and activate the scheme definition.
To do this from the R prompt, one has do these steps manually and install the scheme, install the accompanying R package, load the accompanying R package, and activate the scheme itself (see Figure 1 C for the commands).
The spreadsheet to enter the metadata can be obtained from the app via the “Empty scheme spreadsheet” button. This will download an
.xlsx spreadsheet containing the definition of the scheme and the cells for the metadata which need to be filled in.
In R, the spreadsheet can be obtained by using the
Figure 3 shows two screenshots of the spreadsheet as opened in Excel.