Using the dmdScheme
The functionality for using the dmdScheme is available
either via the online app (which can also be run on an in-house shiny
server), a 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 and
the dmdScheme
package.
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.
Figure 1: Workflow of using dmdScheme (A)
via the web app, (B) via the app locally, (C) via the R prompt. Square
boxes indicate steps which are not common to all three, rounded boxes
indicate steps identical to the different ways, although how they are
executed can differ.
Preparation
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.
Figure 2: Screenshot of the dmdScheme app.
Select scheme
The package 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).
Download new scheme
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
open_new_spreadsheet() command.
Figure 3 shows two screenshots of the spreadsheet as opened in Excel.
