xfer_time when using
envs_userEnvsraster::getdata with geodata
functionsmarkdown to importsrgeos (package expiring)paleobioDB (package off CRAN)rgdal (package expiring)skip_on_cran() added to several testsspooc package (i.e. rbison archived in
CRAN, and BISON data is available via GBIF).What is new in this version?
Stop and start your work whenever you want: This version allows you to save a session partway through the workflow and then restart it. Try this out via the “Save session” tab if you think that is something that matches the way you would run analyses (intermediate-to-advanced users).
Greater reproducibility regarding occurrence records: As a step towards greater documentation and reproducibility in biodiversity informatics, this version of Wallace provides an option of querying GBIF and receiving a DOI for the data provided. If you are already a registered GBIF user, check the “Include Data Source Citations” option under the Query Database (Present) module of the OccData component.
Cross-time transfers: If you will later be interested in transferring your models to estimates of future (or past) climate, try out the updated Transfer component. This version now has data from WorldClim and EcoClimate (which also has reconstructed data for the past). Make your original model with the same climatic data source that you would like to use for transferring across time periods.
Make models for multiple species in the same Wallace session: This advancement supports two important other functionalities: comparisons of species in environmental space (see below). If you are interested in either of these, try making models for more than one species now. To get the data to do this, in the OccData component either run the query multiple times or do it once with scientific names separated by commas. Then, in later components use the pull-down menu in the top center of the interface to indicate the species that you want to work with.
Environmental space comparisons: It may not be as directly linked to conservation as many of the other advances, but this version now has several modules in the EnvSpace component, which allows users to examine characteristics of environmental space across species, like niche overlap. If this matches your research interests (for academic purposes, or to study invasive species, for example), try them out.
Redesigned R-markdown functionalities: Because of the way this version of Wallace is redesigned, it now makes the documentation files in a new way (Reproduce component). In addition to making sure that you can download the documentation in ways readable to humans (like pdf), it would be helpful to the development team to have users download the executable RMD code and confirm that it runs successfully in R (intermediate-to-advanced users).
Summary of new features:
leaflet.extras enables programmatic removal
of drawn polygons again, the Reset button will only reset the data, and
not affect polygons.rgdal is installed
before downloads of rasters are allowed. This turns out to be an issue
with raster package, as the rgdal dependency
for this function doesn’t seem to be functional.system.file() calls to files in the
wallace package to relative paths, which ensures that in
those cases where the user downloads from Github and doesn’t have the
package installed from CRAN, or the package being developed is not the
one installed from CRAN, the correct files can be found. To make this
work, the folders inst/Rmd, inst/css, and
inst/js have been moved to inst/shiny. An
exception is the run_wallace() function, which retains
system.file() because it is not in the
inst/shiny folder.raster package first.repmis and rgdal to package
dependencies.rJava
cannot load.leaflet version 1.0.1. There
was a mysterious problem with zooming to points before clearing markers
and/or plotting points, which resulted in crashing as soon as points are
plotted unless the user had the Github master version of
leaflet installed. Thus the code was rearranged and cleaned
to accomodate the current leaflet version on CRAN.