Frequently Asked Questions • ENMTML

We present here the anwser to some questions that are more common to arise while running ENMTML. If you couldn’t find your issue among those questions, please report it and we will make our best to help you run the package smoothly.
At first the number fo arguments and the folder’s structure may seem a little scary, but with little time you will get the hang of it and will start running ENM models!

Project Folder

We highly recommend you to create a folder for your project!
A general overview of the Project Folder and its containing sub-folders will look similar to this:

Yellow are the Mandatory Folders, you need them to run the package.
Green are the Optional Folders, only required according to your project design.
Blue are Output Folders, those will be created during the modeling routine.

Function Arguments

ENMTML consists of several arguments, which will be checked at the start of the modeling routine.

Take your time to check any Error returned during this argument check and use the help to correctly fill the arguments.

Occurrence File Type

ENMTML imports occurrence data from a TXT file with tabulation as separator (tab-separated)

Data Format

The TXT can have several columns, but three columns are mandatory:

Species name
Longitude
Latitude

They can be named to your preference as those will be inputted in the arguments sp, x, y of the ENMTML function.

Here’s an example of an occurrence table for four sample species.

#> Loading required package: ENMTML
#> Please note that rgdal will be retired during October 2023,
#> plan transition to sf/stars/terra functions using GDAL and PROJ
#> at your earliest convenience.
#> See https://r-spatial.org/r/2023/05/15/evolution4.html and https://github.com/r-spatial/evolution
#> rgdal: version: 1.6-7, (SVN revision 1203)
#> Geospatial Data Abstraction Library extensions to R successfully loaded
#> Loaded GDAL runtime: GDAL 3.6.2, released 2023/01/02
#> Path to GDAL shared files: C:/Users/santi/AppData/Local/R/win-library/4.3/rgdal/gdal
#>  GDAL does not use iconv for recoding strings.
#> GDAL binary built with GEOS: TRUE 
#> Loaded PROJ runtime: Rel. 9.2.0, March 1st, 2023, [PJ_VERSION: 920]
#> Path to PROJ shared files: C:/Users/santi/AppData/Local/R/win-library/4.3/rgdal/proj
#> PROJ CDN enabled: FALSE
#> Linking to sp version:2.1-1
#> To mute warnings of possible GDAL/OSR exportToProj4() degradation,
#> use options("rgdal_show_exportToProj4_warnings"="none") before loading sp or rgdal.
#> Registered S3 methods overwritten by 'adehabitatMA':
#>   method                       from
#>   print.SpatialPixelsDataFrame sp  
#>   print.SpatialPixels          sp
#> rgeos version: 0.6-4, (SVN revision 699)
#>  GEOS runtime version: 3.11.2-CAPI-1.17.2 
#>  Please note that rgeos will be retired during October 2023,
#> plan transition to sf or terra functions using GEOS at your earliest convenience.
#> See https://r-spatial.org/r/2023/05/15/evolution4.html for details.
#>  GEOS using OverlayNG
#>  Linking to sp version: 2.1-1 
#>  Polygon checking: TRUE

species	x	y
Sp_14	-55.37526	-31.708447
Sp_14	-54.20860	-25.041806
Sp_14	-58.29191	-29.125124
Sp_17	-73.12519	-15.041847
Sp_17	-70.87520	-15.458512
Sp_17	-69.12520	-17.708503
Sp_18	-61.37523	-26.625134
Sp_18	-61.29190	-26.958465
Sp_18	-61.37523	-23.125148
Sp_34	-67.29188	-5.041887
Sp_34	-71.20853	-7.458544
Sp_34	-68.20854	-7.208545

Predictors

Predictor File Type
Folder Arrangement
Projections

Predictor File Type

ENMTML accepts predictors from several formats: TIF, BIL, ASC and TXT(tab-separated)

Folder Arrangement

Predictors must be within a single folder, which will be informed through the pred_dir argument.

Projections

Projections are indicated using the proj_dir argument.
As it is common to usually make projections to multiple climate scenarios or extents, the arrangement of Projection folders consists in a major folder with different sub-folders (one for each climatic scenario or extent).
It is essential that the name of the variables in those folder match the names of variables within the pred_dir folder!

Results

Results will be in a folder specified in the result_dir argument, or if you chose not to supply any folder ENMTML will create a folder named Results at the same level of your pred_dir folder (see this at the figure at the Project Folder section.

Model Evaluation and information about the modelling routine can be found in several txt files within the Results folder.
Important sub-folders with result maps are:
- Algorithm: with tif present projections for the selected algorithms and the binary folders for the selected thresholds
- Ensemble: with tif projections for the selected ensembles.
- Projection: with tif projections for the different climatic scenarios/extents

Other sub-folders will be created according to the modeling routine and contain masks related to pseudo-absence allocation and geographical partition of datasets.