1. Introduction
This code aimed at automatizing the creation of input files to run the sensitivity analyses of
Zonation
, similar to those used in El-Gabbas et al. paper:El-Gabbas, Ahmed; Gilbert, Francis; and Dormann, Carsten F. (2020) Spatial conservation prioritisation in data-poor countries: a quantitative sensitivity analysis using multiple taxa. BMC Ecology (under review).
Please note that this appendix is not intended to provide an introduction to
Zonation
software. An introduction to theZonation
software can be found in Di Minin et al., 2014. I expect the reader to be familiar withZonation
and have read the paper in advance.This html file was written in
RMarkdown
. TheRMarkdown
and sample data are available here.
1.1. Abbreviations used
Species weight
WTLoc
: weighted by Egyptian national red-list statusWTWO
: without red-list weightingUncert
: weighted by predictive uncertaintyNoUncert
: without predictive uncertainty weight
Connectivity
BQP
: boundary quality penaltyBQP-WO
: no connectivity analysesBQP-Low
/BQP-Med
/BQP-Strng
: low/medium/strong BQP curves
Modelling algorithms
Mxnt
: MaxentEN
: elastic net
Sampling bias
BiasWO
: environment-only models (no bias correction)Bias0
: bias-free predictions, implementing model-based bias correction
Surrogate groups
MMls
: MammalsRep
: ReptilesButr
: ButterfliesAllSP
: All three groups together
1.2. Input files
Species weights
- Four
*.csv
files for different weighting options are available in the folderZigInputFiles/Data/
. Below is an example on one of these files:ZigInputFiles/Data/WeightsData_EN_Bias0.csv
:
Setting files
- Four
*.dat
setting files are available in the folder:ZigInputFiles/Dat/*.dat
. Below is an example on one of these files (ZigInputFiles/Dat/ABF_Mask.dat
):
[Settings]
removal rule = 2
warp factor = 10
edge removal = 0
add edge points = 50
use SSI = 0
SSI file name = SSI_list.txt
use planning unit layer = 0
planning unit layer file = PLU_file.asc
initial removal percent = 0.0
use cost = 1
cost file = Maps\CostLayer.tif
use mask = 1
mask file = Maps\Mask_PAs.tif
use boundary quality penalty = 1
BQP profiles file = Maps\BQPcurves.txt
BQP mode = 1
BLP = 0
use tree connectivity = 0
tree connectivity file = tree.txt
use interactions = 0
interaction file = interact.spp
annotate name = 0
logit space = 0
treat zero-areas as missing data = 0
z = 0.25
resample species = 0
[Info-gap settings]
Info-gap proportional = 0
use info-gap weights = 0
Info-gap weights file = UCweights.spp
[Outputs]
output proportional loss ranking = 1
Predicted distribution maps
- In this reproducible code, I used 5 species for each surrogate group (butterflies, mammals, reptiles).
- The folder
ZigInputFiles/Maps/
contains predicted distribution maps*.tif
for each combination of species distribution model algorithm and sampling bias correction.
Example map: