parameters.md

Parameters available for the run settings file (.dat-file)

From the manual (p. 97):
"It is very important that all the parameters in your run settings file are written exactly like presented here. If there are errors in the spelling of parameters, the program can not find them and will use default settings instead. The order of parameters on the other hand is not obligatory. If necessary, you can enter comments in your species list file on separate rows starting with the symbol # . Remember also to use decimal points, not commas, in all the input files."

Table below lists all the available parameters by category with default values (if applicable), and a short explanation. For more thorough documentation, please see the manual.
File all_parameters.dat also lists the the same parameters as a proper dat-file.

Parameter value 0/1 means:

0 = off
1 = on

Settings

Parameter	Default	Explanation
removal rule	1	Determines which cell removal rule will be used. 1 = Basic core-area Zonation, 2 = Additive benefit function, 3 = Target-based planning, 4 = Generalized benefit function, 5 = random removal.
warp factor	100	Defines how many cells are removed at a time. If warp factor is 100, it means that 100 cells are removed at each iteration. Thus a lower warp factor leads to a finer solution, but also to a prolonged running time, whereas a high warp factor keeps the running time short, but might result in a more coarse solution.
edge removal	1	Determines whether the program removes cells from the edges of remaining landscape (value = 1) or anywhere from the landscape (value = 0).
add edge points	0	Randomly selects additional cells inside the landscape that will be initially classified as edge-cells, from which removal can proceed. The value of this parameter determines the number of cells that are selected. This parameter allows a compromise between using and not using edge removal.
use SSI	0	Determines whether Species of Special Interest (SSI) are included into the analysis (value = 1) or not (value = 0).
SSI file name	-	Similar to the biodiversity feature list file, except indicates a file that contains the list of SSI species used in the analysis.
use planning unit layer	0	Determines whether a planning unit layer is used (value = 1) or not (value = 0).
planning unit layer file	-	Indicates the planning unit layer file (integer grid) to be used.
use cost	0	Determines whether land costs are included in the analysis (value = 1). If no land costs are used, this parameter should be set to 0. Default = 0.
cost file	-	Indicates the land cost file to be used. Default is that a cost file is not used.
use mask	0	Determines whether a removal mask layer is used (value = 1) or not (value = 0).
mask file	-	Indicates the mask layer file to be used. Default is that a mask file is not used.
use boundary quality penalty	0	Determines whether BQP connectivity is used (value = 1) or not (value = 0).
BQP profiles file	-	Indicates the BQP profiles file to be used.
BQP Mode	1	Determines how the program will calculate the effects of fragmentation from species distribution data.
BLP	0	Defines a penalty given for the boundary length of the reserve. The value of BLP should be a small decimal number. The value of this penalty cannot be decided in advance based on some numeric criterion; rather a suitable value needs to be found by experimentation.
use tree connectivity	0	Determines whether directed connectivity (Neighborhood Quality Penalty; NQP) is used (value = 1) or not (value = 0).
tree connectivity file	-	Indicates which tree connectivity file will be used when including NQP into the analysis.
use interactions	0	Determines whether ecological interactions are included (value = 1) into the analysis or not (value = 0).
interaction file	-	Indicates which interactions definitions file will be used.
annotate name	1	With this option you can mark your output file names to show which analyses have been used to produce them (value = 1).
logit space	0	A special option relevant for probability of occurrence models using logistic link functions. Determines whether the biological values of cells will be transformed from logit space (value = 1) for processing.
treat zero-areas as missing data	0	This option changes all cells with no species occurrences to missing data. This function might be useful in some cases, for example, if the missing data is in fact marked with the value 0 in your species distribution files due to some technical reasons.
z	0.25	This value is used to calculate the extinction risks of species as their distribution sizes are decreasing. z is the exponent of the species-area curve (S = cAz ), which has been widely used in ecological studies.
resample species	0	This option allows you to, for example, test analyses using only a subset of species. The program selects a random set of species from your species list file and uses them to run the analysis.
post-processing list file	-	Indicates the list file of automatically executed post-processing analyses to be performed after landscape ranking.
memory save mode	0	Here you can choose to use Zonation in a memory save mode.
use groups	0	Determines whether a groups file is used (value = 1) or not (value = 0).
groups file	-	Indicates the groups file to be used in the analysis.
use condition layer	0	Determines whether feature-group specific landscape condition is used in the analysis (value = 1) or not (value = 0).
condition file	-	Indicates the file describing linkage of features to landscape condition.
use retention layer	0	Determines whether feature-group specific retention layers are used in the analysis (value = 1) or not (value = 0).
retention file	-	Indicates the file describing linkage of features to landscape retention.
retention layers relative weight	1.0	Determines the relative weight of retention layers (as a group) compared to representation.
mask missing areas	0	Determines whether some areas of the landscape are masked out (filled with missing data) for all input grid layers (value = 1) or not (value = 0).
area mask file	-	Indicates the raster file to be used for masking the areas with missing information.

Info-gap settings

Parameter	Default	Explanation
Info-gap proportional	0	Determines whether the errors in species occurrences are uniform errors (value = 0) or proportional errors (value = 1).
use info-gap weights	1	Determines whether species-specific distribution uncertainty map layers are used in the info-gap analysis (value = 1) or not (value = 0).
Info-gap weights file	-	Indicates the file that includes the list of uncertainty maps.

Community analysis settings

Parameter	Default	Explanation
load similarity matrix	0	Determines whether a similarity matrix for connectivity or community composition is used in the analysis (value = 1) or not (value = 0).
connectivity similarity matrix file	-	Indicates the connectivity similarity matrix file (section 3.3.3.4.) to be used.
apply to connectivity	0	Determines whether the similarity matrix is applied to connectivity in conservation area prioritization (value = 1) or not (value = 0).
connectivity edge effect fix file	-	Indicates the file for edge effect fix for connectivity.
community similarity matrix file	-	Indicates the community similarity matrix file to be used.
apply to representation	0	Determines whether community similarity expansion is applied to the stack of biodiversity features (value = 1) or not (value = 0).

Administrative units

Parameter	Default	Explanation
use ADMUs	0	Determines whether administrative units are accounted for in the analysis (value = 1) or not (value =0).
ADMU mode	1	Determines whether the administrative regions are weak (value = 1) or strong (value = 2).
ADMU layer file	-	Indicates the administrative units layer to be used.
ADMU descriptions file	-	Indicates the file describing weights etc. for the administrative units.
ADMU weight matrix	-	Indicates the file containing a matrix of administrative units x feature weight.
calculate local weights from condition	0
Mode 2 global weight	-	Indicates balance between global representation and local (ADMU-specific) considerations in landscape ranking.
row count for per ADMU output curves	0	Indicates the number of rows for each of the per ADMU curve files, that is, the number of removal levels reported.