MarCon Projects¶

Reference table for MarCon project primary and secondary dictionary keys. Tertiary keys are found in a separate Table 2

New Projects¶

The first step is to import the package and create a MarCon dictionary. This is one giant dictionary that contains all required options, filepaths, etc. These can also be produced using the GUI Marxan Connect

import marxanconpy
import os

project = marxanconpy.marcon.new_project()

Load Projects¶

We can also load pre-existing .MarCon files

path = os.path.dirname(marxanconpy.__file__)
project = marxanconpy.marcon.load_project(os.path.join(path,'data','CF_demographic','tutorial.MarCon'))

Warning: This project file was created with a different version of Marxan Connect. Attempting to update for compatibility
Warning: This project file does not contain all the required fields (marxan). Attempting to update for compatibility

Editing Projects¶

project['filepaths']['aa_filepath'] = "path\to\file.shp"

Saving Projects¶

Understanding Projects¶

MarCon project are a python dictionary with a key strucuture as defined below. You can use the functions in marxanconpy.marcon_ to create, load, and save MarCon projects to file. With those functions the python dictionary can be written to file as a JSON.

Primary and Secondary Keys¶

Table 1: Reference table for MarCon project primary and secondary dictionary keys¶
Primary Key	Secondary Key	Definition
version	marxanconpy	The version number for marxanconpy
version	MarxanConnect	The version number for Marxan Connect
spec_dat		Contains a JSON version of the spec.dat file contents
filepaths	aa_filepath	Filepath for the Avoidance Area shapefile
filepaths	bd_filepath	Filepath for the spatial dependencies file (e.g. boundary.dat)
filepaths	cf_filepath	Filepath for the planning unit vs conservation features file (e.g. puvspr.dat)
filepaths	demo_cu_cm_filepath	Filepath for the demographic connectivity data file scaled to the connectivity units (i.e. not the planning units)
filepaths	demo_cu_file_pu_id	String that represents the column name which corresponds to the planning unit IDs in the demographic connectivity units file
filepaths	demo_cu_filepath	Filepath for the demographic connectivity units (i.e. not the planning units)
filepaths	demo_pu_cm_filepath	Filepath for the demographic connectivity file scaled to the plannings units
filepaths	fa_filepath	Filepath for the focus area shapefile
filepaths	land_cu_file_hab_id	String that represents the column name which corresponds to the planning unit IDs in the landscape connectivity units file
filepaths	land_cu_filepath	Filepath for the landscape connectivity units (i.e. not the planning units)
filepaths	land_pu_cm_filepath	Filepath for the landscape connectivity data file scaled to the planning units
filepaths	land_res_file_hab_id	String that represents the column name which corresponds to the planning unit IDs in the landscape resistance file
filepaths	land_res_filepath	Filepath for the landscape resistance surface file (not yet implemented)
filepaths	land_res_mat_filepath	Filepath for the landscape resistance matrix
filepaths	lp_filepath	Filepath for the local production
filepaths	map	Filepath for the map output
filepaths	marxan_dir	Filepath for the Marxan executable
filepaths	marxan_input	Filepath for the marxan input file (i.e. input.dat)
filepaths	projfile	Filepath for the .MarCon project file
filepaths	projfilename	Filename for the .MarCon project file
filepaths	pu_file_pu_id	String that represents the column name which corresponds to the planning unit IDs in the planning unit file
filepaths	pu_filepath	Filepath for the planning unit shapefile
filepaths	pucsv	Filepath to save a .csv version of all the planning unit specific output
filepaths	pudat_filepath	Filepath for the marxan formated planning unit file (i.e. pu.dat)
filepaths	pushp	Filepath to save a shapefile version of all the planning unit specific output
filepaths	spec_filepath	Filepath for the marxan formated conservation feature file (i.e. spec.dat)
options	aa_status	The status of the avoidance areas (i.e. Locked in, Locked out, or Status-quo)
options	bd_filecheck	Logical, True if you want to export the spatial dependencies file (i.e. boundary.dat)
options	calc_metrics_cu	Logical, True if you want to calculate connectivity metrics scaled to the connectivity units
options	calc_metrics_pu	Logical, True if you want to calculate connectivity metrics scaled to the planning units
options	cf_export	“Export” if you want to export only the connectivity outputs the selected Marxan formated files to the filepaths indicated, or “Append” if you want append the connectivity outputs the selected Marxan formated files to the filepaths indicated without overwritting the original files (the new filenames will have the _appended. format)
options	demo_conmat_format	The format of the demographic connectivity data (i.e. Matrix, Edge List, Edge List with Time, Edge List with Type)
options	demo_conmat_rescale	Identical Grids if no rescaling is necessary, Rescale Connectivity Matrix if the connectivity data needs to be rescaled to the planning units. Use rescaling with caution
options	demo_conmat_rescale_edge	If rescaling, how to handle the edges (i.e. Proportional to overlap or Assume homogeneous connectivity)
options	demo_conmat_type	The format of the demographic connectivity data (i.e. Probability, Migration, Flow)
options	demo_metrics	Third level keys with logicals. True if you want to calculate that specific metric. Tertiary level keys are available in Table 2
options	demo_pu_cm_progress	Logical, True if you want to see a progress bar as demographic connectivity data is rescaled
options	fa_status	The status of the avoidance areas (i.e. Locked in, Locked out, or Status-quo)
options	inputdat_boundary	Nature (i.e. “Asymmetric” “Symmetric”) of the spatial dependencies
options	land_conmat_type	The format of the demographic connectivity data (i.e. Habitat Type + Resistance, Resistance Surface, Connectivity Matrix)
options	land_hab_buff	Buffer distance (m) under which planning units will be considered connected neighbours in the distance calculations. All distance calculations assume travel in straight lines between the centers of neighbouring planning units.
options	land_hab_thresh	Threshold under which habitat connectivity values is considered null. Ranges from 0 to 1. Without a threshold, values for in/out degrees, and betweenness centrality will be homogeneous throughout each habitat type.
options	land_metrics	Third level keys with logicals. True if you want to calculate that specific metric. Tertiary level keys are available in Table 2
options	land_pu_cm_progress	Logical, True if you want to see a progress bar as landscape connectivity data is generated
options	land_res_matrixType	Least-Cost Path if you want to estimate connectivity using resistance values and the spatial arrangement of habitats or Euclidean Distance if you want to estimate connectivity using only the spatial arrangement of habitats
options	map_filecheck	Logical, True if you want to export the map as an image file.
options	marxan	Marxan if you want to use Marxan, or Marxan with Zones if you want to use the Marxan with Zones (experimental)
options	marxan_bit	64-bit if you want to use the 64-bit version of Marxan which is faster, or 32-bit if you want to use the 32-bit version of Marxan
options	metricsCalculated	Logical, True if connectivity metrics have been calculated at least once
options	pucsv_filecheck	Logical, True if you want to export the .csv version of all the planning unit specific output
options	pudat_filecheck	Logical, True if you want to export the marxan formated planning unit file (i.e. pu.dat)
options	pushp_filecheck	Logical, True if you want to export the shapefile version of all the planning unit specific output
connectivityMetrics	best_solution	The best solution from the Marxan output
connectivityMetrics	boundary	The spatial dependencies (i.e. boundary.dat)
connectivityMetrics	select_freq	The selection frequency from the Marxan output
connectivityMetrics	spec_demo_pu	The connectivity metrics calculated from the demographic connectivity data scaled to the planning units. Tertiary level keys are available in Table 2
connectivityMetrics	spec_land_pu	The connectivity metrics calculated from the landscape connectivity data scaled to the planning units. Tertiary level keys are available in Table 2
connectivityMetrics	spec_demo_cu	The connectivity metrics calculated from the demographic connectivity data scaled to the connectivity units. Tertiary level keys are available in Table 2
connectivityMetrics	spec_land_cu	The connectivity metrics calculated from the landscape connectivity data scaled to the connectivity units. Tertiary level keys are available in Table 2

Tertiary Keys¶

Table 2: Reference table for MarCon project tertiary dictionary keys¶
Key	Definition
aa_donors	Avoidance Area Donors
aa_recipients	Avoidance Area Recipients
between_cent	Betweenness Centrality
conn_boundary	Connectivity as Spatial Dependency
eig_vect_cent	Eigenvector Centrality
fa_donors	Focus Area Donors
fa_recipients	Focus Area Recipients
google	Google PageRank
in_degree	In-Degree
inflow	In-flow
local_retention	Local Retention
min_plan_graph	Minimum Planar Graph (deprecated)
out_degree	Out-Degree
outflow	Out-flow
self_recruit	Self-Recruitment
stochasticity	Temporal Connectivity Covariance