README

Data and code for: Sullivan et al. 2021. Consequences of ignoring dispersal variation in 
	network models for landscape connectivity. Conservation Biology.
	
Contact Lauren Sullivan (sullivanll@missouri.edu) for assistance


The following contains code to run the general network model, and then the resulting
	output files (several cleaning steps have been omitted here because of the large size
	of the files).  There is also code to take those output files and create the figures 
	from the paper.



####################  Files


#### Data Files

1.  Prairie Patches in MN
		> "PrairieNearTable_4000m_Geodesic.txt" 
		> edge list of all edge-to-edge distance between each grassland in MN up to 
			4000 m.

	 		 ** Data dictionary for this file:
	  			- "OBJECTID": unique row number
	  			- "IN_FID": ID number for focal patch
	  			- "NEAR_FID": ID number of a neighbor patch within 4000m of the focal patch
	  			- "NEAR_DIST": the nearest distance between the focal patch (IN_FID) and 
	  							its neighbor (NEAR_FID)
	  			- "NEAR_RANK": rank number of neighbor patch to focal patch based on distance


2.  Results Files
	  Network Results	
		> "RESULTS_network_unweighted.txt"
		> "RESULTS_network_weighted_.01.txt"
		> "RESULTS_network_weighted_.0001.txt"
		> "RESULTS_network_weighted_.25.txt"

	 		 ** Data dictionary for these files:
	  			- "disp_dist": the distance d for the iteration
	  			- "no_comp": the number of components
	  			- "max_comp": the max number of components
	  			- "transitivity": the transitivity
	  			- "weighted": 1 = weighted, 0 = not weighted
	  			- "tailcutoff": tail cutoff value, 0.01 = 99% realized, etc.

	  
	  Patch Results - Degree
	  	> "RESULTS_summarized_degree_unweighted.txt"
	  	> "RESULTS_summarized_degree_weighted_.01.txt"
	  	> "RESULTS_summarized_degree_weighted_.0001.txt"
	  	> "RESULTS_summarized_degree_weighted_.25.txt"

	 		 ** Data dictionary for these files:
	  			- "disp_dist": the distance d for the iteration
	  			- "truncation": equivalent to tail cutoff, 0.01 = 99% realized, etc.
	  			- "mean_degree": mean degree value
	  			- "min": min degree value for all patches
	  			- "max": max degree value for all patches
	  			- "q10": degree value at 10th quantile
	  			- "q25": degree value at 25th quantile
	  			- "q50": degree value at 50th quantile
	  			- "q75": degree value at 75th quantile
	  			- "q90": degree value at 90th quantile
	  			
	  				  	
	  Patch Results - Closeness and Inverse Closeness
	    > "RESULTS_summarized_close_unweighted.txt"
	    > "RESULTS_summarized_invclose_weighted_.01.txt"
	    
	 		 ** Data dictionary for these files:
	  			- "disp_dist": the distance d for the iteration
	  			- "truncation": equivalent to tail cutoff, 0.01 = 99% realized, etc.
	  			- "mean_close": mean closeness value
	  			- "min": min closeness value for all patches
	  			- "max": max closeness value for all patches
	  			- "q10": closeness value at 10th quantile
	  			- "q25": closeness value at 25th quantile
	  			- "q50": closeness value at 50th quantile
	  			- "q75": closeness value at 75th quantile
	  			- "q90": closeness value at 90th quantile
	  	

	  	

#### Code Files

1.  network_code.R
		> Code for creating weighted and unweighted networks and calculating network and
			patch metrics.
		> Requires "PrairieNearTable_4000m_Geodesic.txt"
		> When trying to recreate everything, run this code first!
		
2.  figures.R
		> Code for recreating results figures 4 and 5 in the text
		> Requires all Results Files