rename cmfpt folder and update README

README.md

@@ -1,14 +1,20 @@
 This repository contains code to compute the dynamic segregation
 indices based on Class Mean First Passage Times (CMFPT) and Class
-Coverage Times (CCT), as explained in the paper:
+Coverage Times (CCT), as explained in the paper:  
 
-  A. Bassolas, S. Sousa, V. Nicosia
-  "Diffusion segregation and the disproportionate incidence of 
-   COVID-19 in African American communities", Journal of The Royal
-   Society Interface, 
+>  A. Bassolas, S. Sousa, V. Nicosia
+>  "Diffusion segregation and the disproportionate incidence of
+>  COVID-19 in African American communities", Journal of The Royal
+>  Society Interface (in press)."
 
-The code can be copied, used, modified, and redistributed under the 
-terms of the MIT/Expat License. Please see the file LICENSE for 
-additional details. 
+The code can be copied, used, modified, and redistributed under the
+terms of the MIT/Expat License. Please see the file LICENSE for
+additional details.
 
+The data used to run the simulations is freely available at the
+[DRYAD][1] repository and follows the
+formatted supported by the scripts. Please note that references
+to files and folders in the instructions here consider the data
+at the [DRYAD][1] repository.
 
+[1]: https://datadryad.org/stash "DRYAD"

cct/README.md

@@ -1,9 +1,16 @@
+# Data
+
+The reader interested in using the formatted data used on the simulations
+can obtain a copy at the [DRYAD][1] repository.
+References to files and folders consider the data available at the
+repository.
+
+
 # Obtaining the edge-list and node properties for CCT data  
 
-At the repository mentioned at the beginning, the reader will find the script
-`get_adjacencies_connected.py` which returns the edge-list and the nodes
-properties (ethnicity distribution) of the largest connected component. The
-script takes the following inputs:
+The script `get_adjacencies_connected.py` returns the edge-list and the nodes
+properties (ethnicity distribution) of the largest connected component. It
+takes the following inputs:
 
 > shape:     Shapefile of the census tracts at country extent  
 > code_name: The loop uk code (GISJOIN) string to match the tracts  
@@ -13,10 +20,11 @@ script takes the following inputs:
 Obtaining the individual CSV file for each CSA is trivial and can be obtained
 either by filtering the data by the `CSAA` field using the preferred editor or
 using a library such as pandas in python to group rows by the column. The
-CSV files from this process are available in the folder `census_ethnicity_csa`.
+CSV files from this process are available in the folder `census_ethnicity_csa`
+at [DRYAD][1].
 
 The resulting file with the node properties is named by convention
-`nodes_ethnics_agg_censustract_csa_XXX` where XXX refers to the CSA numeric
+`nodes_ethnics_agg_censustract_csa_XXX` where `XXX` refers to the CSA numeric
 code. The column containing the total population was removed so that the output
 file contains:
 
@@ -29,7 +37,12 @@ file contains:
 > Some Other Race;  
 > Two or More Race'  
 
-Note that the `GISJOIN` field is not the same as `GEOID10`, for merging data from NHGIS `GISJOIN` field must be used.
+Note that the `GISJOIN` field is not the same as `GEOID10`, for merging data
+from NHGIS the `GISJOIN` field must be used. The definition of each CSA for
+the adjacency data is available in the file `csacodes_adjacency.csv` and it
+contains the CSA numeric code, description and state. For CSA definitions of
+the commute data please consult the file `csacodes.txt` at the MFPT folder
+in [DRYAD][1].
 
 Edge-list details:
 * Node IDs are defined by the row index of the population table
@@ -48,30 +61,40 @@ script `rw_cct_ctime_jsd.py` and the following input must be provided:
 > epsilon: Threshold value for the JSD divergence;  
 > idx:     range of nodes or single node ID to run the walk from, e.g.: 1, 0-10.  
 
-All the files provided here in this repository are already in input format
+All the files provided in [DRYAD][1] are already in the input format
 needed by the script. An output file for each node will be saved locally at
 the same directory where the code is being executed and follows the format:
 ```
 "Ethnicity" "Time to reach epsilon"
 ```
+where each line corresponds to one repetition of the random walk from node i.
+
 The commute network uses the `rw_cct_ctime_jsd_directed.py` script and the
 corresponding files in the "commute" folder should be used.
 
-
 ---
 
-## List of files in the CCT repository
+## List of files in the DRYAD CCT repository
 
 **Adjacency:**
 
+Adjacency:
 - edges_ids_censustract_csa_XXX: Edge-list with the assigned numeric ID
-- edges_geocode_censustract_csa_XXX: Edge-list with the GISJOIN codes
 - nodes_ethnics_agg_censustract_csa_XXX: Node properties associated with the census tract
+
+Suplementary files:
+- edges_geocode_censustract_csa_XXX: Edge-list with the GISJOIN codes
 - nodes_id_geocode_XXX: Look up codes for node IDs to GISJOIN
 - ethnics_agg_censustract_csa_XXX: Original CSV file with ethnicity data
 
+
 **Commute:**   
-*Note that the commute data here corresponds to the same used on the **MFPT** folder being changed only for convenience to run the `CCT` random walk.*
+*Note that the commute data in the CCT folder corresponds to the same used in
+**MFPT** where reformatting was used for convenience only to run the `CCT`
+random walk.*
 
 - colorethmix_XXX: Node properties
 - network_XXX: Edge-list with the corresponding edge weight
+
+
+[1]: https://datadryad.org/stash "DRYAD"