wiesnerfriedman / FIT_FecalContamination

FIT_FecalContamination

These are the core functions needed to

1. Run the code to obtain the results for the manuscript, "Characterizing differences in sources and contributions to fecal contamination of sediment and surface water with the microbial FIT framework" (associated with the ID es-2022-00224x)

This can be run using the code, RunPaperResults.m

2. Run an example of the "Find" stage of FIT

This can be run using the code, FindExample.m

3. Run examples of the "Inform" stage of FIT with the Overland and River distance with Flow (ORF) model and the Ground hauling, Overland and River distance with Flow (GORF) spatial predictor models

This can be run using the code, InformExample.m

The original source data can be accessed publically via the sites described in the supporting information of the manuscript (See section S6). For data that is not publically accessible, you may request it from the organizations described in the supporting information of the manuscript (See section S6).

Here, we only include the code for obtaining the results of the manuscript. However, to run this code, data needs to be downloaded. The data can be downloaded from https://figshare.com/projects/Characterizing_differences_in_sources_and_contributions_to_fecal_contamination_of_sediment_and_surface_water_with_the_microbial_FIT_framework_DATA/133065

MATLAB Toolboxes that are needed to run the code:

1. Optimization Toolbox
2. Global Optimization Toolbox
3. Bioinformatics Toolbox

Also, I will note here that these functions have been tested in MATLAB version 2020b and up.

Different versions of this code:

version01

Functions added

• coord2dist.m
• FindExample.m
• FindSitesonNetwork.m
• GORFtinypartv2.m
• InformExample.m
• KewauneeObjectiveFunction1.m
• KewauneeObjFunLoad.m
• KewauneePenaltyFunction1.m
• KewauneePenaltyFunction2.m
• KewRoadDistanceMatrix.m
• PrecipitationObjectiveFunctionV2.m
• ReliabilityScore.m
• RunPaperResults.m
• sectionedcoord2dist.m
• sedc2.m
• sedc3.m
• sedc4.m
• SEDCparamOptim.m

version02

File changes

The file name being called to run the core functions was changed to "FITBacteroides.mat" for...

• FindExample.m
• InformExample.m
• RunPaperResults.m

Functions added

The following code was missing and was added:

• CVlinmdl2.m
• randinterval.m

MATLAB Toolboxes required

It was noted that the following MATLAB Toolboxes were required to run the code:

1. Optimization Toolbox
2. Global Optimization Toolbox

version03

Functions added

The following code was missing and was added:

• KewauneeSEDCresults.m

MATLAB Toolboxes required

It was noted that the following MATLAB Toolboxes were required to run the code:

1. Bioinformatics Toolbox