NPHZ_V Codebase
Reproducible Results Scripts and Data
Creative Commons License BY 4.0
https://creativecommons.org/licenses/by/4.0/
Copyright 2014
Joshua Weitz
jsweitz@gatech.edu

Weitz home page
http://ecotheory.biology.gatech.edu

ISME J article
http://www.nature.com/ismej/journal/vaop/ncurrent/abs/ismej2014220a.html

Summary:
This series of scripts can be used to recapitulate all results
in the manuscript.  Note that due to the use of stochastic sampling,
the exact set of results may vary, but not the statistical properties
thereof.  The scripts should be used in the following series of steps:

Step 0, add the correct paths
Load Matlab in this directory
>> addshared_path
Then change directories, as appropriate

Step 1, perform large-scale computation (optional)
-- This code is the analysis subdirectory
-- If you want to skip this step, note that you can use the
   pre-computed data in the data subdirectory
-- Step 1a may take several hours to complete on a desktop/laptop
-- Step 1b should take a few minutes to complete on a desktop/laptop


1a. Perform a nonlinear search for "targeted" parameters (optional).
These results will be stored as:

<targeted.mat>

1b. Perform a LHS sampling of parameter space for "feasible" parameters.  
These results will be stored as:

<param_search_results_flux_LHS.mat>

1c. Place these .mat files in the data directory 
(which is pre-loaded with siminfo_details.mat)

Note - MATLAB will report different types of "warnings", e.g.,

"fmincon stopped because it exceeded the function evaluation limit
options.MaxFunEvals  = 1000 (the selected value)."

or

"fmincon stopped because the size of the current step is less than the
default value of the step size tolerance and constraints are satisfied to
within the default value of the constraint tolerance."

These are normal operations of the minimization procedure.

Step 2, generate figures

* Run figstab_unstab_compare.m
-- Generates stability_solution_analysis.mat
-- Does the stability analysis (Figure SX)

* Run figdists_wv.m
-- Generates Figure 2

* Run master_pipeline_targets.m
-- Generates ss_flux_target.mat

* Run figtarget_fluxes_v2
-- Generates Figure 3

* Run figtarget_fluxes_pvals_v3
-- Generates Figure SX (parameter value bar codes)

* Run figdists_wv_nov_contours_targets.m
-- Generates Figure 4

* Run master_pipeline_taus.m
-- Generates ss_flux_tau_target (with the turnovers)

% Run figcomm_comp_twostack_targets
-- Generates Figure 5 (community structure)

% Run the four export figures
figflux_export_contours_targets_labels.m  
figflux_oreturn_contours_targets_labels.m
figflux_primprod_contours_targets_labels.m
figflux_cturnover_contours_targets_labels.m

% Run figbiomass_turnover.m
Generates biomass turnover in Figure S4

% Run fignpp_baseline.m
Generates NPP figure in SI