initial project version
Need to modify description of sigma
Surface plot entered 2nd commit matlab is freezing
version of combinedclient with sruface plot of varying z and r-transmission
child file committed right after surface plot obtained-runs epidemics
Complete surface plot 3D correct June 5 7:57PM
Comments contain notes from discussion with Nim on 9 June
All code working, but graphs don't make sense. "No" epidemics in tropics, entire graph coming from temperate region. Cannot be correct. Perhaps matrix error?
flucode2014v1.m-Oldest 2014 version-returns total tropical and temp epidemic sizes. Displays a large amount of graphs. Not intended for use with combined client. Not as current as flucode2014v3.

flucode2014v2.m_Returns equilibrium strain id instead of total tropical/temp epi sizes. Designed for use with birthrate_strainid_script_v1.m.

flucode2014v3.m_Most current of the first week's Matlab code. Returns final tropical and temp epi sizes (instead of total) as well as final strian id. Graphs can be switched on or off. Designed for combinedclient2014v1.m. Does not tkae into account seasonality or past infection hisotry (it's predecessors have the same limitation).

combined_client2014v1.m-Compares final tropical/temp epi sizes and mutation rate as a function of tropical and total vaccination rates. Uses flucode2014v3.m.

birthrate_strainid_script_v1.m-Compares final strain id as a function of birthrate. Use with flucode2014v2.m.

find_epi_size2D.m-Runs 2D SIR epidemic

find_epi_size_test_1.m-Test program to graph output of find_epi_size2D.m given different values of Meff.

mutationgraph.m-Test program to graph immune escape and fitness curves for different k values or weights.

negativeassign.m-Assigns a negative value to triples sent to it. Used with combinedclient2014v1.m. Need to change to use Not a Number instead of negative number so that result is not graphed in combinedclient2014v1.m.
latest versions of immune hsiotry files-not sure if it works-not tested yet-disregard earlier versions of these files evevn if they are committed later.
Old wokring combiend client-routine upload
Old initial attempts at immune history matrices-these do not work.
Latest working version of seasonsiality via immune history. Seasonality observed in epidemic sizes! H and B add up to 1 (which is good). Maybe check why antigenic distance graph plateaus at 1.
Working version of 1-region immune history, no seasonality. Use with strain_selection_history_3.m and set the k value to about 1.4.
Spacefill version
Working version as of evening on 6-24-2014-2 regions with immune history, temp region antigenic drift is not mapped. Use with strain_selection_history_3.m and k value of about 1.15.
This version may not work-this is just a save-as.
Same type as persion commit of v2 of immune history flucode 2014. Just a save as, not sure if it works
This is just a save-as-not sure if the code works or not. Give previous commits priority or test it out first.
Save as of old (either pre 2014 or pre-June 2014) flu code starter culture files which happened to be stored in the repository. Not sure what they are/how current they are.