explicitly add T values

age_time_T.py
- add T value range variables and use to define beta
first commit: reduce adult suscep to mimic mild

age_time_suscep.py
- run time-based simulations that reduce susceptibility
of adults in steps of 0.1 from 1 to 0

age_time_suscep_viz.py
- plot OR by time, filtered OR by time, OR by suscep,
incidence by time, prevalence by time, episize by
suscep

age_time_suscep_epitime_viz.py
- filter and align OR at tstep where sim reaches 5% of
total episize
- overlay incidence and filtered/aligned OR
add recreate incidence and suscep beta functions

percolations.py
- recreate incidence from the Itstep results file
- calculate beta for nodes that have less than one
susceptibility values
first commit: store basic reusable network fxns

network_functions.py
- calc_Tc: calculate T_critical for a given network
- calc_Tavg: return avg T value applied to entire network
when susceptibility differs in adults
changed params to explore diff bw perc & time sims

age_time_T.py
age_time_T_viz.py
age_time_suscep.py
age_time_suscep_epitime_viz.py
age_time_suscep_viz.py

Time-based simulations were getting much
larger epidemics sizes than what was
expected from analytical model and percolations.
update new infections at end of tstep

percolations.py
- update new infections and recoveries at end
of time step instead of during the time step
- fixed the error where T = 0.0643 was
producing 30% epidemic sizes instead of 20%
epidemic sizes as expected from percolation
and analytical model

age_time_T.py
- added T1, T2 = 0.0643, 20% episize T value
time sim return only infection & recovery tsteps

percolations.py, age_time_T.py
- return only episize, infection tstep and
recovery tstep
- move all other data processing steps to
age_time_T_viz.py and age_time_T_epitime_viz.py
to streamline and shorten simulation function
data processing moved to viz time sim code

age_time_T_viz.py
- add data processing to front of viz code

pretty_print.py
- no changes to code

perclations.py
- I_tstep and R_tstep_savelists changed to
0 as baseline
age data processing and start of dict generation

age_time_T_viz.py
- added age data processing to beginning
- need to test if data processing step works

age_time_T_epitime_viz.py
- minor changes
data processing added to viz and epitime viz codes

still need to perform major cleanup of all codes for
readability but all of the codes are integrated with
each other

age_time_T.py
- need to remove unused data structures
- need to remove commented out pickle and epiOR data
- minimalist code: runs simulation and saves infection
and recovery tsteps to files in ziparchive

percolations.py
- episim_age_time_susc needs to be updated for new
time sim format
- all other functions that are commented out are in
line to be phased out from time simulation usage
- filter_time_points2 is updated from filter_time_
points to work with episim_age_time function
- episim_age_time function is minimalist and retains
states dictionary for tracking infection
- recreate_epidata function is the primary data
processing function used at the beginning of all
viz codes; returns incidence, OR, results, AR,
and filtered OR dictionaries for epidemic sims only
- patient zero identity and count in incidence is
lost

age_time_T_viz.py
- data processing added to beginning of code
- plots are integrated to work with newly created
dicts and their keys
- epiORtot and epipreval chart functionality is
lost because these are not performed in data
processing.. yet

age_time_T_epitime_viz.py
- data processing added to front of code
- use epiAR dictionary to draw attack rates in
epiORincid chart instead of recreate_incid
function which is now obsolete
- changed x-axes limits
- dict keys changed to reflect new dict structures
add timers, clean and rm comments, timesims run

age_time_T_vix.py
- added comments about dicts created in data
processing step
- added clocks to time data processing (ranges
from 5-45 sec per beta)
- changed plot axes and 5-95% cum infections
for OR filter

age_time_T_epitime_viz.py
- added comments about dicts in data processing
- added clocks to time data processing
- plotting time
- increased incidence Y-axis
- implementation of incidence per 100 is in viz
code instead of in epiincid dict as before

age_time_T.py
- rm comments about how to organize data processing

percolations.py
- rm comments that are unnecessary
- changed filter time point params to 5 & 95% cum
incidence
- np.cumsum implemented where appropriate
change parameters, rm pickles

age_time_T.py
age_time_T_epitime_viz.py
age_time_T_viz.py
- changed parameters to draw charts for different
results
- removed comments for pickling dicts
- removed unneeded packages and modules
child suscep, improve sim efficiency, rm dicts

age_time_suscep.py
- changed parameters - 5 day recovery
- instead of reducing adult suscep as before, increase child
susceptibility relative to all other age groups in steps of
0.1 from 1 to 1.5
- d_age_suscep now accepts age class codes as strings
instead of ints
- add clocks to time different processes
- return only I_tstep and R_tstep from time simulation
- generate reference table for probability of infection
for each susceptible depending on number of infected
contacts (before adjusting for differential susceptibility
values)

percolations.py
> episim_age_time_susc function
- 0 instead of nan for I_tstep and R_tstep when node is not
infected
- update infections at end of time step instead of immediately
- make efficient list comprehensions
> filter_time_points function
- may now be obsolete since suscep time sim no longer filters
time points
> calculate_beta function
- not needed in current implementation of suscep sims
because beta is constant for all individuals; suscep is
multiplied by a susceptible's total probability of getting
at least one infection at each time step
ignore Test/ folder in .gitignore
realign epitime, clean comments

age_time_T_epitime_viz.py
- reassign avg_align_tstep to 0 to draw filtered charts
starting at t=0

age_time_T_viz.py
- clean comments
suscep sims and plots running

age_time_suscep.py
- change parameters for sim

age_time_suscep_viz.py
- change parameters for sim

age_time_suscep_epitime_viz.py
- change parameters for sim
- adjust plotting
- update dicts to accept three item tuple key

percolations.py
- add comments

age_time_T_epitime_viz.py
- minor
no major changes
main code and sim fxn to run realparam time sims

age_time_realistic.py
- main code for realistic time sims
- outputs I_tstep and R_tstep files in zipfile
- real parameters based on Cauchemez 2004

percolations.py
> episim_age_time_realistic function
- real parameters based on Cauchemez 2004
- age-specific sigma, beta, and gamma values, where
non-children are the base value and children have
a larger sigma, beta, and gamma
- children and non-children have different suscep
and recovery parameters and so are considered differently
- sigma is the susceptibility of the individual and
acts as a multiplier in front of P(susceptible
is infected >= 1 times during the time step)
> prob0infections function
- calculate probability of 0 infections for a
single node where children and non-children
neighbors have different beta values
- pairs with episim_age_time_realistic function
results filename has txt extension

age_time_realistic.py
- typo in filename saved Itstep and Rtstep files
as zip instead of txt
yaxis of OR=1 line simplified

age_time_suscep_viz.py
- unnecessary len(xrange(250)) term changed to 250
so for drawing OR line in epiOR and epiORfilt plots