filter_time_points function, incid_ct fix-tim sim

percolations.py
- added filter_time_points function to grab
the time steps at which a certain percent of
the cumulative epidemic size has been infected;
filter_time_points will be used to clear noise
at the beginning and end of the epidemic for
OR, which is a result of the small number of
infections at the beginning and end of an
epidemic
- episim_age_time function was changed to keep
track of incidence correctly; it now counts changes
from S to I, whereas before, it had been counting
changes from I to R
- prior time sims need to be redone
epiOR_filt charts corrected output for timesteps

percolations.py
episim_age_time_function
- cumulative percentiles on which to filter OR
time points are set to 0.2 and 0.8
- filtered_ORlist had infection filter percentiles
instead of time steps at which epidemic had infected
the infection filter percentiles cumulatively, which
 was causing the charts to display incorrectly

age_perc_T_time.py
- number of simulations changed

age_perc_T_time_viz.py
- label of filtered chart now shows cumulative
infection filter percentiles
filtered OR sim figures - changed axes

age_perc_T_time_viz.py
- commented out save for all plots except
filtered OR plots
- show OR by time plot to clear all previously
drawn plots that were commented out (allows
filtered OR plots to be drawn correctly)
- filtered OR plot: shortened y-axis to be able
to better see trends
save time sim infected and recovery tstep results

percolations.py
- episim_age_time function no longer returns binary
list of infections over time simulation
- episim_age_time function now returns list of
infection time step and recovery time step

age_perc_T_time.py
- changed percolation function returns to fit
perc.episim_age_time
- save infection tstep and recovery tstep to
file

pretty_print.py
- added print_sorteddlist_to_file function
because order of simulations matters for infection
and recovery tsteps -- we want the infection
and recovery tstep files to be comparable, such
that row 1 (ie. sim 1) is the same in both files

age_perc_T_time_viz.py
- not sure what changes were made
- plotting should not be different in this file yet
align time-based sim results by epitime

Epidemic time is defined as the alignment of tsteps
at which sims attained 5% of cumulative infections
during the epidemic.

age_perc_T_epitime_viz.py
- new viz script that aligns results on epitime
- relies on pickled data and saved results
- recreates child and adult incidence from Itstep
saved results file from simulations
- chart1: filtered and aligned OR over time
- chart2: filtered and aligned OR over time overlaid
with child and adult incidence over time aligned

percolations.py
- define_epi_time: new function
---> identifies tstep that should be aligned and
returns a dict with a list of 5% tsteps for each
sim where beta value is key
- recreate_incid: new function
---> recreates child and adult incidence from
Itstep results file
---> returns dict with simnumber and age class
as key and incidence at each tstep for a single
sim
finished docstring for recreate_incid

percolations.py
- edited docstring for recreate_incid function
zip results and figures produced from simulations

age_perc_T_time.py
age_perc_T_time_viz.py
- saved results and figures in hierarchical ziparchive

pretty_print.py
- compress_to_ziparchive: new function
---> writes file in folder into ziparchive
---> Figures and results will be in folder AND
in ziparchive. Delete figs and results in
folder manually once no longer needed.