fc: sick behavior sim & viz, sim_params reference

age_time_sickbehavior.py
- infected children and adults have a certain probability
of staying home from school or work, respectively
- tuning parameters: does behavior apply to children, adults,
or both? number of days delay before cutting contacts,
proportion of school/work contacts that are removed after
delay days have passed during infectious period (probability
of being an infected neighbor is adjusted)

simulation_parameters.py
- separate script for designating sim, plotting, processing,
and formatting parameters for simulations
- only pairs with sickbehavior simulations at the moment

percolations.py
- added sick behavior simulation and infected_neighbors_
sickbehav function

viz codes
- same sets of graphs as other sims, but no single
parameter is tuned; charts with tuned parameter were
replaced with histograms of the distribution of results
across the set of simulations for a single parameter set
sickbeh rules corrected for string value d_node_age

percolations
- d_node_age values are strings not ints, list
comprehension rules had referenced int values previously

viz codes
- plot labels are referenced in simulations_parameters

simulation_parameters
- different sims and plots were run
sickbehav- mult seeds, plots|no epi, print params

percolations.py
- episim_age_time_sickbehav function may be seeded
with multiple infections at t=0

sickbehavior viz codes
- control flow: don't draw plots if there were no
epidemics in the experiments

age_time_sickbehavior.py
- print parameters at beginning and end of script
for reference

simulation_parameters.py
- param value changes
fc: sims where prop of imm adults is tuned

age_time_immunity_prop.py
- given a proportion of the adult population, choose
adults randomly to have a fixed level of pre-existing
immunity

viz codes
- epitime_viz also has a chart with the mean retrospective
OR across a set of simulations
fc: sims with immune adults at fixed level

age_time_immunity_single.py
- given a fixed proportion of adults with pre-existing
immunity, tune the magnitude of immunity in equal steps

viz codes
- epitime_viz adds the mean retrospective OR plot
vs immunity value
sim fxns for immunity plots & mnretroOR calc

percolations.py
- mean_retro_OR function reports mean retrospective
OR values for each simulation based on the cumulative
incidence percentage at the start and end of the
retrospective period in the SDI data (averaged across
all seasons in the study)

simulation_parameters.py
- add parameters for mean retro OR calculation and
immunity simulations (single and prop set of sims)