model_run_new: God i don't know hopefully this will work. This version does...

In beeysian/cairnsmozzie: Agent-based model of Wolbachia release in a nice tidy package

Description

God i don't know hopefully this will work. This version does NOT run microclimates. Input is the ABC parameters Output are vectors of interest over time.

Usage

model_run_new(lambda, k, phi, alpha_a, alpha_j, eta)

Arguments

lambda	Shape param for dispersal
k	Parameter for mating
phi	Parameter for trapping
alpha_a	Mortality rate of adult mosquitoes
alpha_j	Mortality rate of juvenile mosquitoes
eta	Clutch size of each egg-laying event. Option to select either high, low, or medium fixed values for each parameter comment this all out after the plots are done. low = -1, medium = 0, high = 1. Mid parameters: End mid parameters Low parameters: End low parameters High parameters: End high parameters This section sets up alternative temperature deviate setup methods —- There are three alternative TD setups for testing purposes: 1) TDs assigned uniformly at random 2) TDs assigned proportionally randomly to how frequently they appear in the "realistic" microclimates setup 3) The grid is partitioned into the different land types, where the size of each partition is proportional to how frequently they appear in the "realistic" microclimates setup. (The order that the partitions appear in is randomly generated). There are three function that do the above. The "tempdev_type" variable can be changed to 0 (keep realistic), 1 (option 1), 2 (option 2) and 3 (option 3). The functions assign land type, then we match it to the associated temperature deviate below. End alternative temperature deviate methods —- —- Set WD for saving graveyard —- Each row will be a timestep, each column will be the time each step takes PLUS the number of agents. ———————— ADDED 12/11/20: EGG HATCH RATE OF 0.8 AS PER PERRAN ROSS This won't error if length(to.adult) == 0 hopefully ———————— 22-09-20: reduce proportion of females laying eggs per day: CHECK ADDED 14/11/20: MAKING JUV DEATH RATE HIGHER FOR THOSE WITH WB add to graveyard remove from mozzie dataframe TESTING 05/11/20: RELEASED ADULTS WITH HIGHER DEATH RATE HHHHHHH ——– END TESTING 05/11/20 HHHH ———————- Begin Step 6 Take 2: a faster way to update microclimates —- For adults/mozzie.dt: everyone has the same EKS update! For juveniles, it's a little bit more involved: Get the temperature deviate for each mozzie Apply the temperature deviate to today's temperature and then convert to Kelvin This is the temperature that will then be fed into the EKM Find EKS score first: for adults, stage = 4 Find the EKS for each adult for today Add to the current enzyme now: for juveniles DOBULE CHECK the below works.... commented the below out 7/1/20 End Step 6 Take 2 :) dataframe for optimisation: MATING ATTEMPT NUMBER 3...... I S2G THIS HAS TO BE THE LAST TIME we do a vectorised for loop. the find_a_mate function works on one agent at a time. Get a list of females who can mate. There's a ~30 apply function to find mates Update female's mate ID Update male's gonoCycle Set up stuff to get graveyard data end graveyard data capture data save graveyard as a csv

beeysian/cairnsmozzie documentation built on Feb. 15, 2021, 12:12 a.m.