run_rot: run_rot to run simulation of the effect of rotations on the...

In ian-hastings/rotations: Simulating the Evolution of Insecticide Resistance under Rotations

Description

can run any number of insecticides/loci

Usage

run_rot(
  max_gen = 200,
  n_insecticides = 4,
  start_freqs = 0.01,
  rot_interval = 0,
  mort_or_freq = "freq",
  mort_thresh = 0.9,
  freq_thresh = 0.5,
  migration = 0.01,
  coverage = 0.8,
  start_insecticide = 1,
  expo_hi = 0.8,
  expo_lo = 0,
  male_expo_prop = 0,
  eff = 0.95,
  dom_sel = 0.5,
  dom_cos = 0.5,
  rr = 0.5,
  cost = 0.1,
  fitSS = 1,
  min_rwr_interval = 0,
  change_interval = 10,
  no_r_below_start = FALSE,
  no_r_below_mut = FALSE,
  exit_rot = FALSE,
  min_gens_switch_back = 0,
  plot = TRUE,
  diagnostics = FALSE,
  logy = NULL,
  add_gens_under50 = FALSE,
  plot_mort = NULL
)

Arguments

max_gen	maximum number of mosquito generations to run the simulation
n_insecticides	number of insecticides (and hence loci)
start_freqs	starting frequencies of resistance either one per insecticide or same for all
rot_interval	frequency of rotation (in generations) if set to zero means sequence, i.e. change when threshold reached
mort_or_freq	whether threshold for insecticide change is mortality 'mort' or resistance frequency 'freq'
mort_thresh	mortality threshold for switching insecticides, default 0.9, only used if mort_or_freq is mort
freq_thresh	resistance frequency threshold for switching insecticides, default 0.5, only used if mort_or_freq is freq
migration	migration rate between treated & untreated areas 0-1. We assume that immigration=emigration.
coverage	proportion of mosquitoes that are covered by the intervention (and 1-C is the proportion of the population in the untreated refugia), if coverage set to 1 no refugia.
start_insecticide	which insecticide to start with
expo_hi	proportion of females exposed to insecticide in hi niche, either single or vector of 1 per insecticide
expo_lo	optional proportion of females exposed to insecticide in lo niche, either single or vector of 1 per insecticide
male_expo_prop	proportion that males are exposed relative to f, default 1, likely to be <1 (could possibly be a vector per insecticide)
eff	effectiveness propn. SS killed by insecticide, one value for all insecticides or individually
dom_sel	dominance of selection, for all insecticides or individually
dom_cos	dominance of cost, for all insecticides or individually
rr	resistance restoration, how much resistance restores fitness of RR in presence of insecticide, for all insecticides or individually
cost	fitness cost of RR in no insecticide, for all insecticides or individually
fitSS	fitness of SS if no insecticide, usually assumed to be 1, for all insecticides or individually
min_rwr_interval	minimum rotate-when-resistant interval to stop short switches, only used when rot_interval==0. set to 0 to have no effect.
change_interval	interval that insecticide can be changed on for both rotation and sequence, default 10 gens 1 year
no_r_below_start	to stop resistance frequencies going below starting values TRUE or FALSE, beware can cause odd results
no_r_below_mut	to stop resistance frequencies going below mutation-selection balance TRUE or FALSE
exit_rot	whether to exit rotation interval if threshold is reached
min_gens_switch_back	minimum num gens before can switch back to an insecticide
plot	whether to plot results
diagnostics	whether to output running info
logy	whether to use log scale for y axis
add_gens_under50	whether to add a label of num generations under 50 pcent resistance
plot_mort	whether to add mortality to plots

Value

dataframe of results

Examples

run_rot(rot_interval=100)
dfr <- run_rot(rot_interval=50, max_gen = 300)
dfr <- run_rot(rot_interval=0, max_gen = 300)
dfr <- run_rot(rot_interval=0, max_gen = 300, migration=0.01)
#running for insecticides with different inputs
dfr <- run_rot(n_insecticides=3, eff=c(1,0.6,0.4), rot_interval=0)

ian-hastings/rotations documentation built on Dec. 14, 2020, 11:42 p.m.