runModel: Run mosquito population model.

In sihoward/mossiemodel-dev: Temperature-dependent mosquito population model

Run mosquito population model.

Description

Run mosquito population model.

Usage

runModel(
  burnin.dates = seq(as.Date("2019-07-01"), as.Date("2020-06-30"), 1),
  burnin.reps = 100,
  run.dates = seq(as.Date("2020-07-01"), max(temp_seq$Date), 1),
  temp_seq = temp_seq[c("Date", "Tmean")],
  b = 100,
  alpha = 0.073,
  beta = 0.0315,
  K_L = 2710200,
  M_max = 1000060,
  MTD = 7.783,
  L_1 = 0,
  L_2 = 0,
  L_3 = 0,
  L_4 = 0,
  L_5 = 0,
  M = 100,
  Mfloor = 100
)

Arguments

burnin.dates	Trim temperature time series to these dates for burn-in.
burnin.reps	Repeat burn-in temperature time series n times.
run.dates	Run temperature time series at these dates after burn-in.
temp_seq	temperature time series
b	number of female eggs per clutch
alpha	adult mortality rate (1/days)
beta	larval mortality rate (1/days)
K_L	larval carrying capacity (numbers/km^2)
M_max	max adult density
MTD	minimum temperature for mosquito development)
L_1	Initial instar densities (1-5)
L_2	see above
L_3	see above
L_4	see above
L_5	see above
M	Initial adult density
Mfloor	Minimum adult density

Examples

library(mosqmod)

# load stored temperatures
temperatures <- data.frame(mosqmod::saved_station_temps)
temperatures <- subset(temperatures, Station == "Dunedin, Musselburgh Ews")

# append temperatures (requires 'cliflo_usrid' & 'cliflo_pwd' environment
# variables to be set if not using request = FALSE)
temp_seq <- mosqmod::append_TempSeq(temp_stored = temperatures, request = FALSE)

# format sequence (fill gaps, format dates etc. )
temp_seq <- formatTempSeq(d = temp_seq)

# get projected temperatures from calendar day mean temperatures

calendar_day_mean_temps <- getCalendarDayMeans(temp_seq)

temp_projected <- project_TempSeq(temp_seq = temp_seq, extend_days = 90,
                                  lookback_days = 90,
                                  calendar_day_mean_temps)

# add projected temperatures
temp_seq <- dplyr::bind_rows(temp_seq, temp_projected)

# run model
res <- runModel(temp_seq = temp_seq,
                burnin.dates = seq(as.Date("2016-07-01"), as.Date("2017-06-30"), 1),
                run.dates = seq(as.Date("2020-07-01"), max(temp_seq$Date), 1))
## Not run: 
mosqmod::plot_popn(resdf = res, include_temp = TRUE, selectPopn = "M")

## End(Not run)

sihoward/mossiemodel-dev documentation built on June 1, 2025, 6:12 p.m.