dynamAedes.m {dynamAedes} | R Documentation |

## Life cycle simulation of *Aedes* mosquitoes

### Description

Function to simulate population dynamics of *Aedes* mosquitoes

### Usage

```
dynamAedes.m(
species = NULL,
intro.eggs = 0,
intro.deggs = 0,
intro.adults = 0,
intro.juveniles = 0,
scale = NULL,
intro.cells = NULL,
jhwv = NULL,
temps.matrix = NULL,
startd = 1,
endd = NA,
cells.coords = NULL,
coords.proj4 = NA,
lat = NA,
long = NA,
road.dist.matrix = NULL,
avgpdisp = NA,
pDispersal = TRUE,
iter = 1,
n.clusters = 1,
cluster.type = "PSOCK",
compressed.output = TRUE,
suffix = NA,
cellsize = 250,
maxadisp = 600,
dispbins = 10,
verbose = 0,
seeding = FALSE
)
```

### Arguments

`species` |
character. Select what species to model: |

`intro.eggs` |
positive integer. number of introduced eggs, default |

`intro.deggs` |
positive integer. number of introduced diapause eggs, default |

`intro.adults` |
positive integer. number of introduced adults, default |

`intro.juveniles` |
positive integer. number of introduced juveniles, default |

`scale` |
character. Define the model spatial scale: punctual/weather station "ws", local "lc", or regional "rg". Active and passive dispersal is enabled only for |

`intro.cells` |
positive integer. One or more cells (id) where to introduce the population at local ("lc") scale. If intro.cells=NULL, then a random cell is used for introduction; If intro.cells is a vector of cell ids then a cell is drawn at random from the vector (with repetition) for introduction in each model iteration. |

`jhwv` |
positive integer. Juvenile-habitat water volume, define the volume (L) of water habitat presents in each spatial unit (parametrised with data retrieved from doi:10.1111/1365-2664.12620). Default |

`temps.matrix` |
matrix. A matrix of daily (average) temperatures (in degrees |

`startd` |
Character date (ISO format "%Y-%m-%d"). Date of start of simulations. |

`endd` |
Character date (ISO format "%Y-%m-%d"). Date of end of simulation. It can be |

`cells.coords` |
matrix. A matrix reporting the spatial coordinates of the temperature observations. |

`coords.proj4` |
string. Proj4 string of cell coordinates used for the calculation of photoperiod. |

`lat` |
numeric. Latitude value of the area of interested used to derive the photoperiod (and thus the diapause eggs allocation function). |

`long` |
numeric. Longitude value of the area of interested used to derive the photoperiod (and thus the diapause eggs allocation function) |

`road.dist.matrix` |
matrix. when |

`avgpdisp` |
optional. when |

`pDispersal` |
boolean. if TRUE (default) then the model considers passive dispersal. |

`iter` |
positive integer. Define the number of model iterations. |

`n.clusters` |
positive integer. Defines the number of parallel processes. |

`cluster.type` |
character. Defines the type of cluster, default "PSOCK". |

`compressed.output` |
logical. Default TRUE, if FALSE provide abundance for each model's subcompartiment; if FALSE abundances are summed per compartment. |

`suffix` |
character. Model output suffix for output RDS. |

`cellsize` |
positive integer. When |

`maxadisp` |
positive integer. When |

`dispbins` |
positive integer. When scale = "lc", defines the resolution of the active dispersal kernel, default dispbins = 10. |

`verbose` |
integer. if 1 then an overview of population dynamics is printed in the console, if 2 more information on population dynamics are printed out. Default is 0 (silent). |

`seeding` |
logical, default |

### Value

Matrix or a list of matrices containing, for each iteration, the number of individuals in each life stage per day (and for each grid cell of the study area if scale="lc" or "rg"). If the argument compressed.output=FALSE (default TRUE), the model returns the daily number of individuals in each life stage sub-compartment.

### Author(s)

Matteo Marcantonio marcantoniomatteo@gmail.com, Daniele Da Re daniele.dare@uclouvain.be

### See Also

Beta regression functions were taken from the R package `aomisc`

, which may be available at https://github.com/OnofriAndreaPG/aomisc.

### Examples

```
## Run dynamAedes at local scale for 5 days
# Make a toy temperature time series
w <- matrix(seq(20,25,length.out=5),ncol=5)*1000
# Run the model
simout <- dynamAedes.m(
species="koreicus",
scale="ws",
intro.eggs=10,
jhwv=2,
temps.matrix=w,
startd="2021-06-21",
endd="2021-06-25",
lat=42,
long=8,
n.clusters=1,
iter=1,
compressed.output=TRUE,
verbose=FALSE)
```

*dynamAedes*version 2.2.9 Index]