defines the activity patterns of vectors and hosts

def_activity_patterns This function creates an object that contains information about mosquito and human activity: the biting rhythms of the mosquitoes and the times when humans are indoors or in bed.

def_activity_patterns(activity = "default_Anopheles_gambiae")

Arguments

activity

can be either a string corresponding to default entries: "default_Anopheles_gambiae", "default_Anopheles_albimanus" or a list object with the following attributes:

  • HBI: ID or proportion of human biting indoors

  • HBO: ID or propotion human biting outdoors

  • humans_indoors: ID or proportion of humans indoors

  • humans_in_bed: ID or proportion of humans in bed

These attribues can be either vectors with the corresponding values at each time point, or an ID corresponding to an entry in the package database object activity_patterns. The function list_activity() can be used to retrieve the available entries for all or specific geographical locations.

Value

list object with the time series attributes:

  • HBI: proportion of human biting indoors

  • HBO: propotion human biting outdoors

  • humans_indoors: proportion of humans indoors

  • humans_in_bed:proportion of humans in bed

Author

Monica Golumbeanu, monica.golumbeanu@unibas.ch

Olivier Briët

Nakul Chitnis, nakul.chitnis@unibas.ch

Tom Smith, thomas.smith@unibas.ch

Examples

# Retrieve default human and mosquito activity patterns
default_rhythms = def_activity_patterns("default_Anopheles_gambiae")
print(default_rhythms)
#> $HBI
#>  [1] 0.000000000 0.000000000 0.000491400 0.000491400 0.005896806 0.007862408
#>  [7] 0.028009828 0.048157248 0.068304668 0.066339066 0.062899263 0.062899263
#> [13] 0.070270270 0.077641278 0.000000000 0.000000000
#> 
#> $HBO
#>  [1] 0.000000000 0.000000000 0.000982801 0.000982801 0.003931204 0.025061425
#>  [7] 0.042260442 0.056019656 0.073710074 0.077149877 0.077149877 0.073710074
#> [13] 0.038329238 0.031449631 0.000000000 0.000000000
#> 
#> $humans_indoors
#>  [1] 0.00000000 0.28380952 0.61904762 0.84761905 0.96190476 1.00000000
#>  [7] 1.00000000 1.00000000 1.00000000 1.00000000 1.00000000 1.00000000
#> [13] 0.96190476 0.00952381 0.00000000 0.00000000
#> 
#> $humans_in_bed
#>  [1] 0.0000000 0.0000000 0.0000000 0.2271333 0.6666333 1.0000000 1.0000000
#>  [8] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.8833167 0.2006667
#> [15] 0.0000000 0.0000000
#>