This document demonstrates how a few simple equations can simulate vector populations and insecticide resistance over time depending on the use of insecticides. Parameters within the simple equations can be modified to generate different patterns.
We intend to tweak the input parameters to generate reasonable scenarios. We are looking for assessment of the scenarios themselves rather than the input parameter values. The input parameters are simply a means by which we can generate reasonable scenarios.
In the following plots time is represented on the x axis, the top panel shows insecticide use, the middle panel shows vector population and the lower panel shows resistance (phenotypic). The code included is there merely to show us as developers how the scenarios were generated.
For an interactive version of the equations used to generate these plots see https://andysouth.shinyapps.io/shinyGame4.
#### load required packages require(resistanceGame)
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plot_sim( run_sim() )
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l_config <- read_config() l_config2 <- config_plan(l_config, t_strt=1, t_stop=20, control_id='irs_pyr') plot_sim( run_sim(l_config=l_config2) )
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l_config2 <- config_plan(l_config, t_strt=1, t_stop=20, control_id='irs_ops') plot_sim( run_sim(l_config=l_config2) )
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l_config2 <- config_plan(l_config, t_strt=seq(1,20,2), t_stop=seq(1,20,2), control_id='irs_pyr') plot_sim( run_sim(l_config=l_config2) )
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l_config2 <- config_plan(l_config, t_strt=seq(1,20), t_stop=seq(1,20), control_id=c('irs_pyr','irs_ops')) plot_sim( run_sim(l_config=l_config2) )
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l_config2 <- config_plan(l_config, t_strt=c(1,11), t_stop=c(10,20), control_id=c('irs_pyr','irs_ops')) plot_sim( run_sim(l_config=l_config2) )
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l_config2 <- config_plan(l_config, t_strt=c(1,11), t_stop=c(10,20), control_id=c('irs_pyr','irs_ddt')) plot_sim( run_sim(l_config=l_config2) )
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plot_sim( run_sim(randomness=0.5) )
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plot_sim( run_sim(randomness=0.5) )
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plot_sim( run_sim(randomness=0.1) )
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l_config2 <- config_plan(l_config, t_strt=1, t_stop=20, control_id='irs_pyr') plot_sim( run_sim(l_config=l_config2, resistance_modifier=0.1) )
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plot_sim( run_sim(l_config=l_config2, resistance_modifier=10) )
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l_config2 <- config_controls(l_config, control_id='new_ai', vector_id='an_gamb', control_kill_rate=0.4) l_config2 <- config_resistances(l_config2, control_id='new_ai', resistance_id="target_site", resistance_strength=0.8, resistance_incr=0.2, resistance_decr=0.1) l_config2 <- config_plan(l_config2, t_strt=1, t_stop=20, control_id='new_ai') plot_sim( run_sim(l_config=l_config2) )
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emergence = c(rep(0.5,6),rep(0,6)) plot_sim( run_sim(emergence=emergence, survival=0.7), plot_emergence=TRUE )
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emergence = seq(0.5,0,-0.05) plot_sim( run_sim(emergence=emergence, survival=0.7), plot_emergence=TRUE )
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emergence = c(rep(0.3,180),rep(0,180)) plot_sim( run_sim(num_tsteps=360,emergence=emergence, survival=0.7), plot_emergence=TRUE )
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emergence = c(rep(0.3,180),rep(0,180)) l_config2 <- config_plan(l_config, t_strt=c(1,181), t_stop=c(180,360), control_id=c('irs_ops','irs_pyr')) plot_sim( run_sim(l_config=l_config2, num_tsteps=360, emergence=emergence, survival=0.7, resist_incr=0.02, resist_decr = 0.01), plot_emergence=TRUE )
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Our generic approach allows us to specify any combination of controls and resistance mechanisms. The controls cause a specified kill rate(s) on specified vector(s). The resistance mechanisms specify which controls they apply to and how fast resistance increases and decreases in the presence and absence respectively of that control. Cross resistance can be specified simply by specifiying multiple controls for one resistance mechanism.
The relationships between vectors, controls and resistance mechanisms are specified in simple configuration files. Here is a simple example of a collection of such configuration files :
places <- read.csv( system.file('extdata','config1','places.csv', package='resistanceGame')) print(places)
vectors <- read.csv( system.file('extdata','config1','vectors.csv', package='resistanceGame')) print(vectors)
controls <- read.csv( system.file('extdata','config1','controls.csv', package='resistanceGame')) print(controls)
resistances <- read.csv( system.file('extdata','config1','resistances.csv', package='resistanceGame')) print(resistances)
control_plan <- read.csv( system.file('extdata','config1','control_plan.csv', package='resistanceGame')) print(control_plan)
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