In AndySouth/resistance: an insecticide resistance population genetics model with 2 loci and 2 insecticides

# options to create final publication quality figures
# causes the document to fail, but the figs do get stored in figs/
library(knitr)
opts_chunk$set(dev="tiff",
               dev.args=list(compression="lzw"),
               dpi=300,
               cache=FALSE,
               fig.path='figs/')

  library(resistance)
  library(ggplot2)

plot_fit_calc( simple=TRUE, effectiveness=0.8, resistance_restoration=0.5, dominance_restoration=0.6, dominance_cost=0.6, cost=0.3 )

TODO decide which of later figures to modify for pubhealth J paper

#2 panel fig A. sequence better, B. mix better

#eff1  0.4  0.8

# add side panels for labels
#layout( matrix(c(1:6,0,7,7,0,8,9),4,3, byrow = TRUE), heights=c(1,1,0.15,0.2), widths=c(0.1,1,1) )

layout( matrix(c(1:2,3,3),2,2, byrow = TRUE), heights=c(1,0.15), widths=c(1,1) )
#layout.show(n=3)


#eff1 0.4 seq better

#plot margins, hight t just a bodge to get graphs down closer to legend
par(mar=c(1.5, 4, 15, 0)) #b,l,t,r default c(5, 4, 4, 2)

runcurtis_f2( max_gen=500,  P_1 = 0.01 , P_2 = 0.01 , h.RS1_A0 = 0.5 , h.RS2_0B = 0.5 , exposure = 0.5 , phi.SS1_A0 = 0.4 , phi.SS2_0B = 0.5 , rr_restoration_ins1 = 0.5 , rr_restoration_ins2 = 0.5 , addCombinedStrategy = FALSE, strategyLabels = c('s','','a','m'), xlabs = TRUE, cex.axis = 0.8, addLegend=FALSE, main='', maxX = 140, labelMixSeqRatio = 1 )

mtext('A.',side=3, adj=0, line=1, cex=0.9) #side=1b,2l,3t,4r

#plot margins, hight t just a bodge to get graphs down closer to legend
par(mar=c(1.5, 4, 15, 0)) #b,l,t,r default c(5, 4, 4, 2)

#eff1 0.8 mix better
runcurtis_f2( max_gen=500,  P_1 = 0.01 , P_2 = 0.01 , h.RS1_A0 = 0.5 , h.RS2_0B = 0.5 , exposure = 0.5 , phi.SS1_A0 = 0.8 , phi.SS2_0B = 0.5 , rr_restoration_ins1 = 0.5 , rr_restoration_ins2 = 0.5 , addCombinedStrategy = FALSE, strategyLabels = c('s','','a','m'), ylab="", ylabs = FALSE, xlabs = TRUE, cex.axis = 0.8, addLegend=FALSE, main='', maxX = 140, labelMixSeqRatio = 1 )

mtext('B.',side=3, adj=0, line=1, cex=0.9) #side=1b,2l,3t,4r


#adding legend in lower panel
#plot margins
par(mar=c(0, 0, 0, 0), pty='m') #b,l,t,r default c(5, 4, 4, 2)

plot( 0, type="n", axes=FALSE, ann=FALSE, pty='m') 

legend( 'bottom', inset=0.1, legend=c("insecticide1 alone   ", "insecticide2 alone   ", "insecticide1 in mix   ", "insecticide2 in mix   "), col=c("red","blue","red","blue"), lty=c(2,2,1,1), pch=c(NA,NA,NA,NA), bty="n", cex=0.9, horiz =TRUE )

AndySouth/resistance documentation built on Nov. 12, 2020, 3:39 a.m.