library(SatTagSim) library(knitr) username = as.character(Sys.info()[7]) setwd(paste0('C:/Users/', username,'/Google Drive/PHD/COLLABORATIONS/SCRS_SIMS/')) # datadir = 'D:/SKYDRIVE_BACKUP/PHD_SIMS/SCRS_SIMS' mycol = colorRampPalette(c("lightcyan", "royalblue", "blue", "lemonchiffon", "orange", "red"), space = "Lab") load('sim_variance_WABFT.Rdata') load('../box4.Rda')
Confidence intervals were constructed for simulations by reducing the number of tracks simulated in a single run and increasing the number of runs to a statistically significant amount.
For each month, 84 fish were released at locaitons proportional to where they were observed that month in the tagging data (n = 1008/run). This was replicated 1000 times for a total of 1,008,000 simulated fish.
For each run, a movement probability matirx was constructed, for a total of 1000 matrices. For each cell in each matrix position, the mean, median, standard deviation and 95% confidence interval were derived. Confidence intervals were defined as the 2.5% - 97.5% range of the 1000 runs.
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ex7 = expand.grid(1:7, 1:7) ## Quantile range ## par(mfrow=c(2,2)) par(mar = c(2,4,2,4)) sapply(1:4, function(x) { image.plot(1:7, 1:7, t(boxmedian[[x]]), col = mycol(49), xlab = '', ylab = '', zlim = c(0, 1)) # text(ex7[,1], ex7[,2], round(as.vector(t(boxmean[[x]]/rowSums(boxmean[[x]]))), 2), font = 2) text(ex7[,1], ex7[,2], paste0(round(t(boxmean[[x]]),2),"\n" ,"(",round(t(boxq.low[[x]]), 2), "-", round(t(boxq.high[[x]]), 2), ")"), font = 2, cex = .65) grid(7,7,col = 'grey50') title(seasons[x]) } )
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ex4 = expand.grid(1:4, 1:4) par(mfrow=c(2,2)) sapply(1:4, function(x) { image.plot(1:4, 1:4, t(boxmean4[[x]]), col = mycol(100), xlab = '', ylab = '', zlim = c(0, 1)) # highlights the mean value # image.plot(1:7, 1:7, round(t(boxq.high[[x]]),2)-round(t(boxq.low[[x]]),2), col = mycol(49), xlab = '', ylab = '', zlim = c(0, 1)) # highlights the 95% CI range # text(ex7[,1], ex7[,2], round(as.vector(t(boxmean[[x]]/rowSums(boxmean[[x]]))), 2), font = 2) text(ex4[,1], ex4[,2], paste0(round(t(boxmean4[[x]]),2),"\n" ,"(",round(t(boxq.low4[[x]]), 2), " - ", round(t(boxq.high4[[x]]), 2), ")"), font = 2) grid(4,4,col = 'grey50') title(seasons[x]) } )
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plot(box7, col = rev(grey.colors(14))[1:7], border = 'orange', add=F, lwd = 3) fields::world(add=T, col = 'cornsilk', fill=T) text(coordinates(box7)[,1], coordinates(box7)[,2], 1:7, col = 'red', cex = 1.5) box() degAxis(1) degAxis(2) title('7-box operating model')
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plot(box4, col = grey.colors(4), border = 'orange', add=F, lwd = 3) fields::world(add=T, col = 'cornsilk', fill=T) text(coordinates(box4)[,1], coordinates(box4)[,2], 1:4, col = 2, cex = 3) box() degAxis(1) degAxis(2) title('4-box operating model')
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