| Previous changeset 98:d33a401c0153 (2017-12-04) Next changeset 100:52114847afff (2017-12-04) |
|
Commit message:
Uploaded |
|
modified:
insect_phenology_model.R |
| b |
| diff -r d33a401c0153 -r 51045fde125e insect_phenology_model.R --- a/insect_phenology_model.R Mon Dec 04 11:54:10 2017 -0500 +++ b/insect_phenology_model.R Mon Dec 04 13:04:11 2017 -0500 |
| [ |
| b'@@ -217,7 +217,7 @@\n g2.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications)\n g0a.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications)\n g1a.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications)\n-g2a.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications)\n+F2_adults.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications)\n \n # Loop through replications.\n for (N.replications in 1:opt$replications) {\n@@ -467,13 +467,13 @@\n }\n } # Else if it is still alive.\n } # End of the individual bug loop.\n- # Find how many died.\n+ # Find the number of deaths.\n num_insects.death <- length(death.vector)\n if (num_insects.death > 0) {\n+ # Remove record of dead.\n vector.matrix <- vector.matrix[-death.vector, ]\n }\n- # Remove record of dead.\n- # Find how many new born.\n+ # Find the number of births.\n num_insects.newborn <- length(birth.vector[,1])\n vector.matrix <- rbind(vector.matrix, birth.vector)\n # Update population size for the next day.\n@@ -481,38 +481,29 @@\n \n # Aggregate results by day.\n tot.pop <- c(tot.pop, num_insects)\n- # Egg.\n- sum_eggs <- sum(vector.matrix[,2] == 0)\n- # Young nymph.\n- sum_young_nymphs <- sum(vector.matrix[,2] == 1)\n- # Old nymph.\n- sum_old_nymphs <- sum(vector.matrix[,2] == 2)\n- # Previtellogenic.\n- sum_previtellogenic <- sum(vector.matrix[,2] == 3)\n- # Vitellogenic.\n- sum_vitellogenic <- sum(vector.matrix[,2] == 4)\n- # Diapausing.\n- sum_diapausing <- sum(vector.matrix[,2] == 5)\n- # Overwintering adult.\n- sum_overwintering_adults <- sum(vector.matrix[,1] == 0)\n- # First generation.\n- sum_first_generation <- sum(vector.matrix[,1] == 1)\n- # Second generation.\n- sum_second_generation <- sum(vector.matrix[,1] == 2)\n- # Sum of all adults.\n+\n+ # All adults population size.\n num_insects.adult <- sum(vector.matrix[,2] == 3) + sum(vector.matrix[,2] == 4) + sum(vector.matrix[,2] == 5)\n \n- # Population sizes.\n- gen0.pop[row] <- sum_overwintering_adults\n- gen1.pop[row] <- sum_first_generation\n- gen2.pop[row] <- sum_second_generation\n+ # Overwintering adult population size.\n+ gen0.pop[row] <- sum(vector.matrix[,1] == 0)\n+ # First generation population size.\n+ gen1.pop[row] <- sum(vector.matrix[,1] == 1)\n+ # Second generation population size.\n+ gen2.pop[row] <- sum(vector.matrix[,1] == 2)\n \n- S0[row] <- sum_eggs\n- S1[row] <- sum_young_nymphs\n- S2[row] <- sum_old_nymphs\n- S3[row] <- sum_previtellogenic\n- S4[row] <- sum_vitellogenic\n- S5[row] <- sum_diapausing\n+ # Egg population size.\n+ S0[row] <- sum(vector.matrix[,2] == 0)\n+ # Young nymph population size.\n+ S1[row] <- sum(vector.matrix[,2] == 1)\n+ # Old nymph population size.\n+ S2[row] <- sum(vector.matrix[,2] == 2)\n+ # Previtellogenic population size.\n+ S3[row] <- sum(vector.matrix[,2] == 3)\n+ # Vitellogenic population size.\n+ S4[row] <- sum(vector.matrix[,2] == 4)\n+ # Diapausing population size.\n+ S5[row] <- sum(vector.matrix[,2] == 5)\n \n g0.adult[row] <- sum(vector.matrix[,1] == 0)\n g1.adult[row] <- sum((vector.matrix[,1] == 1 & vector.matrix[,2] == 3) | (vector.matrix[,1] == 1 & vector.matrix[,2] == 4) | (vector.matrix[,1] == 1 & vector.matrix[,2] == 5))\n@@ -541,34 +532,34 @@\n g2.replications[,N.replications] <- gen2.pop\n g0a.replications[,N.replications] <- g0.adult\n g1a.replications[,N.replications] <- g1.adult\n- g2a.replications[,N.replications] <- g2.adult\n+ F2_adults.replications[,N.replications] <- g2.a'..b'ations)\n+eggs.std_error <- apply(S0.replications, 1, sd) / sqrt(opt$replications)\n # Standard error value for P.\n g0.std_error <- apply(g0.replications, 1, sd) / sqrt(opt$replications)\n # Standard error for F1.\n@@ -580,7 +571,7 @@\n # Standard error for F1 adult.\n g1a.std_error <- apply(g1a.replications, 1, sd) / sqrt(opt$replications)\n # Standard error for F2 adult.\n-g2a.std_error <- apply(g2a.replications, 1, sd) / sqrt(opt$replications)\n+F2_adults.std_error <- apply(F2_adults.replications, 1, sd) / sqrt(opt$replications)\n \n dev.new(width=20, height=30)\n \n@@ -597,25 +588,25 @@\n \n # Subfigure 1: population size by life stage\n title <- paste(opt$insect, ": Total pop. by life stage :", opt$location, ": Lat:", latitude, ":", start_date, "-", end_date, sep=" ")\n-plot(day.all, adult_mean, main=title, type="l", ylim=c(0, max(egg_mean + egg_mean.std_error, nymph_mean + nymph_mean.std_error, adult_mean + adult_mean.std_error)), axes=F, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3)\n+plot(day.all, adults, main=title, type="l", ylim=c(0, max(eggs + eggs.std_error, nymphs + nymphs.std_error, adults + adults.std_error)), axes=F, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3)\n # Young and old nymphs.\n-lines(day.all, nymph_mean, lwd=2, lty=1, col=2)\n+lines(day.all, nymphs, lwd=2, lty=1, col=2)\n # Eggs\n-lines(day.all, egg_mean, lwd=2, lty=1, col=4)\n+lines(day.all, eggs, lwd=2, lty=1, col=4)\n axis(1, at=c(1:12) * 30 - 15, cex.axis=3, labels=c("Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec"))\n axis(2, cex.axis=3)\n legend("topleft", c("Egg", "Nymph", "Adult"), lty=c(1, 1, 1), col=c(4, 2, 1), cex=3)\n if (opt$std_error_plot == 1) {\n # Add Standard error lines to plot\n # Standard error for adults\n- lines (day.all, adult_mean+adult_mean.std_error, lty=2)\n- lines (day.all, adult_mean-adult_mean.std_error, lty=2)\n+ lines (day.all, adults+adults.std_error, lty=2)\n+ lines (day.all, adults-adults.std_error, lty=2)\n # Standard error for nymphs\n- lines (day.all, nymph_mean+nymph_mean.std_error, col=2, lty=2)\n- lines (day.all, nymph_mean-nymph_mean.std_error, col=2, lty=2)\n+ lines (day.all, nymphs+nymphs.std_error, col=2, lty=2)\n+ lines (day.all, nymphs-nymphs.std_error, col=2, lty=2)\n # Standard error for eggs\n- lines (day.all, egg_mean+egg_mean.std_error, col=4, lty=2)\n- lines (day.all, egg_mean-egg_mean.std_error, col=4, lty=2)\n+ lines (day.all, eggs+eggs.std_error, col=4, lty=2)\n+ lines (day.all, eggs-eggs.std_error, col=4, lty=2)\n }\n \n # Subfigure 2: population size by generation\n@@ -641,9 +632,9 @@\n \n # Subfigure 3: adult population size by generation\n title <- paste(opt$insect, ": Adult pop. by generation :", opt$location, ": Lat:", latitude, ":", start_date, "-", end_date, sep=" ")\n-plot(day.all, g0a, ylim=c(0, max(F2_adult_mean) + 100), main=title, type="l", axes=F, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3)\n+plot(day.all, g0a, ylim=c(0, max(F2_adults) + 100), main=title, type="l", axes=F, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3)\n lines(day.all, g1a, lwd = 2, lty = 1, col=2)\n-lines(day.all, F2_adult_mean, lwd = 2, lty = 1, col=4)\n+lines(day.all, F2_adults, lwd = 2, lty = 1, col=4)\n axis(1, at=c(1:12) * 30 - 15, cex.axis=3, labels = c("Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec"))\n axis(2, cex.axis=3)\n legend("topleft", c("P", "F1", "F2"), lty=c(1, 1, 1), col=c(1, 2, 4), cex=3)\n@@ -656,8 +647,8 @@\n lines (day.all, g1a+g1a.std_error, col=2, lty=2)\n lines (day.all, g1a-g1a.std_error, col=2, lty=2)\n # Standard error for eggs\n- lines (day.all, F2_adult_mean+g2a.std_error, col=4, lty=2)\n- lines (day.all, F2_adult_mean-g2a.std_error, col=4, lty=2)\n+ lines (day.all, F2_adults+F2_adults.std_error, col=4, lty=2)\n+ lines (day.all, F2_adults-F2_adults.std_error, col=4, lty=2)\n }\n \n # Turn off device driver to flush output.\n' |