| Previous changeset 102:ce996e90f5a7 (2017-12-05) Next changeset 104:d6e37828b094 (2017-12-05) |
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modified:
insect_phenology_model.R |
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| diff -r ce996e90f5a7 -r 4d9e40d8af0f insect_phenology_model.R --- a/insect_phenology_model.R Tue Dec 05 10:32:04 2017 -0500 +++ b/insect_phenology_model.R Tue Dec 05 11:01:23 2017 -0500 |
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| b'@@ -83,9 +83,9 @@\n # Mean temperature for current row.\n curr_mean_temp <- 0.5 * (curr_min_temp + curr_max_temp)\n # Initialize degree day accumulation\n- degree_days <- 0\n+ averages <- 0\n if (curr_max_temp < threshold) {\n- degree_days <- 0\n+ averages <- 0\n }\n else {\n # Initialize hourly temperature.\n@@ -138,9 +138,9 @@\n }\n }\n }\n- degree_days <- sum(dh) / 24\n+ averages <- sum(dh) / 24\n }\n- return(c(curr_mean_temp, degree_days))\n+ return(c(curr_mean_temp, averages))\n }\n \n mortality.adult = function(temperature) {\n@@ -197,15 +197,19 @@\n group1, group2, group3, group1_std_error, group2_std_error, group3_std_error) {\n if (chart_type == "pop_size_by_life_stage") {\n title <- paste(insect, ": Total pop. by life stage :", location, ": Lat:", latitude, ":", start_date, "-", end_date, sep=" ")\n- legend("topleft", c("Egg", "Nymph", "Adult"), lty=c(1, 1, 1), col=c(4, 2, 1), cex=3)\n+ legend_text <- c("Egg", "Nymph", "Adult")\n+ columns <- c(4, 2, 1)\n } else if (chart_type == "pop_size_by_generation") {\n title <- paste(insect, ": Total pop. by generation :", location, ": Lat:", latitude, ":", start_date, "-", end_date, sep=" ")\n- legend("topleft", c("P", "F1", "F2"), lty=c(1, 1, 1), col=c(1, 2, 4), cex=3)\n+ legend_text <- c("P", "F1", "F2")\n+ columns <- col=c(1, 2, 4)\n } else if (chart_type == "adult_pop_size_by_generation") {\n title <- paste(insect, ": Adult pop. by generation :", location, ": Lat:", latitude, ":", start_date, "-", end_date, sep=" ")\n- legend("topleft", c("P", "F1", "F2"), lty=c(1, 1, 1), col=c(1, 2, 4), cex=3)\n+ legend_text <- c("P", "F1", "F2")\n+ columns <- col=c(1, 2, 4)\n }\n plot(days, group1, main=title, type="l", ylim=c(0, maxval), axes=F, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3)\n+ legend("topleft", legend_text, lty=c(1, 1, 1), columns, cex=3)\n lines(days, group2, lwd=2, lty=1, col=2)\n lines(days, group3, 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@@ -237,17 +241,20 @@\n Previtellogenic.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications)\n Vitellogenic.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications)\n Diapausing.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications)\n+\n newborn.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications)\n+adult.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications)\n death.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications)\n-adult.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications)\n-population.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications)\n+\n P.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications)\n+P_adults.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications)\n F1.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications)\n+F1_adults.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications)\n F2.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications)\n-P_adults.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications)\n-F1_adults.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+population.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications)\n+\n # Process replications.\n for (N.replications in 1:opt$replications) {\n # D'..b',7 +501,7 @@\n }\n # Event 4 growing of diapausing adult (unimportant, but still necessary).\n if (vector.individual[2] == 5) {\n- vector.individual[3] <- vector.individual[3] + degree_days.temp\n+ vector.individual[3] <- vector.individual[3] + averages.temp\n vector.individual[4] <- vector.individual[4] + 1\n vector.matrix[i,] <- vector.individual\n }\n@@ -544,7 +555,7 @@\n N.adult[row] <- num_insects.adult\n } # End of days specified in the input temperature data.\n \n- degree_days.cum <- cumsum(degree_days.day)\n+ averages.cum <- cumsum(averages.day)\n \n # Define the output values.\n Eggs.replications[,N.replications] <- Eggs\n@@ -565,40 +576,48 @@\n F2_adults.replications[,N.replications] <- F2.adult\n }\n \n-# Mean value for adults.\n-adults <- apply((Previtellogenic.replications+Vitellogenic.replications+Diapausing.replications), 1, mean)\n-# Mean value for nymphs.\n-nymphs <- apply((YoungNymphs.replications+OldNymphs.replications), 1, mean)\n # Mean value for eggs.\n eggs <- apply(Eggs.replications, 1, mean)\n+# Standard error for eggs.\n+eggs.std_error <- apply(Eggs.replications, 1, sd) / sqrt(opt$replications)\n+\n+# Mean value for nymphs.\n+nymphs <- apply((YoungNymphs.replications+OldNymphs.replications), 1, mean)\n+# Standard error for nymphs.\n+nymphs.std_error <- apply((YoungNymphs.replications+OldNymphs.replications) / sqrt(opt$replications), 1, sd)\n+\n+# Mean value for adults.\n+adults <- apply((Previtellogenic.replications+Vitellogenic.replications+Diapausing.replications), 1, mean)\n+# Standard error for adults.\n+adults.std_error <- apply((Previtellogenic.replications+Vitellogenic.replications+Diapausing.replications), 1, sd) / sqrt(opt$replications)\n+\n # Mean value for P.\n P <- apply(P.replications, 1, mean)\n+# Standard error for P.\n+P.std_error <- apply(P.replications, 1, sd) / sqrt(opt$replications)\n+\n+# Mean value for P adults.\n+P_adults <- apply(P_adults.replications, 1, mean)\n+# Standard error for P_adult.\n+P_adults.std_error <- apply(P_adults.replications, 1, sd) / sqrt(opt$replications)\n+\n # Mean value for F1.\n F1 <- apply(F1.replications, 1, mean)\n-# Mean value for F2.\n-F2 <- apply(F2.replications, 1, mean)\n-# Mean value for P adults.\n-P_adults <- apply(P_adults.replications, 1, mean)\n+# Standard error for F1.\n+F1.std_error <- apply(F1.replications, 1, sd) / sqrt(opt$replications)\n+\n # Mean value for F1 adults.\n F1_adults <- apply(F1_adults.replications, 1, mean)\n+# Standard error for F1 adult.\n+F1_adults.std_error <- apply(F1_adults.replications, 1, sd) / sqrt(opt$replications)\n+\n+# Mean value for F2.\n+F2 <- apply(F2.replications, 1, mean)\n+# Standard error for F2.\n+F2.std_error <- apply(F2.replications, 1, sd) / sqrt(opt$replications)\n+\n # Mean value for F2 adults.\n F2_adults <- apply(F2_adults.replications, 1, mean)\n-# Standard error for adults.\n-adults.std_error <- apply((Previtellogenic.replications+Vitellogenic.replications+Diapausing.replications), 1, sd) / sqrt(opt$replications)\n-# Standard error for nymphs.\n-nymphs.std_error <- apply((YoungNymphs.replications+OldNymphs.replications) / sqrt(opt$replications), 1, sd)\n-# Standard error for eggs.\n-eggs.std_error <- apply(Eggs.replications, 1, sd) / sqrt(opt$replications)\n-# Standard error value for P.\n-P.std_error <- apply(P.replications, 1, sd) / sqrt(opt$replications)\n-# Standard error for F1.\n-F1.std_error <- apply(F1.replications, 1, sd) / sqrt(opt$replications)\n-# Standard error for F2.\n-F2.std_error <- apply(F2.replications, 1, sd) / sqrt(opt$replications)\n-# Standard error for P adult.\n-P_adults.std_error <- apply(P_adults.replications, 1, sd) / sqrt(opt$replications)\n-# Standard error for F1 adult.\n-F1_adults.std_error <- apply(F1_adults.replications, 1, sd) / sqrt(opt$replications)\n # Standard error for F2 adult.\n F2_adults.std_error <- apply(F2_adults.replications, 1, sd) / sqrt(opt$replications)\n \n' |