Mercurial > repos > greg > insect_phenology_model
changeset 102:ce996e90f5a7 draft
Uploaded
| author | greg |
|---|---|
| date | Tue, 05 Dec 2017 10:32:04 -0500 |
| parents | 691b677d8f83 |
| children | 4d9e40d8af0f |
| files | insect_phenology_model.R |
| diffstat | 1 files changed, 232 insertions(+), 252 deletions(-) [+] |
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--- a/insect_phenology_model.R Mon Dec 04 13:34:28 2017 -0500 +++ b/insect_phenology_model.R Tue Dec 05 10:32:04 2017 -0500 @@ -3,14 +3,14 @@ suppressPackageStartupMessages(library("optparse")) option_list <- list( - make_option(c("-a", "--adult_mort"), action="store", dest="adult_mort", type="integer", help="Adjustment rate for adult mortality"), - make_option(c("-b", "--adult_accum"), action="store", dest="adult_accum", type="integer", help="Adjustment of degree-days accumulation (old nymph->adult)"), - make_option(c("-c", "--egg_mort"), action="store", dest="egg_mort", type="integer", help="Adjustment rate for egg mortality"), + make_option(c("-a", "--adult_mortality"), action="store", dest="adult_mortality", type="integer", help="Adjustment rate for adult mortality"), + make_option(c("-b", "--adult_accumulation"), action="store", dest="adult_accumulation", type="integer", help="Adjustment of degree-days accumulation (old nymph->adult)"), + make_option(c("-c", "--egg_mortality"), action="store", dest="egg_mortality", type="integer", help="Adjustment rate for egg mortality"), make_option(c("-e", "--location"), action="store", dest="location", help="Selected location"), make_option(c("-f", "--min_clutch_size"), action="store", dest="min_clutch_size", type="integer", help="Adjustment of minimum clutch size"), make_option(c("-i", "--max_clutch_size"), action="store", dest="max_clutch_size", type="integer", help="Adjustment of maximum clutch size"), - make_option(c("-j", "--nymph_mort"), action="store", dest="nymph_mort", type="integer", help="Adjustment rate for nymph mortality"), - make_option(c("-k", "--old_nymph_accum"), action="store", dest="old_nymph_accum", type="integer", help="Adjustment of degree-days accumulation (young nymph->old nymph)"), + make_option(c("-j", "--nymph_mortality"), action="store", dest="nymph_mortality", type="integer", help="Adjustment rate for nymph mortality"), + make_option(c("-k", "--old_nymph_accumulation"), action="store", dest="old_nymph_accumulation", type="integer", help="Adjustment of degree-days accumulation (young nymph->old nymph)"), make_option(c("-n", "--num_days"), action="store", dest="num_days", type="integer", help="Total number of days in the temperature dataset"), make_option(c("-o", "--output"), action="store", dest="output", help="Output dataset"), make_option(c("-p", "--oviposition"), action="store", dest="oviposition", type="integer", help="Adjustment for oviposition rate"), @@ -18,7 +18,7 @@ make_option(c("-s", "--replications"), action="store", dest="replications", type="integer", help="Number of replications"), make_option(c("-t", "--std_error_plot"), action="store", dest="std_error_plot", help="Plot Standard error"), make_option(c("-v", "--input"), action="store", dest="input", help="Temperature data for selected location"), - make_option(c("-y", "--young_nymph_accum"), action="store", dest="young_nymph_accum", type="integer", help="Adjustment of degree-days accumulation (egg->young nymph)"), + make_option(c("-y", "--young_nymph_accumulation"), action="store", dest="young_nymph_accumulation", type="integer", help="Adjustment of degree-days accumulation (egg->young nymph)"), make_option(c("-x", "--insect"), action="store", dest="insect", help="Insect name") ) @@ -26,23 +26,6 @@ args <- parse_args(parser, positional_arguments=TRUE) opt <- args$options -parse_input_data = function(input_file, num_rows) { - # Read in the input temperature datafile into a data frame. - temperature_data_frame <- read.csv(file=input_file, header=T, strip.white=TRUE, sep=",") - num_columns <- dim(temperature_data_frame)[2] - if (num_columns == 6) { - # The input data has the following 6 columns: - # LATITUDE, LONGITUDE, DATE, DOY, TMIN, TMAX - # Set the column names for access when adding daylight length.. - colnames(temperature_data_frame) <- c("LATITUDE","LONGITUDE", "DATE", "DOY", "TMIN", "TMAX") - # Add a column containing the daylight length for each day. - temperature_data_frame <- add_daylight_length(temperature_data_frame, num_columns, num_rows) - # Reset the column names with the additional column for later access. - colnames(temperature_data_frame) <- c("LATITUDE","LONGITUDE", "DATE", "DOY", "TMIN", "TMAX", "DAYLEN") - } - return(temperature_data_frame) -} - add_daylight_length = function(temperature_data_frame, num_columns, num_rows) { # Return a vector of daylight length (photoperido profile) for # the number of days specified in the input temperature data @@ -57,28 +40,51 @@ theta <- 0.2163108 + 2 * atan(0.9671396 * tan(0.00860 * (doy - 186))) phi <- asin(0.39795 * cos(theta)) # Compute the length of daylight for the day of the year. - daylight_length_vector[i] <- 24 - (24 / pi * acos((sin(p * pi / 180) + sin(latitude * pi / 180) * sin(phi)) / (cos(latitude * pi / 180) * cos(phi)))) + darkness_length <- 24 / pi * acos((sin(p * pi / 180) + sin(latitude * pi / 180) * sin(phi)) / (cos(latitude * pi / 180) * cos(phi))) + daylight_length_vector[i] <- 24 - darkness_length } # Append daylight_length_vector as a new column to temperature_data_frame. temperature_data_frame[, num_columns+1] <- daylight_length_vector return(temperature_data_frame) } +dev.egg = function(temperature) { + dev.rate = -0.9843 * temperature + 33.438 + return(dev.rate) +} + +dev.emerg = function(temperature) { + emerg.rate <- -0.5332 * temperature + 24.147 + return(emerg.rate) +} + +dev.old = function(temperature) { + n34 <- -0.6119 * temperature + 17.602 + n45 <- -0.4408 * temperature + 19.036 + dev.rate = mean(n34 + n45) + return(dev.rate) +} + +dev.young = function(temperature) { + n12 <- -0.3728 * temperature + 14.68 + n23 <- -0.6119 * temperature + 25.249 + dev.rate = mean(n12 + n23) + return(dev.rate) +} + get_temperature_at_hour = function(latitude, temperature_data_frame, row, num_days) { # Base development threshold for Brown Marmolated Stink Bug # insect phenology model. - # TODO: Pass insect on the command line to accomodate more - # the just the Brown Marmolated Stink Bub. threshold <- 14.17 # Minimum temperature for current row. - dnp <- temperature_data_frame$TMIN[row] + curr_min_temp <- temperature_data_frame$TMIN[row] # Maximum temperature for current row. - dxp <- temperature_data_frame$TMAX[row] + curr_max_temp <- temperature_data_frame$TMAX[row] # Mean temperature for current row. - dmean <- 0.5 * (dnp + dxp) + curr_mean_temp <- 0.5 * (curr_min_temp + curr_max_temp) # Initialize degree day accumulation degree_days <- 0 - if (dxp < threshold) { + if (curr_max_temp < threshold) { degree_days <- 0 } else { @@ -98,12 +104,12 @@ risetime <- 12 - y / 2 # Sunset time. settime <- 12 + y / 2 - ts <- (dxp - dnp) * sin(pi * (settime - 5) / (y + 2 * a)) + dnp + ts <- (curr_max_temp - curr_min_temp) * sin(pi * (settime - 5) / (y + 2 * a)) + curr_min_temp for (i in 1:24) { if (i > risetime && i < settime) { # Number of hours after Tmin until sunset. m <- i - 5 - T[i] = (dxp - dnp) * sin(pi * m / (y + 2 * a)) + dnp + T[i] = (curr_max_temp - curr_min_temp) * sin(pi * m / (y + 2 * a)) + curr_min_temp if (T[i] < 8.4) { dh[i] <- 0 } @@ -113,7 +119,7 @@ } else if (i > settime) { n <- i - settime - T[i] = dnp + (ts - dnp) * exp( - b * n / z) + T[i] = curr_min_temp + (ts - curr_min_temp) * exp( - b * n / z) if (T[i] < 8.4) { dh[i] <- 0 } @@ -123,7 +129,7 @@ } else { n <- i + 24 - settime - T[i]=dnp + (ts - dnp) * exp( - b * n / z) + T[i] = curr_min_temp + (ts - curr_min_temp) * exp( - b * n / z) if (T[i] < 8.4) { dh[i] <- 0 } @@ -134,64 +140,87 @@ } degree_days <- sum(dh) / 24 } - return(c(dmean, degree_days)) -} - -dev.egg = function(temperature) { - dev.rate= -0.9843 * temperature + 33.438 - return(dev.rate) + return(c(curr_mean_temp, degree_days)) } -dev.young = function(temperature) { - n12 <- -0.3728 * temperature + 14.68 - n23 <- -0.6119 * temperature + 25.249 - dev.rate = mean(n12 + n23) - return(dev.rate) -} - -dev.old = function(temperature) { - n34 <- -0.6119 * temperature + 17.602 - n45 <- -0.4408 * temperature + 19.036 - dev.rate = mean(n34 + n45) - return(dev.rate) -} - -dev.emerg = function(temperature) { - emerg.rate <- -0.5332 * temperature + 24.147 - return(emerg.rate) +mortality.adult = function(temperature) { + if (temperature < 12.7) { + mortality.probability = 0.002 + } + else { + mortality.probability = temperature * 0.0005 + 0.02 + } + return(mortality.probability) } mortality.egg = function(temperature) { if (temperature < 12.7) { - mort.prob = 0.8 + mortality.probability = 0.8 } else { - mort.prob = 0.8 - temperature / 40.0 - if (mort.prob < 0) { - mort.prob = 0.01 + mortality.probability = 0.8 - temperature / 40.0 + if (mortality.probability < 0) { + mortality.probability = 0.01 } } - return(mort.prob) + return(mortality.probability) } mortality.nymph = function(temperature) { if (temperature < 12.7) { - mort.prob = 0.03 + mortality.probability = 0.03 } else { - mort.prob = temperature * 0.0008 + 0.03 + mortality.probability = temperature * 0.0008 + 0.03 } - return(mort.prob) + return(mortality.probability) +} + +parse_input_data = function(input_file, num_rows) { + # Read in the input temperature datafile into a data frame. + temperature_data_frame <- read.csv(file=input_file, header=T, strip.white=TRUE, sep=",") + num_columns <- dim(temperature_data_frame)[2] + if (num_columns == 6) { + # The input data has the following 6 columns: + # LATITUDE, LONGITUDE, DATE, DOY, TMIN, TMAX + # Set the column names for access when adding daylight length.. + colnames(temperature_data_frame) <- c("LATITUDE","LONGITUDE", "DATE", "DOY", "TMIN", "TMAX") + # Add a column containing the daylight length for each day. + temperature_data_frame <- add_daylight_length(temperature_data_frame, num_columns, num_rows) + # Reset the column names with the additional column for later access. + colnames(temperature_data_frame) <- c("LATITUDE","LONGITUDE", "DATE", "DOY", "TMIN", "TMAX", "DAYLEN") + } + return(temperature_data_frame) } -mortality.adult = function(temperature) { - if (temperature < 12.7) { - mort.prob = 0.002 +render_chart = function(chart_type, insect, location, latitude, start_date, end_date, days, maxval, plot_std_error, + group1, group2, group3, group1_std_error, group2_std_error, group3_std_error) { + if (chart_type == "pop_size_by_life_stage") { + title <- paste(insect, ": Total pop. by life stage :", location, ": Lat:", latitude, ":", start_date, "-", end_date, sep=" ") + legend("topleft", c("Egg", "Nymph", "Adult"), lty=c(1, 1, 1), col=c(4, 2, 1), cex=3) + } else if (chart_type == "pop_size_by_generation") { + title <- paste(insect, ": Total pop. by generation :", location, ": Lat:", latitude, ":", start_date, "-", end_date, sep=" ") + legend("topleft", c("P", "F1", "F2"), lty=c(1, 1, 1), col=c(1, 2, 4), cex=3) + } else if (chart_type == "adult_pop_size_by_generation") { + title <- paste(insect, ": Adult pop. by generation :", location, ": Lat:", latitude, ":", start_date, "-", end_date, sep=" ") + legend("topleft", c("P", "F1", "F2"), lty=c(1, 1, 1), col=c(1, 2, 4), cex=3) } - else { - mort.prob = temperature * 0.0005 + 0.02 + 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) + lines(days, group2, lwd=2, lty=1, col=2) + lines(days, group3, lwd=2, lty=1, col=4) + 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")) + axis(2, cex.axis=3) + if (plot_std_error==1) { + # Standard error for group1. + lines(days, group1+group1_std_error, lty=2) + lines (days, group1-group1_std_error, lty=2) + # Standard error for group2. + lines(days, group2+group2_std_error, col=2, lty=2) + lines(days, group2-group2_std_error, col=2, lty=2) + # Standard error for group3. + lines(days, group3+group3_std_error, col=4, lty=2) + lines(days, group3-group3_std_error, col=4, lty=2) } - return(mort.prob) } temperature_data_frame <- parse_input_data(opt$input, opt$num_days) @@ -202,16 +231,16 @@ cat("Number of days: ", opt$num_days, "\n") # Initialize matrices. -S0.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) -S1.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) -S2.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) -S3.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) -S4.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) -S5.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) +Eggs.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) +YoungNymphs.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) +OldNymphs.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) +Previtellogenic.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) +Vitellogenic.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) +Diapausing.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) newborn.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) death.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) adult.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) -pop.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) +population.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) P.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) F1.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) F2.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) @@ -219,7 +248,7 @@ F1_adults.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) F2_adults.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) -# Loop through replications. +# Process replications. for (N.replications in 1:opt$replications) { # During each replication start with 1000 individuals. # TODO: user definable as well? @@ -235,12 +264,12 @@ overwintering_adult.population <- rep(0, opt$num_days) first_generation.population <- rep(0, opt$num_days) second_generation.population <- rep(0, opt$num_days) - S0 <- rep(0, opt$num_days) - S1 <- rep(0, opt$num_days) - S2 <- rep(0, opt$num_days) - S3 <- rep(0, opt$num_days) - S4 <- rep(0, opt$num_days) - S5 <- rep(0, opt$num_days) + Eggs <- rep(0, opt$num_days) + YoungNymphs <- rep(0, opt$num_days) + OldNymphs <- rep(0, opt$num_days) + Previtellogenic <- rep(0, opt$num_days) + Vitellogenic <- rep(0, opt$num_days) + Diapausing <- rep(0, opt$num_days) P.adult <- rep(0, opt$num_days) F1.adult <- rep(0, opt$num_days) F2.adult <- rep(0, opt$num_days) @@ -265,79 +294,79 @@ # All individuals. for (i in 1:num_insects) { # Find individual record. - vector.ind <- vector.matrix[i,] + vector.individual <- vector.matrix[i,] # First of all, still alive? # Adjustment for late season mortality rate. if (latitude < 40.0) { - post.mort <- 1 + post.mortality <- 1 day.kill <- 300 } else { - post.mort <- 2 + post.mortality <- 2 day.kill <- 250 } - if (vector.ind[2] == 0) { + if (vector.individual[2] == 0) { # Egg. - death.prob = opt$egg_mort * mortality.egg(mean.temp) + death.probability = opt$egg_mortality * mortality.egg(mean.temp) } - else if (vector.ind[2] == 1 | vector.ind[2] == 2) { - death.prob = opt$nymph_mort * mortality.nymph(mean.temp) + else if (vector.individual[2] == 1 | vector.individual[2] == 2) { + death.probability = opt$nymph_mortality * mortality.nymph(mean.temp) } - else if (vector.ind[2] == 3 | vector.ind[2] == 4 | vector.ind[2] == 5) { + else if (vector.individual[2] == 3 | vector.individual[2] == 4 | vector.individual[2] == 5) { # For adult. if (doy < day.kill) { - death.prob = opt$adult_mort * mortality.adult(mean.temp) + death.probability = opt$adult_mortality * mortality.adult(mean.temp) } else { # Increase adult mortality after fall equinox. - death.prob = opt$adult_mort * post.mort * mortality.adult(mean.temp) + death.probability = opt$adult_mortality * post.mortality * mortality.adult(mean.temp) } } # (or dependent on temperature and life stage?) u.d <- runif(1) - if (u.d < death.prob) { + if (u.d < death.probability) { death.vector <- c(death.vector, i) } else { # Aggregrate index of dead bug. # Event 1 end of diapause. - if (vector.ind[1] == 0 && vector.ind[2] == 3) { + if (vector.individual[1] == 0 && vector.individual[2] == 3) { # Overwintering adult (previttelogenic). - if (photoperiod > opt$photoperiod && vector.ind[3] > 68 && doy < 180) { + if (photoperiod > opt$photoperiod && vector.individual[3] > 68 && doy < 180) { # Add 68C to become fully reproductively matured. # Transfer to vittelogenic. - vector.ind <- c(0, 4, 0, 0, 0) - vector.matrix[i,] <- vector.ind + vector.individual <- c(0, 4, 0, 0, 0) + vector.matrix[i,] <- vector.individual } else { # Add to degree_days. - vector.ind[3] <- vector.ind[3] + degree_days.temp + vector.individual[3] <- vector.individual[3] + degree_days.temp # Add 1 day in current stage. - vector.ind[4] <- vector.ind[4] + 1 - vector.matrix[i,] <- vector.ind + vector.individual[4] <- vector.individual[4] + 1 + vector.matrix[i,] <- vector.individual } } - if (vector.ind[1] != 0 && vector.ind[2] == 3) { + if (vector.individual[1] != 0 && vector.individual[2] == 3) { # Not overwintering adult (previttelogenic). - current.gen <- vector.ind[1] - if (vector.ind[3] > 68) { + current.gen <- vector.individual[1] + if (vector.individual[3] > 68) { # Add 68C to become fully reproductively matured. # Transfer to vittelogenic. - vector.ind <- c(current.gen, 4, 0, 0, 0) - vector.matrix[i,] <- vector.ind + vector.individual <- c(current.gen, 4, 0, 0, 0) + vector.matrix[i,] <- vector.individual } else { # Add to degree_days. - vector.ind[3] <- vector.ind[3] + degree_days.temp + vector.individual[3] <- vector.individual[3] + degree_days.temp # Add 1 day in current stage. - vector.ind[4] <- vector.ind[4] + 1 - vector.matrix[i,] <- vector.ind + vector.individual[4] <- vector.individual[4] + 1 + vector.matrix[i,] <- vector.individual } } # Event 2 oviposition -- where population dynamics comes from. - if (vector.ind[2] == 4 && vector.ind[1] == 0 && mean.temp > 10) { + if (vector.individual[2] == 4 && vector.individual[1] == 0 && mean.temp > 10) { # Vittelogenic stage, overwintering generation. - if (vector.ind[4] == 0) { + if (vector.individual[4] == 0) { # Just turned in vittelogenic stage. num_insects.birth = round(runif(1, 2 + opt$min_clutch_size, 8 + opt$max_clutch_size)) } @@ -350,16 +379,16 @@ } } # Add to degree_days. - vector.ind[3] <- vector.ind[3] + degree_days.temp + vector.individual[3] <- vector.individual[3] + degree_days.temp # Add 1 day in current stage. - vector.ind[4] <- vector.ind[4] + 1 - vector.matrix[i,] <- vector.ind + vector.individual[4] <- vector.individual[4] + 1 + vector.matrix[i,] <- vector.individual if (num_insects.birth > 0) { # Add new birth -- might be in different generations. - new.gen <- vector.ind[1] + 1 + new.gen <- vector.individual[1] + 1 # Egg profile. - new.ind <- c(new.gen, 0, 0, 0, 0) - new.vector <- rep(new.ind, num_insects.birth) + new.individual <- c(new.gen, 0, 0, 0, 0) + new.vector <- rep(new.individual, num_insects.birth) # Update batch of egg profile. new.vector <- t(matrix(new.vector, nrow=5)) # Group with total eggs laid in that day. @@ -367,11 +396,11 @@ } } # Event 2 oviposition -- for generation 1. - if (vector.ind[2] == 4 && vector.ind[1] == 1 && mean.temp > 12.5 && doy < 222) { + if (vector.individual[2] == 4 && vector.individual[1] == 1 && mean.temp > 12.5 && doy < 222) { # Vittelogenic stage, 1st generation - if (vector.ind[4] == 0) { + if (vector.individual[4] == 0) { # Just turned in vittelogenic stage. - num_insects.birth=round(runif(1, 2 + opt$min_clutch_size, 8 + opt$max_clutch_size)) + num_insects.birth = round(runif(1, 2+opt$min_clutch_size, 8+opt$max_clutch_size)) } else { # Daily probability of birth. @@ -382,16 +411,16 @@ } } # Add to degree_days. - vector.ind[3] <- vector.ind[3] + degree_days.temp + vector.individual[3] <- vector.individual[3] + degree_days.temp # Add 1 day in current stage. - vector.ind[4] <- vector.ind[4] + 1 - vector.matrix[i,] <- vector.ind + vector.individual[4] <- vector.individual[4] + 1 + vector.matrix[i,] <- vector.individual if (num_insects.birth > 0) { # Add new birth -- might be in different generations. - new.gen <- vector.ind[1] + 1 + new.gen <- vector.individual[1] + 1 # Egg profile. - new.ind <- c(new.gen, 0, 0, 0, 0) - new.vector <- rep(new.ind, num_insects.birth) + new.individual <- c(new.gen, 0, 0, 0, 0) + new.vector <- rep(new.individual, num_insects.birth) # Update batch of egg profile. new.vector <- t(matrix(new.vector, nrow=5)) # Group with total eggs laid in that day. @@ -399,78 +428,78 @@ } } # Event 3 development (with diapause determination). - # Event 3.1 egg development to young nymph (vector.ind[2]=0 -> egg). - if (vector.ind[2] == 0) { + # Event 3.1 egg development to young nymph (vector.individual[2]=0 -> egg). + if (vector.individual[2] == 0) { # Egg stage. # Add to degree_days. - vector.ind[3] <- vector.ind[3] + degree_days.temp - if (vector.ind[3] >= (68 + opt$young_nymph_accum)) { + vector.individual[3] <- vector.individual[3] + degree_days.temp + if (vector.individual[3] >= (68+opt$young_nymph_accumulation)) { # From egg to young nymph, degree-days requirement met. - current.gen <- vector.ind[1] + current.gen <- vector.individual[1] # Transfer to young nymph stage. - vector.ind <- c(current.gen, 1, 0, 0, 0) + vector.individual <- c(current.gen, 1, 0, 0, 0) } else { # Add 1 day in current stage. - vector.ind[4] <- vector.ind[4] + 1 + vector.individual[4] <- vector.individual[4] + 1 } - vector.matrix[i,] <- vector.ind + vector.matrix[i,] <- vector.individual } - # Event 3.2 young nymph to old nymph (vector.ind[2]=1 -> young nymph: determines diapause). - if (vector.ind[2] == 1) { + # Event 3.2 young nymph to old nymph (vector.individual[2]=1 -> young nymph: determines diapause). + if (vector.individual[2] == 1) { # Young nymph stage. # Add to degree_days. - vector.ind[3] <- vector.ind[3] + degree_days.temp - if (vector.ind[3] >= (250 + opt$old_nymph_accum)) { + vector.individual[3] <- vector.individual[3] + degree_days.temp + if (vector.individual[3] >= (250+opt$old_nymph_accumulation)) { # From young to old nymph, degree_days requirement met. - current.gen <- vector.ind[1] + current.gen <- vector.individual[1] # Transfer to old nym stage. - vector.ind <- c(current.gen, 2, 0, 0, 0) + vector.individual <- c(current.gen, 2, 0, 0, 0) if (photoperiod < opt$photoperiod && doy > 180) { - vector.ind[5] <- 1 + vector.individual[5] <- 1 } # Prepare for diapausing. } else { # Add 1 day in current stage. - vector.ind[4] <- vector.ind[4] + 1 + vector.individual[4] <- vector.individual[4] + 1 } - vector.matrix[i,] <- vector.ind + vector.matrix[i,] <- vector.individual } # Event 3.3 old nymph to adult: previttelogenic or diapausing? - if (vector.ind[2] == 2) { + if (vector.individual[2] == 2) { # Old nymph stage. # Add to degree_days. - vector.ind[3] <- vector.ind[3] + degree_days.temp - if (vector.ind[3] >= (200 + opt$adult_accum)) { + vector.individual[3] <- vector.individual[3] + degree_days.temp + if (vector.individual[3] >= (200+opt$adult_accumulation)) { # From old to adult, degree_days requirement met. - current.gen <- vector.ind[1] - if (vector.ind[5] == 0) { + current.gen <- vector.individual[1] + if (vector.individual[5] == 0) { # Non-diapausing adult -- previttelogenic. - vector.ind <- c(current.gen, 3, 0, 0, 0) + vector.individual <- c(current.gen, 3, 0, 0, 0) } else { # Diapausing. - vector.ind <- c(current.gen, 5, 0, 0, 1) + vector.individual <- c(current.gen, 5, 0, 0, 1) } } else { # Add 1 day in current stage. - vector.ind[4] <- vector.ind[4] + 1 + vector.individual[4] <- vector.individual[4] + 1 } - vector.matrix[i,] <- vector.ind + vector.matrix[i,] <- vector.individual } # Event 4 growing of diapausing adult (unimportant, but still necessary). - if (vector.ind[2] == 5) { - vector.ind[3] <- vector.ind[3] + degree_days.temp - vector.ind[4] <- vector.ind[4] + 1 - vector.matrix[i,] <- vector.ind + if (vector.individual[2] == 5) { + vector.individual[3] <- vector.individual[3] + degree_days.temp + vector.individual[4] <- vector.individual[4] + 1 + vector.matrix[i,] <- vector.individual } } # Else if it is still alive. } # End of the individual bug loop. # Find the number of deaths. num_insects.death <- length(death.vector) if (num_insects.death > 0) { - # Remove record of dead. + # Remove record of dead. vector.matrix <- vector.matrix[-death.vector, ] } # Find the number of births. @@ -481,52 +510,53 @@ # Aggregate results by day. total.population <- c(total.population, num_insects) - # All adults population size. - num_insects.adult <- sum(vector.matrix[,2] == 3) + sum(vector.matrix[,2] == 4) + sum(vector.matrix[,2] == 5) - + num_insects.adult <- sum(vector.matrix[,2]==3)+sum(vector.matrix[,2]==4)+sum(vector.matrix[,2]==5) # Overwintering adult population size. - overwintering_adult.population[row] <- sum(vector.matrix[,1] == 0) + overwintering_adult.population[row] <- sum(vector.matrix[,1]==0) # First generation population size. - first_generation.population[row] <- sum(vector.matrix[,1] == 1) + first_generation.population[row] <- sum(vector.matrix[,1]==1) # Second generation population size. - second_generation.population[row] <- sum(vector.matrix[,1] == 2) - + second_generation.population[row] <- sum(vector.matrix[,1]==2) # Egg population size. - S0[row] <- sum(vector.matrix[,2]==0) + Eggs[row] <- sum(vector.matrix[,2]==0) # Young nymph population size. - S1[row] <- sum(vector.matrix[,2]==1) + YoungNymphs[row] <- sum(vector.matrix[,2]==1) # Old nymph population size. - S2[row] <- sum(vector.matrix[,2]==2) + OldNymphs[row] <- sum(vector.matrix[,2]==2) # Previtellogenic population size. - S3[row] <- sum(vector.matrix[,2]==3) + Previtellogenic[row] <- sum(vector.matrix[,2]==3) # Vitellogenic population size. - S4[row] <- sum(vector.matrix[,2]==4) + Vitellogenic[row] <- sum(vector.matrix[,2]==4) # Diapausing population size. - S5[row] <- sum(vector.matrix[,2]==5) - + Diapausing[row] <- sum(vector.matrix[,2]==5) + # P adult population size. P.adult[row] <- sum(vector.matrix[,1]==0) + # F1 adult population size. F1.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)) + # F2 adult population size F2.adult[row] <- sum((vector.matrix[,1]==2 & vector.matrix[,2]==3) | (vector.matrix[,1]==2 & vector.matrix[,2]==4) | (vector.matrix[,1]==2 & vector.matrix[,2]==5)) - + # Newborn population size. N.newborn[row] <- num_insects.newborn + # Dead population size. N.death[row] <- num_insects.death + # Adult population size. N.adult[row] <- num_insects.adult - } # end of days specified in the input temperature data + } # End of days specified in the input temperature data. degree_days.cum <- cumsum(degree_days.day) - # Collect all the outputs. - S0.replications[,N.replications] <- S0 - S1.replications[,N.replications] <- S1 - S2.replications[,N.replications] <- S2 - S3.replications[,N.replications] <- S3 - S4.replications[,N.replications] <- S4 - S5.replications[,N.replications] <- S5 + # Define the output values. + Eggs.replications[,N.replications] <- Eggs + YoungNymphs.replications[,N.replications] <- YoungNymphs + OldNymphs.replications[,N.replications] <- OldNymphs + Previtellogenic.replications[,N.replications] <- Previtellogenic + Vitellogenic.replications[,N.replications] <- Vitellogenic + Diapausing.replications[,N.replications] <- Diapausing newborn.replications[,N.replications] <- N.newborn death.replications[,N.replications] <- N.death adult.replications[,N.replications] <- N.adult - pop.replications[,N.replications] <- total.population + population.replications[,N.replications] <- total.population P.replications[,N.replications] <- overwintering_adult.population F1.replications[,N.replications] <- first_generation.population F2.replications[,N.replications] <- second_generation.population @@ -536,11 +566,11 @@ } # Mean value for adults. -adults <- apply((S3.replications + S4.replications + S5.replications), 1, mean) +adults <- apply((Previtellogenic.replications+Vitellogenic.replications+Diapausing.replications), 1, mean) # Mean value for nymphs. -nymphs <- apply((S1.replications + S2.replications), 1, mean) +nymphs <- apply((YoungNymphs.replications+OldNymphs.replications), 1, mean) # Mean value for eggs. -eggs <- apply(S0.replications, 1, mean) +eggs <- apply(Eggs.replications, 1, mean) # Mean value for P. P <- apply(P.replications, 1, mean) # Mean value for F1. @@ -553,13 +583,12 @@ F1_adults <- apply(F1_adults.replications, 1, mean) # Mean value for F2 adults. F2_adults <- apply(F2_adults.replications, 1, mean) - # Standard error for adults. -adults.std_error <- apply((S3.replications + S4.replications + S5.replications), 1, sd) / sqrt(opt$replications) +adults.std_error <- apply((Previtellogenic.replications+Vitellogenic.replications+Diapausing.replications), 1, sd) / sqrt(opt$replications) # Standard error for nymphs. -nymphs.std_error <- apply((S1.replications + S2.replications) / sqrt(opt$replications), 1, sd) +nymphs.std_error <- apply((YoungNymphs.replications+OldNymphs.replications) / sqrt(opt$replications), 1, sd) # Standard error for eggs. -eggs.std_error <- apply(S0.replications, 1, sd) / sqrt(opt$replications) +eggs.std_error <- apply(Eggs.replications, 1, sd) / sqrt(opt$replications) # Standard error value for P. P.std_error <- apply(P.replications, 1, sd) / sqrt(opt$replications) # Standard error for F1. @@ -573,11 +602,10 @@ # Standard error for F2 adult. F2_adults.std_error <- apply(F2_adults.replications, 1, sd) / sqrt(opt$replications) -dev.new(width=20, height=30) +dev.new(width=20, height=40) # Start PDF device driver to save charts to output. -pdf(file=opt$output, width=20, height=30, bg="white") - +pdf(file=opt$output, width=20, height=40, bg="white") par(mar=c(5, 6, 4, 4), mfrow=c(3, 1)) # Data analysis and visualization plots @@ -587,69 +615,21 @@ end_date <- temperature_data_frame$DATE[opt$num_days] # Subfigure 1: population size by life stage -title <- paste(opt$insect, ": Total pop. by life stage :", opt$location, ": Lat:", latitude, ":", start_date, "-", end_date, sep=" ") -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) -# Young and old nymphs. -lines(day.all, nymphs, lwd=2, lty=1, col=2) -# Eggs -lines(day.all, eggs, lwd=2, lty=1, col=4) -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")) -axis(2, cex.axis=3) -legend("topleft", c("Egg", "Nymph", "Adult"), lty=c(1, 1, 1), col=c(4, 2, 1), cex=3) -if (opt$std_error_plot == 1) { - # Add Standard error lines to plot - # Standard error for adults - lines (day.all, adults+adults.std_error, lty=2) - lines (day.all, adults-adults.std_error, lty=2) - # Standard error for nymphs - lines (day.all, nymphs+nymphs.std_error, col=2, lty=2) - lines (day.all, nymphs-nymphs.std_error, col=2, lty=2) - # Standard error for eggs - lines (day.all, eggs+eggs.std_error, col=4, lty=2) - lines (day.all, eggs-eggs.std_error, col=4, lty=2) -} +maxval <- max(eggs+eggs.std_error, nymphs+nymphs.std_error, adults+adults.std_error) +render_chart("pop_size_by_life_stage", opt$insect, opt$location, latitude, start_date, end_date, days.all, maxval, + opt$std_error_plot, adults, nymphs, eggs, adults.std_error, nymphs.std_error, eggs.std_error) # Subfigure 2: population size by generation -title <- paste(opt$insect, ": Total pop. by generation :", opt$location, ": Lat:", latitude, ":", start_date, "-", end_date, sep=" ") -plot(day.all, P, main=title, type="l", ylim=c(0, max(F2)), axes=F, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3) -lines(day.all, F1, lwd = 2, lty = 1, col=2) -lines(day.all, F2, lwd = 2, lty = 1, col=4) -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")) -axis(2, cex.axis=3) -legend("topleft", c("P", "F1", "F2"), lty=c(1, 1, 1), col=c(1, 2, 4), cex=3) -if (opt$std_error_plot == 1) { - # Add Standard error lines to plot - # Standard error for adults - lines (day.all, P+P.std_error, lty=2) - lines (day.all, P-P.std_error, lty=2) - # Standard error for nymphs - lines (day.all, F1+F1.std_error, col=2, lty=2) - lines (day.all, F1-F1.std_error, col=2, lty=2) - # Standard error for eggs - lines (day.all, F2+F2.std_error, col=4, lty=2) - lines (day.all, F2-F2.std_error, col=4, lty=2) -} +maxval <- max(F2) +render_chart("pop_size_by_generation", opt$insect, opt$location, latitude, start_date, end_date, days.all, maxval, + opt$std_error_plot, P, F1, F2, P.std_error, F1.std_error, F2.std_error) + # Subfigure 3: adult population size by generation -title <- paste(opt$insect, ": Adult pop. by generation :", opt$location, ": Lat:", latitude, ":", start_date, "-", end_date, sep=" ") -plot(day.all, P_adults, 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) -lines(day.all, F1_adults, lwd = 2, lty = 1, col=2) -lines(day.all, F2_adults, lwd = 2, lty = 1, col=4) -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")) -axis(2, cex.axis=3) -legend("topleft", c("P", "F1", "F2"), lty=c(1, 1, 1), col=c(1, 2, 4), cex=3) -if (opt$std_error_plot == 1) { - # Add Standard error lines to plot - # Standard error for adults - lines (day.all, P_adults+P_adults.std_error, lty=2) - lines (day.all, P_adults-P_adults.std_error, lty=2) - # Standard error for nymphs - lines (day.all, F1_adults+F1_adults.std_error, col=2, lty=2) - lines (day.all, F1_adults-F1_adults.std_error, col=2, lty=2) - # Standard error for eggs - lines (day.all, F2_adults+F2_adults.std_error, col=4, lty=2) - lines (day.all, F2_adults-F2_adults.std_error, col=4, lty=2) -} +maxval <- max(F2_adults) + 100 +render_chart("adult_pop_size_by_generation", opt$insect, opt$location, latitude, start_date, end_date, days.all, maxval, + opt$std_error_plot, P_adults, F1_adults, F2_adults, P_adults.std_error, F1_adults.std_error, F2_adults2.std_error) + # Turn off device driver to flush output. dev.off()