Mercurial > repos > greg > insect_phenology_model
changeset 6:fe3f86012394 draft
Uploaded
| author | greg |
|---|---|
| date | Wed, 06 Dec 2017 10:07:21 -0500 |
| parents | 1878a03f9c9f |
| children | ad26f07a7dd8 |
| files | insect_phenology_model.R insect_phenology_model.xml test-data/output.pdf |
| diffstat | 3 files changed, 446 insertions(+), 441 deletions(-) [+] |
line wrap: on
line diff
--- a/insect_phenology_model.R Wed Nov 22 13:22:49 2017 -0500 +++ b/insect_phenology_model.R Wed Dec 06 10:07:21 2017 -0500 @@ -3,46 +3,30 @@ 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 DD 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("-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 DD 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"), - make_option(c("-q", "--photoperiod"), action="store", dest="photoperiod", type="double", help="Critical photoperiod for diapause induction/termination"), - make_option(c("-s", "--replications"), action="store", dest="replications", type="integer", help="Number of replications"), - make_option(c("-t", "--se_plot"), action="store", dest="se_plot", help="Plot SE"), - 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 DD accumulation (egg->young nymph)"), - make_option(c("-x", "--insect"), action="store", dest="insect", help="Insect name") + make_option(c("--adult_mortality"), action="store", dest="adult_mortality", type="integer", help="Adjustment rate for adult mortality"), + make_option(c("--adult_accumulation"), action="store", dest="adult_accumulation", type="integer", help="Adjustment of degree-days accumulation (old nymph->adult)"), + make_option(c("--egg_mortality"), action="store", dest="egg_mortality", type="integer", help="Adjustment rate for egg mortality"), + make_option(c("--input"), action="store", dest="input", help="Temperature data for selected location"), + make_option(c("--insect"), action="store", dest="insect", help="Insect name"), + make_option(c("--insects_per_replication"), action="store", dest="insects_per_replication", type="integer", help="Number of insects with which to start each replication"), + make_option(c("--location"), action="store", dest="location", help="Selected location"), + make_option(c("--min_clutch_size"), action="store", dest="min_clutch_size", type="integer", help="Adjustment of minimum clutch size"), + make_option(c("--max_clutch_size"), action="store", dest="max_clutch_size", type="integer", help="Adjustment of maximum clutch size"), + make_option(c("--nymph_mortality"), action="store", dest="nymph_mortality", type="integer", help="Adjustment rate for nymph mortality"), + make_option(c("--old_nymph_accumulation"), action="store", dest="old_nymph_accumulation", type="integer", help="Adjustment of degree-days accumulation (young nymph->old nymph)"), + make_option(c("--num_days"), action="store", dest="num_days", type="integer", help="Total number of days in the temperature dataset"), + make_option(c("--output"), action="store", dest="output", help="Output dataset"), + make_option(c("--oviposition"), action="store", dest="oviposition", type="integer", help="Adjustment for oviposition rate"), + make_option(c("--photoperiod"), action="store", dest="photoperiod", type="double", help="Critical photoperiod for diapause induction/termination"), + make_option(c("--replications"), action="store", dest="replications", type="integer", help="Number of replications"), + make_option(c("--std_error_plot"), action="store", dest="std_error_plot", help="Plot Standard error"), + make_option(c("--young_nymph_accumulation"), action="store", dest="young_nymph_accumulation", type="integer", help="Adjustment of degree-days accumulation (egg->young nymph)") ) parser <- OptionParser(usage="%prog [options] file", option_list=option_list) 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 @@ -57,29 +41,52 @@ 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 - dd <- 0 - if (dxp < threshold) { - dd <- 0 + averages <- 0 + if (curr_max_temp < threshold) { + averages <- 0 } else { # Initialize hourly temperature. @@ -98,12 +105,12 @@ 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 } @@ -111,9 +118,9 @@ dh[i] <- T[i] - 8.4 } } - else if (i > settime) { + 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 +130,7 @@ } 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 } @@ -132,99 +139,153 @@ } } } - dd <- sum(dh) / 24 + averages <- sum(dh) / 24 } - return(c(dmean, dd)) -} - -dev.egg = function(temperature) { - dev.rate= -0.9843 * temperature + 33.438 - return(dev.rate) + return(c(curr_mean_temp, averages)) } -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_text <- c("Egg", "Nymph", "Adult") + columns <- c(4, 2, 1) + } else if (chart_type == "pop_size_by_generation") { + title <- paste(insect, ": Total pop. by generation :", location, ": Lat:", latitude, ":", start_date, "-", end_date, sep=" ") + legend_text <- c("P", "F1", "F2") + columns <- c(1, 2, 4) + } 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_text <- c("P", "F1", "F2") + columns <- c(1, 2, 4) } - 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) + legend("topleft", legend_text, lty=c(1, 1, 1), col=columns, cex=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$num_days) -# All latitude values are the same, -# so get the value from the first row. +# All latitude values are the same, so get the value from the first row. latitude <- temperature_data_frame$LATITUDE[1] -cat("Number of days: ", opt$num_days, "\n") +# Initialize matrices. +Eggs.replications <- matrix(rep(0, opt$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$replications) -# Initialize matrix for results from all replications. -S0.rep <- S1.rep <- S2.rep <- S3.rep <- S4.rep <- S5.rep <- matrix(rep(0, opt$num_days * opt$replications), ncol = opt$replications) -newborn.rep <- death.rep <- adult.rep <- pop.rep <- g0.rep <- g1.rep <- g2.rep <- g0a.rep <- g1a.rep <- g2a.rep <- matrix(rep(0, opt$num_days * opt$replications), ncol=opt$replications) +newborn.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) +adult.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) +death.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) + +P.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) +P_adults.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) +F1.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) +F1_adults.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) +F2.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) +F2_adults.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) + +population.replications <- matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications) -# Loop through replications. -for (N.rep in 1:opt$replications) { - # During each replication start with 1000 individuals. - # TODO: user definable as well? - n <- 1000 - # Generation, Stage, DD, T, Diapause. - vec.ini <- c(0, 3, 0, 0, 0) - # Overwintering, previttelogenic, DD=0, T=0, no-diapause. - vec.mat <- rep(vec.ini, n) +# Process replications. +for (N.replications in 1:opt$replications) { + # Start with the user-defined number of insects per replication. + num_insects <- opt$insects_per_replication + # Generation, Stage, degree-days, T, Diapause. + vector.ini <- c(0, 3, 0, 0, 0) + # Overwintering, previttelogenic, degree-days=0, T=0, no-diapause. + vector.matrix <- rep(vector.ini, num_insects) # Complete matrix for the population. - vec.mat <- base::t(matrix(vec.mat, nrow=5)) + vector.matrix <- base::t(matrix(vector.matrix, nrow=5)) # Time series of population size. - tot.pop <- NULL - gen0.pop <- rep(0, opt$num_days) - gen1.pop <- rep(0, opt$num_days) - gen2.pop <- rep(0, opt$num_days) - S0 <- S1 <- S2 <- S3 <- S4 <- S5 <- rep(0, opt$num_days) - g0.adult <- g1.adult <- g2.adult <- rep(0, opt$num_days) - N.newborn <- N.death <- N.adult <- rep(0, opt$num_days) - dd.day <- 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$num_days) + + N.newborn <- rep(0, opt$num_days) + N.adult <- rep(0, opt$num_days) + N.death <- rep(0, opt$num_days) + + overwintering_adult.population <- rep(0, opt$num_days) + first_generation.population <- rep(0, opt$num_days) + second_generation.population <- 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) + + total.population <- NULL + + averages.day <- rep(0, opt$num_days) # All the days included in the input temperature dataset. for (row in 1:opt$num_days) { # Get the integer day of the year for the current row. @@ -233,415 +294,357 @@ photoperiod <- temperature_data_frame$DAYLEN[row] temp.profile <- get_temperature_at_hour(latitude, temperature_data_frame, row, opt$num_days) mean.temp <- temp.profile[1] - dd.temp <- temp.profile[2] - dd.day[row] <- dd.temp + averages.temp <- temp.profile[2] + averages.day[row] <- averages.temp # Trash bin for death. - death.vec <- NULL + death.vector <- NULL # Newborn. - birth.vec <- NULL + birth.vector <- NULL # All individuals. - for (i in 1:n) { - # Find individual record. - vec.ind <- vec.mat[i,] - # First of all, still alive? - # Adjustment for late season mortality rate. + for (i in 1:num_insects) { + # Individual record. + vector.individual <- vector.matrix[i,] + # Adjustment for late season mortality rate (still alive?). if (latitude < 40.0) { - post.mort <- 1 + post.mortality <- 1 day.kill <- 300 } else { - post.mort <- 2 + post.mortality <- 2 day.kill <- 250 } - if (vec.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 (vec.ind[2] == 1 | vec.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 (vec.ind[2] == 3 | vec.ind[2] == 4 | vec.ind[2] == 5) { - # For adult. + else if (vector.individual[2] == 3 | vector.individual[2] == 4 | vector.individual[2] == 5) { + # 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?) + # Dependent on temperature and life stage? u.d <- runif(1) - if (u.d < death.prob) { - death.vec <- c(death.vec, i) - } + if (u.d < death.probability) { + death.vector <- c(death.vector, i) + } else { - # Aggregrate index of dead bug. - # Event 1 end of diapause. - if (vec.ind[1] == 0 && vec.ind[2] == 3) { + # End of diapause. + if (vector.individual[1] == 0 && vector.individual[2] == 3) { # Overwintering adult (previttelogenic). - if (photoperiod > opt$photoperiod && vec.ind[3] > 68 && doy < 180) { + if (photoperiod > opt$photoperiod && vector.individual[3] > 68 && doy < 180) { # Add 68C to become fully reproductively matured. # Transfer to vittelogenic. - vec.ind <- c(0, 4, 0, 0, 0) - vec.mat[i,] <- vec.ind + vector.individual <- c(0, 4, 0, 0, 0) + vector.matrix[i,] <- vector.individual } else { - # Add to dd. - vec.ind[3] <- vec.ind[3] + dd.temp + # Add to # Add average temperature for current day. + vector.individual[3] <- vector.individual[3] + averages.temp # Add 1 day in current stage. - vec.ind[4] <- vec.ind[4] + 1 - vec.mat[i,] <- vec.ind + vector.individual[4] <- vector.individual[4] + 1 + vector.matrix[i,] <- vector.individual } } - if (vec.ind[1] != 0 && vec.ind[2] == 3) { + if (vector.individual[1] != 0 && vector.individual[2] == 3) { # Not overwintering adult (previttelogenic). - current.gen <- vec.ind[1] - if (vec.ind[3] > 68) { + current.gen <- vector.individual[1] + if (vector.individual[3] > 68) { # Add 68C to become fully reproductively matured. # Transfer to vittelogenic. - vec.ind <- c(current.gen, 4, 0, 0, 0) - vec.mat[i,] <- vec.ind + vector.individual <- c(current.gen, 4, 0, 0, 0) + vector.matrix[i,] <- vector.individual } else { - # Add to dd. - vec.ind[3] <- vec.ind[3] + dd.temp + # Add average temperature for current day. + vector.individual[3] <- vector.individual[3] + averages.temp # Add 1 day in current stage. - vec.ind[4] <- vec.ind[4] + 1 - vec.mat[i,] <- vec.ind + vector.individual[4] <- vector.individual[4] + 1 + vector.matrix[i,] <- vector.individual } } - # Event 2 oviposition -- where population dynamics comes from. - if (vec.ind[2] == 4 && vec.ind[1] == 0 && mean.temp > 10) { + # Oviposition -- where population dynamics comes from. + if (vector.individual[2] == 4 && vector.individual[1] == 0 && mean.temp > 10) { # Vittelogenic stage, overwintering generation. - if (vec.ind[4] == 0) { + if (vector.individual[4] == 0) { # Just turned in vittelogenic stage. - n.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. p.birth = opt$oviposition * 0.01 u1 <- runif(1) if (u1 < p.birth) { - n.birth=round(runif(1, 2, 8)) + num_insects.birth = round(runif(1, 2, 8)) } } - # Add to dd. - vec.ind[3] <- vec.ind[3] + dd.temp + # Add average temperature for current day. + vector.individual[3] <- vector.individual[3] + averages.temp # Add 1 day in current stage. - vec.ind[4] <- vec.ind[4] + 1 - vec.mat[i,] <- vec.ind - if (n.birth > 0) { + vector.individual[4] <- vector.individual[4] + 1 + vector.matrix[i,] <- vector.individual + if (num_insects.birth > 0) { # Add new birth -- might be in different generations. - new.gen <- vec.ind[1] + 1 + new.gen <- vector.individual[1] + 1 # Egg profile. - new.ind <- c(new.gen, 0, 0, 0, 0) - new.vec <- rep(new.ind, n.birth) + new.individual <- c(new.gen, 0, 0, 0, 0) + new.vector <- rep(new.individual, num_insects.birth) # Update batch of egg profile. - new.vec <- t(matrix(new.vec, nrow=5)) + new.vector <- t(matrix(new.vector, nrow=5)) # Group with total eggs laid in that day. - birth.vec <- rbind(birth.vec, new.vec) + birth.vector <- rbind(birth.vector, new.vector) } } - # Event 2 oviposition -- for generation 1. - if (vec.ind[2] == 4 && vec.ind[1] == 1 && mean.temp > 12.5 && doy < 222) { + # Oviposition -- for generation 1. + if (vector.individual[2] == 4 && vector.individual[1] == 1 && mean.temp > 12.5 && doy < 222) { # Vittelogenic stage, 1st generation - if (vec.ind[4] == 0) { + if (vector.individual[4] == 0) { # Just turned in vittelogenic stage. - n.birth=round(runif(1, 2 + opt$min_clutch_size, 8 + opt$max_clutch_size)) + num_insects.birth = round(runif(1, 2+opt$min_clutch_size, 8+opt$max_clutch_size)) } else { # Daily probability of birth. p.birth = opt$oviposition * 0.01 u1 <- runif(1) if (u1 < p.birth) { - n.birth = round(runif(1, 2, 8)) + num_insects.birth = round(runif(1, 2, 8)) } } - # Add to dd. - vec.ind[3] <- vec.ind[3] + dd.temp + # Add average temperature for current day. + vector.individual[3] <- vector.individual[3] + averages.temp # Add 1 day in current stage. - vec.ind[4] <- vec.ind[4] + 1 - vec.mat[i,] <- vec.ind - if (n.birth > 0) { + 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 <- vec.ind[1] + 1 + new.gen <- vector.individual[1] + 1 # Egg profile. - new.ind <- c(new.gen, 0, 0, 0, 0) - new.vec <- rep(new.ind, n.birth) + new.individual <- c(new.gen, 0, 0, 0, 0) + new.vector <- rep(new.individual, num_insects.birth) # Update batch of egg profile. - new.vec <- t(matrix(new.vec, nrow=5)) + new.vector <- t(matrix(new.vector, nrow=5)) # Group with total eggs laid in that day. - birth.vec <- rbind(birth.vec, new.vec) + birth.vector <- rbind(birth.vector, new.vector) } } - # Event 3 development (with diapause determination). - # Event 3.1 egg development to young nymph (vec.ind[2]=0 -> egg). - if (vec.ind[2] == 0) { - # Egg stage. - # Add to dd. - vec.ind[3] <- vec.ind[3] + dd.temp - if (vec.ind[3] >= (68 + opt$young_nymph_accum)) { - # From egg to young nymph, DD requirement met. - current.gen <- vec.ind[1] + # Egg to young nymph. + if (vector.individual[2] == 0) { + # Add average temperature for current day. + vector.individual[3] <- vector.individual[3] + averages.temp + if (vector.individual[3] >= (68+opt$young_nymph_accumulation)) { + # From egg to young nymph, degree-days requirement met. + current.gen <- vector.individual[1] # Transfer to young nymph stage. - vec.ind <- c(current.gen, 1, 0, 0, 0) + vector.individual <- c(current.gen, 1, 0, 0, 0) } else { # Add 1 day in current stage. - vec.ind[4] <- vec.ind[4] + 1 + vector.individual[4] <- vector.individual[4] + 1 } - vec.mat[i,] <- vec.ind + vector.matrix[i,] <- vector.individual } - # Event 3.2 young nymph to old nymph (vec.ind[2]=1 -> young nymph: determines diapause). - if (vec.ind[2] == 1) { - # young nymph stage. - # add to dd. - vec.ind[3] <- vec.ind[3] + dd.temp - if (vec.ind[3] >= (250 + opt$old_nymph_accum)) { - # From young to old nymph, dd requirement met. - current.gen <- vec.ind[1] + # Young nymph to old nymph. + if (vector.individual[2] == 1) { + # Add average temperature for current day. + vector.individual[3] <- vector.individual[3] + averages.temp + if (vector.individual[3] >= (250+opt$old_nymph_accumulation)) { + # From young to old nymph, degree_days requirement met. + current.gen <- vector.individual[1] # Transfer to old nym stage. - vec.ind <- c(current.gen, 2, 0, 0, 0) + vector.individual <- c(current.gen, 2, 0, 0, 0) if (photoperiod < opt$photoperiod && doy > 180) { - vec.ind[5] <- 1 + vector.individual[5] <- 1 } # Prepare for diapausing. } else { # Add 1 day in current stage. - vec.ind[4] <- vec.ind[4] + 1 + vector.individual[4] <- vector.individual[4] + 1 } - vec.mat[i,] <- vec.ind - } - # Event 3.3 old nymph to adult: previttelogenic or diapausing? - if (vec.ind[2] == 2) { - # Old nymph stage. - # add to dd. - vec.ind[3] <- vec.ind[3] + dd.temp - if (vec.ind[3] >= (200 + opt$adult_accum)) { - # From old to adult, dd requirement met. - current.gen <- vec.ind[1] - if (vec.ind[5] == 0) { - # Non-diapausing adult -- previttelogenic. - vec.ind <- c(current.gen, 3, 0, 0, 0) + vector.matrix[i,] <- vector.individual + } + # Old nymph to adult: previttelogenic or diapausing? + if (vector.individual[2] == 2) { + # Add average temperature for current day. + vector.individual[3] <- vector.individual[3] + averages.temp + if (vector.individual[3] >= (200+opt$adult_accumulation)) { + # From old to adult, degree_days requirement met. + current.gen <- vector.individual[1] + if (vector.individual[5] == 0) { + # Previttelogenic. + vector.individual <- c(current.gen, 3, 0, 0, 0) } else { # Diapausing. - vec.ind <- c(current.gen, 5, 0, 0, 1) + vector.individual <- c(current.gen, 5, 0, 0, 1) } } else { # Add 1 day in current stage. - vec.ind[4] <- vec.ind[4] + 1 + vector.individual[4] <- vector.individual[4] + 1 } - vec.mat[i,] <- vec.ind + vector.matrix[i,] <- vector.individual } - # Event 4 growing of diapausing adult (unimportant, but still necessary). - if (vec.ind[2] == 5) { - vec.ind[3] <- vec.ind[3] + dd.temp - vec.ind[4] <- vec.ind[4] + 1 - vec.mat[i,] <- vec.ind + # Growing of diapausing adult (unimportant, but still necessary). + if (vector.individual[2] == 5) { + vector.individual[3] <- vector.individual[3] + averages.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 how many died. - n.death <- length(death.vec) - if (n.death > 0) { - vec.mat <- vec.mat[-death.vec, ] + + # Number of deaths. + num_insects.death <- length(death.vector) + if (num_insects.death > 0) { + # Remove record of dead. + vector.matrix <- vector.matrix[-death.vector, ] } - # Remove record of dead. - # Find how many new born. - n.newborn <- length(birth.vec[,1]) - vec.mat <- rbind(vec.mat, birth.vec) + # Number of births. + num_insects.newborn <- length(birth.vector[,1]) + vector.matrix <- rbind(vector.matrix, birth.vector) # Update population size for the next day. - n <- n - n.death + n.newborn + num_insects <- num_insects - num_insects.death + num_insects.newborn # Aggregate results by day. - tot.pop <- c(tot.pop, n) - # Egg. - s0 <- sum(vec.mat[,2] == 0) - # Young nymph. - s1 <- sum(vec.mat[,2] == 1) - # Old nymph. - s2 <- sum(vec.mat[,2] == 2) - # Previtellogenic. - s3 <- sum(vec.mat[,2] == 3) - # Vitellogenic. - s4 <- sum(vec.mat[,2] == 4) - # Diapausing. - s5 <- sum(vec.mat[,2] == 5) - # Overwintering adult. - gen0 <- sum(vec.mat[,1] == 0) - # First generation. - gen1 <- sum(vec.mat[,1] == 1) - # Second generation. - gen2 <- sum(vec.mat[,1] == 2) - # Sum of all adults. - n.adult <- sum(vec.mat[,2] == 3) + sum(vec.mat[,2] == 4) + sum(vec.mat[,2] == 5) + # Egg population size. + Eggs[row] <- sum(vector.matrix[,2]==0) + # Young nymph population size. + YoungNymphs[row] <- sum(vector.matrix[,2]==1) + # Old nymph population size. + OldNymphs[row] <- sum(vector.matrix[,2]==2) + # Previtellogenic population size. + Previtellogenic[row] <- sum(vector.matrix[,2]==3) + # Vitellogenic population size. + Vitellogenic[row] <- sum(vector.matrix[,2]==4) + # Diapausing population size. + Diapausing[row] <- sum(vector.matrix[,2]==5) - # Generation 0 pop size. - gen0.pop[row] <- gen0 - gen1.pop[row] <- gen1 - gen2.pop[row] <- gen2 + # Newborn population size. + N.newborn[row] <- num_insects.newborn + # Adult population size. + N.adult[row] <- sum(vector.matrix[,2]==3) + sum(vector.matrix[,2]==4) + sum(vector.matrix[,2]==5) + # Dead population size. + N.death[row] <- num_insects.death + + total.population <- c(total.population, num_insects) + + # Overwintering adult population size. + overwintering_adult.population[row] <- sum(vector.matrix[,1]==0) + # First generation population size. + first_generation.population[row] <- sum(vector.matrix[,1]==1) + # Second generation population size. + second_generation.population[row] <- sum(vector.matrix[,1]==2) - S0[row] <- s0 - S1[row] <- s1 - S2[row] <- s2 - S3[row] <- s3 - S4[row] <- s4 - S5[row] <- s5 + # 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)) + } # End of days specified in the input temperature data. - g0.adult[row] <- sum(vec.mat[,1] == 0) - g1.adult[row] <- sum((vec.mat[,1] == 1 & vec.mat[,2] == 3) | (vec.mat[,1] == 1 & vec.mat[,2] == 4) | (vec.mat[,1] == 1 & vec.mat[,2] == 5)) - g2.adult[row] <- sum((vec.mat[,1]== 2 & vec.mat[,2] == 3) | (vec.mat[,1] == 2 & vec.mat[,2] == 4) | (vec.mat[,1] == 2 & vec.mat[,2] == 5)) - - N.newborn[row] <- n.newborn - N.death[row] <- n.death - N.adult[row] <- n.adult - } # end of days specified in the input temperature data - - dd.cum <- cumsum(dd.day) + averages.cum <- cumsum(averages.day) - # Collect all the outputs. - S0.rep[,N.rep] <- S0 - S1.rep[,N.rep] <- S1 - S2.rep[,N.rep] <- S2 - S3.rep[,N.rep] <- S3 - S4.rep[,N.rep] <- S4 - S5.rep[,N.rep] <- S5 - newborn.rep[,N.rep] <- N.newborn - death.rep[,N.rep] <- N.death - adult.rep[,N.rep] <- N.adult - pop.rep[,N.rep] <- tot.pop - g0.rep[,N.rep] <- gen0.pop - g1.rep[,N.rep] <- gen1.pop - g2.rep[,N.rep] <- gen2.pop - g0a.rep[,N.rep] <- g0.adult - g1a.rep[,N.rep] <- g1.adult - g2a.rep[,N.rep] <- g2.adult + # 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 + adult.replications[,N.replications] <- N.adult + death.replications[,N.replications] <- N.death + + P.replications[,N.replications] <- overwintering_adult.population + P_adults.replications[,N.replications] <- P.adult + F1.replications[,N.replications] <- first_generation.population + F1_adults.replications[,N.replications] <- F1.adult + F2.replications[,N.replications] <- second_generation.population + F2_adults.replications[,N.replications] <- F2.adult + + population.replications[,N.replications] <- total.population } -# Data analysis and visualization can currently -# plot only within a single calendar year. -# TODO: enhance this to accomodate multiple calendar years. -start_date <- temperature_data_frame$DATE[1] -end_date <- temperature_data_frame$DATE[opt$num_days] +# Mean value for eggs. +eggs <- apply(Eggs.replications, 1, mean) +# Standard error for eggs. +eggs.std_error <- apply(Eggs.replications, 1, sd) / sqrt(opt$replications) + +# Mean value for nymphs. +nymphs <- apply((YoungNymphs.replications+OldNymphs.replications), 1, mean) +# Standard error for nymphs. +nymphs.std_error <- apply((YoungNymphs.replications+OldNymphs.replications) / sqrt(opt$replications), 1, sd) -n.yr <- 1 -day.all <- c(1:opt$num_days * n.yr) +# Mean value for adults. +adults <- apply((Previtellogenic.replications+Vitellogenic.replications+Diapausing.replications), 1, mean) +# Standard error for adults. +adults.std_error <- apply((Previtellogenic.replications+Vitellogenic.replications+Diapausing.replications), 1, sd) / sqrt(opt$replications) + +# Mean value for P. +P <- apply(P.replications, 1, mean) +# Standard error for P. +P.std_error <- apply(P.replications, 1, sd) / sqrt(opt$replications) -# mean value for adults -sa <- apply((S3.rep + S4.rep + S5.rep), 1, mean) -# mean value for nymphs -sn <- apply((S1.rep + S2.rep), 1,mean) -# mean value for eggs -se <- apply(S0.rep, 1, mean) -# mean value for P -g0 <- apply(g0.rep, 1, mean) -# mean value for F1 -g1 <- apply(g1.rep, 1, mean) -# mean value for F2 -g2 <- apply(g2.rep, 1, mean) -# mean value for P adult -g0a <- apply(g0a.rep, 1, mean) -# mean value for F1 adult -g1a <- apply(g1a.rep, 1, mean) -# mean value for F2 adult -g2a <- apply(g2a.rep, 1, mean) +# Mean value for P adults. +P_adults <- apply(P_adults.replications, 1, mean) +# Standard error for P_adult. +P_adults.std_error <- apply(P_adults.replications, 1, sd) / sqrt(opt$replications) + +# Mean value for F1. +F1 <- apply(F1.replications, 1, mean) +# Standard error for F1. +F1.std_error <- apply(F1.replications, 1, sd) / sqrt(opt$replications) -# SE for adults -sa.se <- apply((S3.rep + S4.rep + S5.rep), 1, sd) / sqrt(opt$replications) -# SE for nymphs -sn.se <- apply((S1.rep + S2.rep) / sqrt(opt$replications), 1, sd) -# SE for eggs -se.se <- apply(S0.rep, 1, sd) / sqrt(opt$replications) -# SE value for P -g0.se <- apply(g0.rep, 1, sd) / sqrt(opt$replications) -# SE for F1 -g1.se <- apply(g1.rep, 1, sd) / sqrt(opt$replications) -# SE for F2 -g2.se <- apply(g2.rep, 1, sd) / sqrt(opt$replications) -# SE for P adult -g0a.se <- apply(g0a.rep, 1, sd) / sqrt(opt$replications) -# SE for F1 adult -g1a.se <- apply(g1a.rep, 1, sd) / sqrt(opt$replications) -# SE for F2 adult -g2a.se <- apply(g2a.rep, 1, sd) / sqrt(opt$replications) +# Mean value for F1 adults. +F1_adults <- apply(F1_adults.replications, 1, mean) +# Standard error for F1 adult. +F1_adults.std_error <- apply(F1_adults.replications, 1, sd) / sqrt(opt$replications) + +# Mean value for F2. +F2 <- apply(F2.replications, 1, mean) +# Standard error for F2. +F2.std_error <- apply(F2.replications, 1, sd) / sqrt(opt$replications) + +# Mean value for F2 adults. +F2_adults <- apply(F2_adults.replications, 1, mean) +# Standard error for F2 adult. +F2_adults.std_error <- apply(F2_adults.replications, 1, sd) / sqrt(opt$replications) + +# Display the total number of days in the Galaxy history item blurb. +cat("Number of days: ", opt$num_days, "\n") dev.new(width=20, height=30) # Start PDF device driver to save charts to output. pdf(file=opt$output, width=20, height=30, bg="white") - -par(mar = c(5, 6, 4, 4), mfrow=c(3, 1)) +par(mar=c(5, 6, 4, 4), mfrow=c(3, 1)) -# Subfigure 1: population size by life stage -title <- paste(opt$insect, ": Total pop. by life stage :", opt$location, ": Lat:", latitude, ":", start_date, "-", end_date, sep=" ") -plot(day.all, sa, main=title, type="l", ylim=c(0, max(se + se.se, sn + sn.se, sa + sa.se)), axes=F, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3) -# Young and old nymphs. -lines(day.all, sn, lwd=2, lty=1, col=2) -# Eggs -lines(day.all, se, lwd=2, lty=1, col=4) -axis(1, at=c(1:12) * 30 - 15, cex.axis=3, labels=c("Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec")) -axis(2, cex.axis=3) -leg.text <- c("Egg", "Nymph", "Adult") -legend("topleft", leg.text, lty=c(1, 1, 1), col=c(4, 2, 1), cex=3) -if (opt$se_plot == 1) { - # Add SE lines to plot - # SE for adults - lines (day.all, sa + sa.se, lty=2) - lines (day.all, sa - sa.se, lty=2) - # SE for nymphs - lines (day.all, sn + sn.se, col=2, lty=2) - lines (day.all, sn - sn.se, col=2, lty=2) - # SE for eggs - lines (day.all, se + se.se, col=4, lty=2) - lines (day.all, se - se.se, col=4, lty=2) -} +# Data analysis and visualization plots only within a single calendar year. +days <- c(1:opt$num_days) +start_date <- temperature_data_frame$DATE[1] +end_date <- temperature_data_frame$DATE[opt$num_days] -# 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, g0, main=title, type="l", ylim=c(0, max(g2)), axes=F, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3) -lines(day.all, g1, lwd = 2, lty = 1, col=2) -lines(day.all, g2, 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) -leg.text <- c("P", "F1", "F2") -legend("topleft", leg.text, lty=c(1, 1, 1), col=c(1, 2, 4), cex=3) -if (opt$se_plot == 1) { - # Add SE lines to plot - # SE for adults - lines (day.all, g0+g0.se, lty=2) - lines (day.all, g0-g0.se, lty=2) - # SE for nymphs - lines (day.all, g1+g1.se, col=2, lty=2) - lines (day.all, g1-g1.se, col=2, lty=2) - # SE for eggs - lines (day.all, g2+g2.se, col=4, lty=2) - lines (day.all, g2-g2.se, col=4, lty=2) -} - -# Subfigure 3: adult population size by generation -title <- paste(opt$insect, ": Adult pop. by generation :", opt$location, ": Lat:", latitude, ":", start_date, "-", end_date, sep=" ") -plot(day.all, g0a, ylim=c(0, max(g2a) + 100), main=title, type="l", axes=F, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3) -lines(day.all, g1a, lwd = 2, lty = 1, col=2) -lines(day.all, g2a, lwd = 2, lty = 1, col=4) -axis(1, at=c(1:12) * 30 - 15, cex.axis=3, labels = c("Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec")) -axis(2, cex.axis=3) -leg.text <- c("P", "F1", "F2") -legend("topleft", leg.text, lty=c(1, 1, 1), col=c(1, 2, 4), cex=3) -if (opt$se_plot == 1) { - # Add SE lines to plot - # SE for adults - lines (day.all, g0a+g0a.se, lty=2) - lines (day.all, g0a-g0a.se, lty=2) - # SE for nymphs - lines (day.all, g1a+g1a.se, col=2, lty=2) - lines (day.all, g1a-g1a.se, col=2, lty=2) - # SE for eggs - lines (day.all, g2a+g2a.se, col=4, lty=2) - lines (day.all, g2a-g2a.se, col=4, lty=2) -} +# Subfigure 1: population size by life stage. +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, maxval, + opt$std_error_plot, adults, nymphs, eggs, adults.std_error, nymphs.std_error, eggs.std_error) +# Subfigure 2: population size by generation. +maxval <- max(F2) +render_chart("pop_size_by_generation", opt$insect, opt$location, latitude, start_date, end_date, days, maxval, + opt$std_error_plot, P, F1, F2, P.std_error, F1.std_error, F2.std_error) +# Subfigure 3: adult population size by generation. +maxval <- max(F2_adults) + 100 +render_chart("adult_pop_size_by_generation", opt$insect, opt$location, latitude, start_date, end_date, days, maxval, + opt$std_error_plot, P_adults, F1_adults, F2_adults, P_adults.std_error, F1_adults.std_error, F2_adults.std_error) # Turn off device driver to flush output. dev.off()
--- a/insect_phenology_model.xml Wed Nov 22 13:22:49 2017 -0500 +++ b/insect_phenology_model.xml Wed Dec 06 10:07:21 2017 -0500 @@ -5,23 +5,24 @@ </requirements> <command detect_errors="exit_code"><![CDATA[ Rscript '$__tool_directory__/insect_phenology_model.R' --a $adult_mort --b $adult_accum --c $egg_mort --e '$location' --f $max_clutch_size --i $min_clutch_size --j $nymph_mort --k $old_nymph_accum --n $input.metadata.data_lines --o '$output' --p $oviposition --q $photoperiod --s $replications --t $se_plot --v '$input' --y $young_nymph_accum --x '$insect']]></command> +--adult_mortality $adult_mortality +--adult_accumulation $adult_accumulation +--egg_mortality $egg_mortality +--input '$input' +--insect '$insect' +--insects_per_replication $insects_per_replication +--location '$location' +--max_clutch_size $max_clutch_size +--min_clutch_size $min_clutch_size +--nymph_mortality $nymph_mortality +--num_days $input.metadata.data_lines +--old_nymph_accumulation $old_nymph_accumulation +--output '$output' +--oviposition $oviposition +--photoperiod $photoperiod +--replications $replications +--std_error_plot $std_error_plot +--young_nymph_accumulation $young_nymph_accumulation]]></command> <inputs> <param name="input" type="data" format="csv" label="Temperature data" /> <param name="location" type="text" value="" optional="false" label="Location" /> @@ -29,17 +30,18 @@ <option value="Brown Marmolated Stink Bug" selected="True">Brown Marmolated Stink Bug</option> </param> <param name="replications" type="integer" value="10" min="1" label="Number of replications" /> + <param name="insects_per_replication" type="integer" value="1000" min="1" label="Number of insects with which to start each replication" /> <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination" /> - <param name="egg_mort" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" /> - <param name="nymph_mort" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality" /> - <param name="adult_mort" type="integer" value="1" min="0" label="Adjustment rate for adult mortality" /> + <param name="egg_mortality" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" /> + <param name="nymph_mortality" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality" /> + <param name="adult_mortality" type="integer" value="1" min="0" label="Adjustment rate for adult mortality" /> <param name="oviposition" type="integer" value="1" min="0" label="Adjustment oviposition rate" /> <param name="min_clutch_size" type="integer" value="0" min="0" label="Adjustment of minimum clutch size" /> <param name="max_clutch_size" type="integer" value="0" min="0" label="Adjustment of maximum clutch size" /> - <param name="young_nymph_accum" type="integer" value="0" min="0" label="Adjustment of DD accumulation (egg->young nymph)" /> - <param name="old_nymph_accum" type="integer" value="0" min="0" label="Adjustment of DD accumulation (young nymph->old nymph)" /> - <param name="adult_accum" type="integer" value="0" min="0" label="Adjustment of DD accumulation (old nymph->adult)" /> - <param name="se_plot" type="select" label="Plot SE?"> + <param name="young_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (egg->young nymph)" /> + <param name="old_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (young nymph->old nymph)" /> + <param name="adult_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (old nymph->adult)" /> + <param name="std_error_plot" type="select" label="Plot standard error?"> <option value="1" selected="True">Yes</option> <option value="0">No</option> </param> @@ -57,7 +59,7 @@ </tests> <help> **What it does** - + Provides an agent-based stochastic model expressing stage-specific phenology and population dynamics for an insect species across geographic regions. ----- @@ -66,7 +68,9 @@ * **Location** - the location associated with the selected temperature data. * **Temperature data** - select the dataset from your history containing the temperature data. + * **Select insect** - currently only the Brown Marmolated Stink Bug can be analyzed. * **Number of replications** - number of replications. + * **Number of insects with which to start each replication** - the analysis for each replication will start with this number of insects. * **Critical photoperiod for diapause induction/termination** - critical photoperiod for diapause induction/termination. * **Adjustment rate for egg mortality** - adjustment rate for egg mortality. * **Adjustment rate for nymph mortality** - adjustment rate for nymph mortality. @@ -74,11 +78,11 @@ * **Adjustment oviposition rate** - adjustment oviposition rate. * **Adjustment of minimum clutch size** - adjustment of minimum clutch size. * **Adjustment of maximum clutch size** - adjustment of maximum clutch size - * **Adjustment of DD accumulation (egg->young nymph)** - adjustment of DD accumulation (egg->young nymph). - * **Adjustment of DD accumulation (young nymph->old nymph)** - adjustment of DD accumulation (young nymph->old nymph). - * **Adjustment of DD accumulation (old nymph->adult)** - adjustment of DD accumulation (old nymph->adult). - * **Plot SE** - add SE lines to plot for eggs, nymphs and adults. - + * **Adjustment of degree-days accumulation (egg->young nymph)** - adjustment of degree-days accumulation (egg->young nymph). + * **Adjustment of degree-days accumulation (young nymph->old nymph)** - adjustment of degree-days accumulation (young nymph->old nymph). + * **Adjustment of degree-days accumulation (old nymph->adult)** - adjustment of degree-days accumulation (old nymph->adult). + * **Plot standard error** - add standard error lines to plot. + </help> <citations> <citation type="doi">10.3389/fphys.2016.00165</citation>
--- a/test-data/output.pdf Wed Nov 22 13:22:49 2017 -0500 +++ b/test-data/output.pdf Wed Dec 06 10:07:21 2017 -0500 @@ -1,19 +1,16 @@ +%PDF 1 0 obj << +/CreationDate +/ModDate /Title (R Graphics Output) +/Producer /Creator (R) ->> -endobj -2 0 obj << /Type /Catalog /Pages 3 0 R >> endobj 7 0 obj << /Type /Page /Parent 3 0 R /Contents 8 0 R /Resources 4 0 R >> endobj -8 0 obj -<< ->> -stream 3 0 obj << /Type /Pages /Kids [ 7 0 R ] /Count 1 /MediaBox [0 0 1440 2160] >> endobj @@ -52,3 +49,4 @@ trailer << /Size 12 /Info 1 0 R /Root 2 0 R >> startxref +%%EOF