Mercurial > repos > greg > insect_phenology_model
changeset 3:24fa0d35a8bf draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 09 Nov 2017 14:20:42 -0500 |
| parents | 07444af6824f |
| children | e7b1fc0133bb |
| files | insect_phenology_model.R insect_phenology_model.xml test-data/asheville2014.csv test-data/output.pdf test-data/state_college.csv tool-data/locations.txt.sample tool-data/years.txt.sample |
| diffstat | 7 files changed, 372 insertions(+), 614 deletions(-) [+] |
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--- a/insect_phenology_model.R Mon Aug 14 13:47:50 2017 -0400 +++ b/insect_phenology_model.R Thu Nov 09 14:20:42 2017 -0500 @@ -6,19 +6,18 @@ 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("-d", "--latitude"), action="store", dest="latitude", type="double", help="Latitude of selected location"), 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("-u", "--year"), action="store", dest="year", type="integer", help="Starting year"), - make_option(c("-v", "--temperature_dataset"), action="store", dest="temperature_dataset", help="Temperature data for selected location"), + 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)") ) @@ -26,40 +25,42 @@ args <- parse_args(parser, positional_arguments=TRUE) opt <- args$options -data.input=function(loc, year, temperature.dataset) +convert_csv_to_rdata=function(temperature_data, data_matrix) { - expdata <- matrix(rep(0, 365 * 3), nrow=365) - namedat <- paste(loc, year, ".Rdat", sep="") - temp.data <- read.csv(file=temperature.dataset, header=T) - - expdata[,1] <- c(1:365) + # Integer day of the year. + data_matrix[,1] <- c(1:opt$num_days) # Minimum - expdata[,2] <- temp.data[c(1:365), 3] + data_matrix[,2] <- temperature_data[c(1:opt$num_days), 5] # Maximum - expdata[,3] <- temp.data[c(1:365), 2] - save(expdata, file=namedat) + data_matrix[,3] <- temperature_data[c(1:opt$num_days), 6] + namedat <- "tempdata.Rdat" + save(data_matrix, file=namedat) namedat } -daylength=function(latitude) +daylength=function(latitude, num_days) { - # from Forsythe 1995 + # From Forsythe 1995. p=0.8333 dl <- NULL - for (i in 1:365) { + for (i in 1:num_days) { theta <- 0.2163108 + 2 * atan(0.9671396 * tan(0.00860 * (i - 186))) phi <- asin(0.39795 * cos(theta)) dl[i] <- 24 - 24 / pi * acos((sin(p * pi / 180) + sin(latitude * pi / 180) * sin(phi)) / (cos(latitude * pi / 180) * cos(phi))) } - dl # return a vector of daylength in 365 days + # Return a vector of daylength for the number of + # days specified in the input temperature data. + dl } -hourtemp=function(latitude, date, temperature_file_path) +hourtemp=function(latitude, date, temperature_file_path, num_days) { load(temperature_file_path) - threshold <- 14.17 # base development threshold for BMSB - dnp <- expdata[date, 2] # daily minimum - dxp <- expdata[date, 3] # daily maximum + # Base development threshold for Brown Marmolated Stink Bug + # insect phenology model. + threshold <- 14.17 + dnp <- data_matrix[date, 2] # daily minimum + dxp <- data_matrix[date, 3] # daily maximum dmean <- 0.5 * (dnp + dxp) dd <- 0 # initialize degree day accumulation @@ -67,22 +68,30 @@ dd <- 0 } else { - dlprofile <- daylength(latitude) # extract daylength data for entire year - T <- NULL # initialize hourly temperature - dh <- NULL #initialize degree hour vector - # date <- 200 - y <- dlprofile[date] # calculate daylength in given date - z <- 24 - y # night length - a <- 1.86 # lag coefficient - b <- 2.20 # night coefficient - #tempdata <- read.csv("tempdata.csv") #import raw data set - # Should be outside function otherwise its redundant - risetime <- 12 - y / 2 # sunrise time - settime <- 12 + y / 2 # sunset time + # Extract daylength data for the number of + # days specified in the input temperature data. + dlprofile <- daylength(latitude, num_days) + # Initialize hourly temperature. + T <- NULL + # Initialize degree hour vector. + dh <- NULL + # Calculate daylength in given date. + y <- dlprofile[date] + # Night length. + z <- 24 - y + # Lag coefficient. + a <- 1.86 + # Night coefficient. + b <- 2.20 + # Sunrise time. + risetime <- 12 - y / 2 + # Sunset time. + settime <- 12 + y / 2 ts <- (dxp - dnp) * sin(pi * (settime - 5) / (y + 2 * a)) + dnp for (i in 1:24) { if (i > risetime && i<settime) { - m <- i - 5 # number of hours after Tmin until sunset + # Number of hours after Tmin until sunset. + m <- i - 5 T[i]=(dxp - dnp) * sin(pi * m / (y + 2 * a)) + dnp if (T[i]<8.4) { dh[i] <- 0 @@ -189,73 +198,64 @@ return } -cat("Replications: ", opt$replications, "\n") -cat("Photoperiod: ", opt$photoperiod, "\n") -cat("Oviposition rate: ", opt$oviposition, "\n") -cat("Egg mortality rate: ", opt$egg_mort, "\n") -cat("Nymph mortality rate: ", opt$nymph_mort, "\n") -cat("Adult mortality rate: ", opt$adult_mort, "\n") -cat("Min clutch size: ", opt$min_clutch_size, "\n") -cat("Max clutch size: ", opt$max_clutch_size, "\n") -cat("(egg->young nymph): ", opt$young_nymph_accum, "\n") -cat("(young nymph->old nymph): ", opt$old_nymph_accum, "\n") -cat("(old nymph->adult): ", opt$adult_accum, "\n") +# Read in the input temperature datafile into a Data Frame object. +temperature_data <- read.csv(file=opt$input, header=T, sep=",") +start_date <- temperature_data[c(1:1), 3] +end_date <- temperature_data[c(opt$num_days:opt$num_days), 3] +raw_data_matrix <- matrix(rep(0, opt$num_days * 6), nrow=opt$num_days) +temperature_file_path <- convert_csv_to_rdata(temperature_data, raw_data_matrix) +latitude <- temperature_data[1, 1] -# Read in the input temperature datafile -temperature_file_path <- data.input(opt$location, opt$year, opt$temperature_dataset) +cat("Number of days: ", opt$num_days, "\n") -# Initialize matrix for results from all replications -S0.rep <- S1.rep <- S2.rep <- S3.rep <- S4.rep <- S5.rep <- matrix(rep(0, 365 * 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, 365 * 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) # loop through replications for (N.rep in 1:opt$replications) { - # during each replication - # start with 1000 individuals -- user definable as well? + # During each replication start with 1000 individuals. + # TODO: user definable as well? n <- 1000 - # Generation, Stage, DD, T, Diapause + # Generation, Stage, DD, T, Diapause. vec.ini <- c(0, 3, 0, 0, 0) - # overwintering, previttelogenic, DD=0, T=0, no-diapause + # Overwintering, previttelogenic, DD=0, T=0, no-diapause. vec.mat <- rep(vec.ini, n) - # complete matrix for the population - vec.mat <- t(matrix(vec.mat, nrow=5)) - # complete photoperiod profile in a year, requires daylength function - ph.p <- daylength(opt$latitude) + # Complete matrix for the population. + vec.mat <- base::t(matrix(vec.mat, nrow=5)) + # Complete photoperiod profile in a year, requires daylength function. + ph.p <- daylength(latitude, opt$num_days) - # time series of population size + # Time series of population size. tot.pop <- NULL - # gen.0 pop size - gen0.pop <- rep(0, 365) - gen1.pop <- rep(0, 365) - gen2.pop <- rep(0, 365) - S0 <- S1 <- S2 <- S3 <- S4 <- S5 <- rep(0, 365) - g0.adult <- g1.adult <- g2.adult <- rep(0, 365) - N.newborn <- N.death <- N.adult <- rep(0, 365) - dd.day <- rep(0, 365) + gen0.pop <- rep(0, opt$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) - # start tick - ptm <- proc.time() - - # all the days - for (day in 1:365) { - # photoperiod in the day + # All the days included in the input temperature dataset. + for (day in 1:opt$num_days) { + # Photoperiod in the day. photoperiod <- ph.p[day] - temp.profile <- hourtemp(opt$latitude, day, temperature_file_path) + temp.profile <- hourtemp(latitude, day, temperature_file_path, opt$num_days) mean.temp <- temp.profile[1] dd.temp <- temp.profile[2] dd.day[day] <- dd.temp - # trash bin for death + # Trash bin for death. death.vec <- NULL - # new born + # Newborn. birth.vec <- NULL - # all individuals + # All individuals. for (i in 1:n) { - # find individual record + # Find individual record. vec.ind <- vec.mat[i,] - # first of all, still alive? - # adjustment for late season mortality rate - if (opt$latitude < 40.0) { + # First of all, still alive? + # Adjustment for late season mortality rate. + if (latitude < 40.0) { post.mort <- 1 day.kill <- 300 } @@ -264,19 +264,19 @@ day.kill <- 250 } if (vec.ind[2] == 0) { - # egg + # Egg. death.prob = opt$egg_mort * mortality.egg(mean.temp) } else if (vec.ind[2] == 1 | vec.ind[2] == 2) { death.prob = opt$nymph_mort * mortality.nymph(mean.temp) } else if (vec.ind[2] == 3 | vec.ind[2] == 4 | vec.ind[2] == 5) { - # for adult + # For adult. if (day < day.kill) { death.prob = opt$adult_mort * mortality.adult(mean.temp) } else { - # increase adult mortality after fall equinox + # Increase adult mortality after fall equinox. death.prob = opt$adult_mort * post.mort * mortality.adult(mean.temp) } } @@ -286,218 +286,216 @@ death.vec <- c(death.vec, i) } else { - # aggregrate index of dead bug - # event 1 end of diapause + # Aggregrate index of dead bug. + # Event 1 end of diapause. if (vec.ind[1] == 0 && vec.ind[2] == 3) { - # overwintering adult (previttelogenic) + # Overwintering adult (previttelogenic). if (photoperiod > opt$photoperiod && vec.ind[3] > 68 && day < 180) { - # add 68C to become fully reproductively matured - # transfer to vittelogenic + # Add 68C to become fully reproductively matured. + # Transfer to vittelogenic. vec.ind <- c(0, 4, 0, 0, 0) vec.mat[i,] <- vec.ind } else { - # add to DD + # Add to dd. vec.ind[3] <- vec.ind[3] + dd.temp - # add 1 day in current stage + # Add 1 day in current stage. vec.ind[4] <- vec.ind[4] + 1 vec.mat[i,] <- vec.ind } } if (vec.ind[1] != 0 && vec.ind[2] == 3) { - # NOT overwintering adult (previttelogenic) + # Not overwintering adult (previttelogenic). current.gen <- vec.ind[1] if (vec.ind[3] > 68) { - # add 68C to become fully reproductively matured - # transfer to vittelogenic + # Add 68C to become fully reproductively matured. + # Transfer to vittelogenic. vec.ind <- c(current.gen, 4, 0, 0, 0) vec.mat[i,] <- vec.ind } else { - # add to DD + # Add to dd. vec.ind[3] <- vec.ind[3] + dd.temp - # add 1 day in current stage + # Add 1 day in current stage. vec.ind[4] <- vec.ind[4] + 1 vec.mat[i,] <- vec.ind } } - # event 2 oviposition -- where population dynamics comes from + # Event 2 oviposition -- where population dynamics comes from. if (vec.ind[2] == 4 && vec.ind[1] == 0 && mean.temp > 10) { - # vittelogenic stage, overwintering generation + # Vittelogenic stage, overwintering generation. if (vec.ind[4] == 0) { - # just turned in vittelogenic stage + # Just turned in vittelogenic stage. n.birth=round(runif(1, 2 + opt$min_clutch_size, 8 + opt$max_clutch_size)) } else { - # daily probability of birth + # Daily probability of birth. p.birth = opt$oviposition * 0.01 u1 <- runif(1) if (u1 < p.birth) { n.birth=round(runif(1, 2, 8)) } } - # add to DD + # Add to dd. vec.ind[3] <- vec.ind[3] + dd.temp - # add 1 day in current stage + # Add 1 day in current stage. vec.ind[4] <- vec.ind[4] + 1 vec.mat[i,] <- vec.ind if (n.birth > 0) { - # add new birth -- might be in different generations - # generation + 1 + # Add new birth -- might be in different generations. new.gen <- vec.ind[1] + 1 - # egg profile + # Egg profile. new.ind <- c(new.gen, 0, 0, 0, 0) new.vec <- rep(new.ind, n.birth) - # update batch of egg profile + # Update batch of egg profile. new.vec <- t(matrix(new.vec, nrow=5)) - # group with total eggs laid in that day + # Group with total eggs laid in that day. birth.vec <- rbind(birth.vec, new.vec) } } - # event 2 oviposition -- for gen 1. + # Event 2 oviposition -- for gen 1. if (vec.ind[2] == 4 && vec.ind[1] == 1 && mean.temp > 12.5 && day < 222) { - # vittelogenic stage, 1st generation + # Vittelogenic stage, 1st generation if (vec.ind[4] == 0) { - # just turned in vittelogenic stage + # Just turned in vittelogenic stage. n.birth=round(runif(1, 2 + opt$min_clutch_size, 8 + opt$max_clutch_size)) } else { - # daily probability of birth + # Daily probability of birth. p.birth = opt$oviposition * 0.01 u1 <- runif(1) if (u1 < p.birth) { n.birth = round(runif(1, 2, 8)) } } - # add to DD + # Add to dd. vec.ind[3] <- vec.ind[3] + dd.temp - # add 1 day in current stage + # Add 1 day in current stage. vec.ind[4] <- vec.ind[4] + 1 vec.mat[i,] <- vec.ind if (n.birth > 0) { - # add new birth -- might be in different generations - # generation + 1 + # Add new birth -- might be in different generations. new.gen <- vec.ind[1] + 1 - # egg profile + # Egg profile. new.ind <- c(new.gen, 0, 0, 0, 0) new.vec <- rep(new.ind, n.birth) - # update batch of egg profile + # Update batch of egg profile. new.vec <- t(matrix(new.vec, nrow=5)) - # group with total eggs laid in that day + # Group with total eggs laid in that day. birth.vec <- rbind(birth.vec, new.vec) } } - # event 3 development (with diapause determination) - # event 3.1 egg development to young nymph (vec.ind[2]=0 -> egg) + # Event 3 development (with diapause determination). + # Event 3.1 egg development to young nymph (vec.ind[2]=0 -> egg). if (vec.ind[2] == 0) { - # egg stage - # add to DD + # Egg stage. + # Add to dd. vec.ind[3] <- vec.ind[3] + dd.temp if (vec.ind[3] >= (68 + opt$young_nymph_accum)) { - # from egg to young nymph, DD requirement met + # From egg to young nymph, DD requirement met. current.gen <- vec.ind[1] - # transfer to young nym stage + # Transfer to young nymph stage. vec.ind <- c(current.gen, 1, 0, 0, 0) } else { - # add 1 day in current stage + # Add 1 day in current stage. vec.ind[4] <- vec.ind[4] + 1 } vec.mat[i,] <- vec.ind } - # event 3.2 young nymph to old nymph (vec.ind[2]=1 -> young nymph: determines diapause) + # 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 + # young nymph stage. + # add to dd. vec.ind[3] <- vec.ind[3] + dd.temp if (vec.ind[3] >= (250 + opt$old_nymph_accum)) { - # from young to old nymph, DD requirement met + # From young to old nymph, dd requirement met. current.gen <- vec.ind[1] - # transfer to old nym stage + # Transfer to old nym stage. vec.ind <- c(current.gen, 2, 0, 0, 0) if (photoperiod < opt$photoperiod && day > 180) { vec.ind[5] <- 1 - } # prepare for diapausing + } # Prepare for diapausing. } else { - # add 1 day in current stage + # Add 1 day in current stage. vec.ind[4] <- vec.ind[4] + 1 } vec.mat[i,] <- vec.ind } - # event 3.3 old nymph to adult: previttelogenic or diapausing? + # Event 3.3 old nymph to adult: previttelogenic or diapausing? if (vec.ind[2] == 2) { - # old nymph stage - # add to DD + # 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 + # From old to adult, dd requirement met. current.gen <- vec.ind[1] if (vec.ind[5] == 0) { - # non-diapausing adult -- previttelogenic + # Non-diapausing adult -- previttelogenic. vec.ind <- c(current.gen, 3, 0, 0, 0) } else { - # diapausing + # Diapausing. vec.ind <- c(current.gen, 5, 0, 0, 1) } } else { - # add 1 day in current stage + # Add 1 day in current stage. vec.ind[4] <- vec.ind[4] + 1 } vec.mat[i,] <- vec.ind } - # event 4 growing of diapausing adult (unimportant, but still necessary)## + # 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 } - } # else if it is still alive - } # end of the individual bug loop + } # Else if it is still alive. + } # End of the individual bug loop. - # find how many died + # Find how many died. n.death <- length(death.vec) if (n.death > 0) { vec.mat <- vec.mat[-death.vec, ] } - # remove record of dead - # find how many new born + # Remove record of dead. + # Find how many new born. n.newborn <- length(birth.vec[,1]) vec.mat <- rbind(vec.mat, birth.vec) - # update population size for the next day + # Update population size for the next day. n <- n - n.death + n.newborn - # aggregate results by day + # Aggregate results by day. tot.pop <- c(tot.pop, n) - # egg + # Egg. s0 <- sum(vec.mat[,2] == 0) - # young nymph + # Young nymph. s1 <- sum(vec.mat[,2] == 1) - # old nymph + # Old nymph. s2 <- sum(vec.mat[,2] == 2) - # previtellogenic + # Previtellogenic. s3 <- sum(vec.mat[,2] == 3) - # vitellogenic + # Vitellogenic. s4 <- sum(vec.mat[,2] == 4) - # diapausing + # Diapausing. s5 <- sum(vec.mat[,2] == 5) - # overwintering adult + # Overwintering adult. gen0 <- sum(vec.mat[,1] == 0) - # first generation + # First generation. gen1 <- sum(vec.mat[,1] == 1) - # second generation + # Second generation. gen2 <- sum(vec.mat[,1] == 2) - # sum of all adults + # Sum of all adults. n.adult <- sum(vec.mat[,2] == 3) + sum(vec.mat[,2] == 4) + sum(vec.mat[,2] == 5) - # gen.0 pop size + # Gen eration 0 pop size. gen0.pop[day] <- gen0 gen1.pop[day] <- gen1 gen2.pop[day] <- gen2 @@ -514,11 +512,10 @@ N.newborn[day] <- n.newborn N.death[day] <- n.death N.adult[day] <- n.adult - #print(c(N.rep, day, n, n.adult)) - } # end of 365 days + } # end of days specified in the input temperature data dd.cum <- cumsum(dd.day) - # collect all the outputs + # Collect all the outputs. S0.rep[,N.rep] <- S0 S1.rep[,N.rep] <- S1 S2.rep[,N.rep] <- S2 @@ -537,15 +534,11 @@ g2a.rep[,N.rep] <- g2.adult } -# save(dd.day, dd.cum, S0.rep, S1.rep, S2.rep, S3.rep, S4.rep, S5.rep, newborn.rep, death.rep, adult.rep, pop.rep, g0.rep, g1.rep, g2.rep, g0a.rep, g1a.rep, g2a.rep, file=opt$output) -# maybe do not need to export this bit, but for now just leave it as-is -# do we need to export this Rdat file? - # Data analysis and visualization # default: plot 1 year of result # but can be expanded to accommodate multiple years n.yr <- 1 -day.all <- c(1:365 * n.yr) +day.all <- c(1:opt$num_days * n.yr) # mean value for adults sa <- apply((S3.rep + S4.rep + S5.rep), 1, mean) @@ -593,30 +586,32 @@ par(mar = c(5, 6, 4, 4), mfrow=c(3, 1)) # Subfigure 2: population size by life stage -plot(day.all, sa, main = "BSMB Total Population Size by Life Stage", type = "l", ylim = c(0, max(se + se.se, sn + sn.se, sa + sa.se)), axes = F, lwd = 2, xlab = "", ylab = "Number", cex = 2, cex.lab = 2, cex.axis = 2, cex.main = 2) -# Young and old nymphs -lines(day.all, sn, lwd = 2, lty = 1, col = 2) +title <- paste("BSMB Total Population Size by Life Stage:", opt$location, ", Latitude:", latitude, ", Temperature Dates:", start_date, "to", 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="Number", cex=2, cex.lab=2, cex.axis=2, cex.main=2) +# 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 = 2, labels = c("Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec")) +lines(day.all, se, lwd=2, lty=1, col=4) +axis(1, at = c(1:12) * 30 - 15, cex.axis=2, labels=c("Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec")) axis(2, cex.axis = 2) leg.text <- c("Egg", "Nymph", "Adult") -legend("topleft", leg.text, lty = c(1, 1, 1), col = c(4, 2, 1), cex = 2) +legend("topleft", leg.text, lty=c(1, 1, 1), col=c(4, 2, 1), cex=2) if (opt$se_plot == 1) { # add SE lines to plot # SE for adults - lines (day.all, sa + sa.se, lty = 2) - lines (day.all, sa - sa.se, lty = 2) + lines (day.all, sa + sa.se, lty=2) + lines (day.all, sa - sa.se, lty=2) # SE for nymphs - lines (day.all, sn + sn.se, col = 2, lty = 2) - lines (day.all, sn - sn.se, col = 2, lty = 2) + lines (day.all, sn + sn.se, col=2, lty=2) + lines (day.all, sn - sn.se, col=2, lty=2) # SE for eggs - lines (day.all, se + se.se, col = 4, lty = 2) - lines (day.all, se - se.se, col = 4, lty = 2) + lines (day.all, se + se.se, col=4, lty=2) + lines (day.all, se - se.se, col=4, lty=2) } # Subfigure 3: population size by generation -plot(day.all, g0, main = "BSMB Total Population Size by Generation", type = "l", ylim = c(0, max(g2)), axes = F, lwd = 2, xlab = "", ylab = "Number", cex = 2, cex.lab = 2, cex.axis = 2, cex.main = 2) +title <- paste("BSMB Total Population Size by Generation:", opt$location, ", Latitude:", latitude, ", Temperature Dates:", start_date, "to", end_date, sep=" ") +plot(day.all, g0, main=title, type="l", ylim=c(0, max(g2)), axes=F, lwd=2, xlab="", ylab="Number", cex=2, cex.lab=2, cex.axis=2, cex.main=2) 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 = 2, labels = c("Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec")) @@ -637,7 +632,8 @@ } # Subfigure 4: adult population size by generation -plot(day.all, g0a, ylim = c(0, max(g2a) + 100), main = "BSMB Adult Population Size by Generation", type = "l", axes = F, lwd = 2, xlab = "Year", ylab = "Number", cex = 2, cex.lab = 2, cex.axis = 2, cex.main = 2) +title <- paste("BSMB Adult Population Size by Generation:", opt$location, ", Latitude:", latitude, ", Temperature Dates:", start_date, "to", end_date, sep=" ") +plot(day.all, g0a, ylim=c(0, max(g2a) + 100), main=title, type="l", axes=F, lwd=2, xlab="Year", ylab="Number", cex=2, cex.lab=2, cex.axis=2, cex.main=2) lines(day.all, g1a, lwd = 2, lty = 1, col = 2) lines(day.all, g2a, lwd = 2, lty = 1, col = 4) axis(1, at = c(1:12) * 30 - 15, cex.axis = 2, labels = c("Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec"))
--- a/insect_phenology_model.xml Mon Aug 14 13:47:50 2017 -0400 +++ b/insect_phenology_model.xml Thu Nov 09 14:20:42 2017 -0500 @@ -1,34 +1,31 @@ <?xml version="."?> -<tool id="insect_phenology_model" name="Insect phenology model" version="1.0.0"> +<tool id="insect_phenology_model" name="Insect phenology model" version="1.1.0"> <description>expressing stage-specific phenology and population dynamics</description> <requirements> - <requirement type="package" version="1.3.2">r-optparse</requirement> + <requirement type="package" version="1.4.4">r-optparse</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ Rscript '$__tool_directory__/insect_phenology_model.R' -a $adult_mort -b $adult_accum -c $egg_mort --d $latitude -e '$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 --u $year --v '$temperature_data' +-v '$input' -y $young_nymph_accum ]]></command> <inputs> <param name="location" type="text" value="" optional="false" label="Location" /> - <param name="latitude" type="float" value="0.0" label="Latitude of selected location" /> - <param name="temperature_data" type="data" format="csv" label="Temperature data" /> - <param name="year" type="integer" value="2017" min="1995" label="Temperature data year" /> + <param name="input" type="data" format="csv" label="Temperature data" /> <param name="replications" type="integer" value="10" min="1" label="Number of replications" /> <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination" /> <param name="egg_mort" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" /> @@ -46,14 +43,13 @@ </param> </inputs> <outputs> - <data name="output" format="pdf" label="${tool.name} ${location}, ${year} lat:${latitude} on ${on_string}" /> + <data name="output" format="pdf" label="${tool.name} ${location}, on ${on_string}" /> </outputs> <tests> <test> - <param name="temperature_data" value="asheville2014.csv" ftype="csv" /> - <param name="location" value="asheville:35.58" /> - <param name="year" value="2014" /> - <param name="replications" value="3" /> + <param name="input" value="state_college.csv" ftype="csv" /> + <param name="location" value="State College PA" /> + <param name="replications" value="10" /> <output name="output" file="output.pdf" ftype="pdf" compare="contains" /> </test> </tests> @@ -68,7 +64,6 @@ * **Location** - the location associated with the selected temperature data. * **Temperature data** - select the dataset from your history containing the temperature data. - * **Temperature data year** - the year during which the temperature data was recorded. * **Number of replications** - number of replications. * **Critical photoperiod for diapause induction/termination** - critical photoperiod for diapause induction/termination. * **Adjustment rate for egg mortality** - adjustment rate for egg mortality. @@ -85,5 +80,7 @@ </help> <citations> <citation type="doi">10.3389/fphys.2016.00165</citation> + <citation type="doi">10.1175/JTECH-D-11-00103.1</citation> + <citation type="doi">10.7289/V5D21VHZ</citation> </citations> </tool>
--- a/test-data/asheville2014.csv Mon Aug 14 13:47:50 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,366 +0,0 @@ -"","TMAX","TMIN" -"100746",3.9,-1.7 -"100747",7.8,-3.3 -"100748",7.8,-7.8 -"100749",-3.9,-11.1 -"100750",6.7,-6.7 -"100751",11.1,5 -"100752",8.3,-17.2 -"100753",-6.7,-18.3 -"100754",8.3,-12.8 -"100755",10.6,-5 -"100756",12.2,1.7 -"100757",15,6.1 -"100758",12.8,3.3 -"100759",12.8,-0.6 -"100760",10.6,0.6 -"100761",3.3,-3.3 -"100762",6.1,-6.7 -"100763",9.4,-3.9 -"100764",2.8,-8.3 -"100765",7.2,-2.8 -"100766",16.7,-3.3 -"100767",6.1,-8.9 -"100768",-2.8,-12.8 -"100769",-2.8,-12.8 -"100770",-2.2,-16.7 -"100771",3.3,-10 -"100772",12.2,-3.9 -"100773",9.4,-6.1 -"100774",-5.6,-9.4 -"100775",-3.3,-13.3 -"100776",3.9,-14.4 -"100777",10.6,-7.2 -"100778",16.1,-3.9 -"100779",17.8,-1.1 -"100780",15,2.8 -"100781",7.2,2.8 -"100782",12.8,-2.8 -"100783",0.6,-4.4 -"100784",5.6,-3.9 -"100785",10,0 -"100786",11.7,-1.1 -"100787",3.3,-1.1 -"100788",1.1,-1.1 -"100789",-1.1,-5 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--- a/test-data/output.pdf Mon Aug 14 13:47:50 2017 -0400 +++ b/test-data/output.pdf Thu Nov 09 14:20:42 2017 -0500 @@ -1,8 +1,5 @@ -%PDF-1.4 -%ρ\r 1 0 obj << -/Title (R Graphics Output) /Creator (R) >> endobj @@ -12,8 +9,6 @@ 7 0 obj << /Type /Page /Parent 3 0 R /Contents 8 0 R /Resources 4 0 R >> endobj -8 0 obj -endobj 3 0 obj << /Type /Pages /Kids [ 7 0 R ] /Count 1 /MediaBox [0 0 1440 1440] >> endobj @@ -28,7 +23,8 @@ 5 0 obj [/ICCBased 6 0 R] endobj -6 0 obj +9 0 obj +<< /Type /Encoding /BaseEncoding /WinAnsiEncoding /Differences [ 45/minus 96/quoteleft 144/dotlessi /grave /acute /circumflex /tilde /macron /breve /dotaccent @@ -43,8 +39,6 @@ << /Type /Font /Subtype /Type1 /Name /F3 /BaseFont /Helvetica-Bold /Encoding 9 0 R >> endobj -xref -0 12 trailer << /Size 12 /Info 1 0 R /Root 2 0 R >> startxref
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--- a/tool-data/locations.txt.sample Mon Aug 14 13:47:50 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +0,0 @@ -Asheville NC asheville_nc:35.58 -Bridgeton NJ bridgeton_nj:39.43 -Davis CA davis_ca:38.55 -Geneva NY geneva_ny:42.88 -Homestead FL homestead_fl:25.47 -NJ_companion nj_companion:39.62 -NJ_management nj_management:39.66 -PA_companion pa_companion:39.98 -PA_management pa_management:39.97 -Riverside CA riverside_ca:33.95 -Salem OR salem_or:44.93 -VA_companion va_companion:39.15 -VA_management va_management:39.13 -Wenatchee WA wneatchee_wa:47.42 -WV_companion wv_companion:39.38 -WV_management wv_management:39.52
--- a/tool-data/years.txt.sample Mon Aug 14 13:47:50 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,31 +0,0 @@ -1995 1995 -1996 1996 -1997 1997 -1998 1998 -1999 1999 -2000 2000 -2001 2001 -2002 2002 -2003 2003 -2004 2004 -2005 2005 -2006 2006 -2007 2007 -2008 2008 -2009 2009 -2010 2010 -2011 2011 -2012 2012 -2013 2013 -2014 2014 -2015 2015 -2016 2016 -2017 2017 -2018 2018 -2019 2019 -2020 2020 -2021 2021 -2022 2022 -2023 2023 -2024 2024 -2025 2025