| Next changeset 1:3debfb664792 (2017-08-09) |
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Commit message:
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added:
.shed.yml insect_phenology_model.R insect_phenology_model.xml test-data/asheville2014.csv test-data/output.pdf tool-data/locations.txt.sample tool-data/years.txt.sample |
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| diff -r 000000000000 -r 244c373f2a34 .shed.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Tue Aug 08 13:14:39 2017 -0400 |
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| @@ -0,0 +1,13 @@ +name: insect_phenology_model +owner: greg +description: | + Contains a tool that provides an agent-based stochastic model expressing stage-specific phenology and population dynamics + for an insect species across geographic regions. +homepage_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/entomology/insect_phenology_model +long_description: | + Contains a tool that provides an agent-based stochastic model expressing stage-specific phenology and population dynamics + for an insect species across geographic regions. +remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/entomology/insect_phenology_model +type: unrestricted +categories: +- Entomology |
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| diff -r 000000000000 -r 244c373f2a34 insect_phenology_model.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/insect_phenology_model.R Tue Aug 08 13:14:39 2017 -0400 |
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| b'@@ -0,0 +1,661 @@\n+#!/usr/bin/env Rscript\r\n+\r\n+suppressPackageStartupMessages(library("optparse"))\r\n+\r\n+option_list <- list(\r\n+ make_option(c("-a", "--adult_mort"), action="store", dest="adult_mort", type="integer", help="Adjustment rate for adult mortality"),\r\n+ make_option(c("-b", "--adult_accum"), action="store", dest="adult_accum", type="integer", help="Adjustment of DD accumulation (old nymph->adult)"),\r\n+ make_option(c("-c", "--egg_mort"), action="store", dest="egg_mort", type="integer", help="Adjustment rate for egg mortality"),\r\n+ make_option(c("-d", "--latitude"), action="store", dest="latitude", type="double", help="Latitude of selected location"),\r\n+ make_option(c("-e", "--location"), action="store", dest="location", help="Selected location"),\r\n+ make_option(c("-f", "--min_clutch_size"), action="store", dest="min_clutch_size", type="integer", help="Adjustment of minimum clutch size"),\r\n+ make_option(c("-i", "--max_clutch_size"), action="store", dest="max_clutch_size", type="integer", help="Adjustment of maximum clutch size"),\r\n+ make_option(c("-j", "--nymph_mort"), action="store", dest="nymph_mort", type="integer", help="Adjustment rate for nymph mortality"),\r\n+ make_option(c("-k", "--old_nymph_accum"), action="store", dest="old_nymph_accum", type="integer", help="Adjustment of DD accumulation (young nymph->old nymph)"),\r\n+ make_option(c("-o", "--output"), action="store", dest="output", help="Output dataset"),\r\n+ make_option(c("-p", "--oviposition"), action="store", dest="oviposition", type="integer", help="Adjustment for oviposition rate"),\r\n+ make_option(c("-q", "--photoperiod"), action="store", dest="photoperiod", type="double", help="Critical photoperiod for diapause induction/termination"),\r\n+ make_option(c("-s", "--replications"), action="store", dest="replications", type="integer", help="Number of replications"),\r\n+ make_option(c("-t", "--se_plot"), action="store", dest="se_plot", help="Plot SE"),\r\n+ make_option(c("-u", "--year"), action="store", dest="year", type="integer", help="Starting year"),\r\n+ make_option(c("-v", "--temperature_dataset"), action="store", dest="temperature_dataset", help="Temperature data for selected location"),\r\n+ make_option(c("-y", "--young_nymph_accum"), action="store", dest="young_nymph_accum", type="integer", help="Adjustment of DD accumulation (egg->young nymph)")\r\n+)\r\n+\r\n+parser <- OptionParser(usage="%prog [options] file", option_list=option_list)\r\n+args <- parse_args(parser, positional_arguments=TRUE)\r\n+opt <- args$options\r\n+\r\n+data.input=function(loc, year, temperature.dataset)\r\n+{\r\n+ expdata <- matrix(rep(0, 365 * 3), nrow=365)\r\n+ namedat <- paste(loc, year, ".Rdat", sep="")\r\n+ temp.data <- read.csv(file=temperature.dataset, header=T)\r\n+\r\n+ expdata[,1] <- c(1:365)\r\n+ # Minimum\r\n+ expdata[,2] <- temp.data[c(1:365), 3]\r\n+ # Maximum\r\n+ expdata[,3] <- temp.data[c(1:365), 2]\r\n+ save(expdata, file=namedat)\r\n+ namedat\r\n+}\r\n+\r\n+daylength=function(latitude)\r\n+{\r\n+ # from Forsythe 1995\r\n+ p=0.8333\r\n+ dl <- NULL\r\n+ for (i in 1:365) {\r\n+ theta <- 0.2163108 + 2 * atan(0.9671396 * tan(0.00860 * (i - 186)))\r\n+ phi <- asin(0.39795 * cos(theta))\r\n+ dl[i] <- 24 - 24 / pi * acos((sin(p * pi / 180) + sin(latitude * pi / 180) * sin(phi)) / (cos(latitude * pi / 180) * cos(phi)))\r\n+ }\r\n+ dl # return a vector of daylength in 365 days\r\n+}\r\n+\r\n+hourtemp=function(latitude, date, temperature_file_path)\r\n+{\r\n+ load(temperature_file_path)\r\n+ threshold <- 14.17 # base development threshold for BMSB\r\n+ dnp <- expdata[date, 2] # daily minimum\r\n+ dxp <- expdata[date, 3] # daily maximum\r\n+ dmean <- 0.5 * (dnp + dxp)\r\n+ dd <- 0 # initialize degree day accumulation\r\n+\r\n+ if (dxp<threshold) {\r\n+ dd <- 0\r\n+ }\r\n+ else {\r\n+ dlprofile <- daylength(latitude) # extract daylength data for entire year\r\n+ T <- NULL # initialize hourly temperatur'..b'+se.se <- apply(S0.rep, 1, sd) / sqrt(opt$replications)\r\n+# SE value for P\r\n+g0.se <- apply(g0.rep, 1, sd) / sqrt(opt$replications)\r\n+# SE for F1\r\n+g1.se <- apply(g1.rep, 1, sd) / sqrt(opt$replications)\r\n+# SE for F2\r\n+g2.se <- apply(g2.rep, 1, sd) / sqrt(opt$replications)\r\n+# SE for P adult\r\n+g0a.se <- apply(g0a.rep, 1, sd) / sqrt(opt$replications)\r\n+# SE for F1 adult\r\n+g1a.se <- apply(g1a.rep, 1, sd) / sqrt(opt$replications)\r\n+# SE for F2 adult\r\n+g2a.se <- apply(g2a.rep, 1, sd) / sqrt(opt$replications)\r\n+\r\n+dev.new(width=20, height=20)\r\n+\r\n+# Start PDF device driver to save charts to output.\r\n+pdf(file=opt$output, height=20, width=20, bg="white")\r\n+\r\n+par(mar = c(5, 6, 4, 4), mfrow=c(3, 1))\r\n+\r\n+# Subfigure 2: population size by life stage\r\n+plot(day.all, sa, main = "BSMB Total Population Size by Life Stage", type = "l", ylim = c(0, max(se + se.se, sn + sn.se, sa + sa.se)), axes = F, lwd = 2, xlab = "", ylab = "Number", cex = 2, cex.lab = 2, cex.axis = 2, cex.main = 2)\r\n+# Young and old nymphs\r\n+lines(day.all, sn, lwd = 2, lty = 1, col = 2)\r\n+# Eggs\r\n+lines(day.all, se, lwd = 2, lty = 1, col = 4)\r\n+axis(1, at = c(1:12) * 30 - 15, cex.axis = 2, labels = c("Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec"))\r\n+axis(2, cex.axis = 2)\r\n+leg.text <- c("Egg", "Nymph", "Adult")\r\n+legend("topleft", leg.text, lty = c(1, 1, 1), col = c(4, 2, 1), cex = 2)\r\n+if (opt$se_plot == 1) {\r\n+ # add SE lines to plot\r\n+ # SE for adults\r\n+ lines (day.all, sa + sa.se, lty = 2)\r\n+ lines (day.all, sa - sa.se, lty = 2) \r\n+ # SE for nymphs\r\n+ lines (day.all, sn + sn.se, col = 2, lty = 2)\r\n+ lines (day.all, sn - sn.se, col = 2, lty = 2) \r\n+ # SE for eggs\r\n+ lines (day.all, se + se.se, col = 4, lty = 2)\r\n+ lines (day.all, se - se.se, col = 4, lty = 2) \r\n+}\r\n+\r\n+# Subfigure 3: population size by generation\r\n+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)\r\n+lines(day.all, g1, lwd = 2, lty = 1, col = 2)\r\n+lines(day.all, g2, lwd = 2, lty = 1, col = 4)\r\n+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"))\r\n+axis(2, cex.axis = 2)\r\n+leg.text <- c("P", "F1", "F2")\r\n+legend("topleft", leg.text, lty = c(1, 1, 1), col =c(1, 2, 4), cex = 2)\r\n+if (opt$se_plot == 1) {\r\n+ # add SE lines to plot\r\n+ # SE for adults\r\n+ lines (day.all, g0 + g0.se, lty = 2)\r\n+ lines (day.all, g0 - g0.se, lty = 2) \r\n+ # SE for nymphs\r\n+ lines (day.all, g1 + g1.se, col = 2, lty = 2)\r\n+ lines (day.all, g1 - g1.se, col = 2, lty = 2) \r\n+ # SE for eggs\r\n+ lines (day.all, g2 + g2.se, col = 4, lty = 2)\r\n+ lines (day.all, g2 - g2.se, col = 4, lty = 2) \r\n+}\r\n+\r\n+# Subfigure 4: adult population size by generation\r\n+plot(day.all, g0a, ylim = c(0, max(g2a) + 100), main = "BSMB Adult Population Size by Generation", type = "l", axes = F, lwd = 2, xlab = "Year", ylab = "Number", cex = 2, cex.lab = 2, cex.axis = 2, cex.main = 2)\r\n+lines(day.all, g1a, lwd = 2, lty = 1, col = 2)\r\n+lines(day.all, g2a, lwd = 2, lty = 1, col = 4)\r\n+axis(1, at = c(1:12) * 30 - 15, cex.axis = 2, labels = c("Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec"))\r\n+axis(2, cex.axis = 2)\r\n+leg.text <- c("P", "F1", "F2")\r\n+legend("topleft", leg.text, lty = c(1, 1, 1), col = c(1, 2, 4), cex = 2)\r\n+if (opt$se_plot == 1) {\r\n+ # add SE lines to plot\r\n+ # SE for adults\r\n+ lines (day.all, g0a + g0a.se, lty = 2)\r\n+ lines (day.all, g0a - g0a.se, lty = 2) \r\n+ # SE for nymphs\r\n+ lines (day.all, g1a + g1a.se, col = 2, lty = 2)\r\n+ lines (day.all, g1a - g1a.se, col = 2, lty = 2) \r\n+ # SE for eggs\r\n+ lines (day.all, g2a + g2a.se, col = 4, lty = 2)\r\n+ lines (day.all, g2a - g2a.se, col = 4, lty = 2) \r\n+}\r\n+\r\n+# Turn off device driver to flush output.\r\n+dev.off()\r\n' |
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| diff -r 000000000000 -r 244c373f2a34 insect_phenology_model.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/insect_phenology_model.xml Tue Aug 08 13:14:39 2017 -0400 |
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| @@ -0,0 +1,101 @@ +<?xml version="."?> +<tool id="insect_phenology_model" name="Insect phenology model" version="1.0.0"> + <description>expressing stage-specific phenology and population dynamics</description> + <requirements> + <requirement type="package" version="1.3.0">r-optparse</requirement> + </requirements> + <command><![CDATA[ +#set loc_lat_items = str($location).split(':') +#set loc = $loc_lat_items[0] +#set lat = $loc_lat_items[1] +Rscript '$__tool_directory__/insect_phenology_model.R' +-a $adult_mort +-b $adult_accum +-c $egg_mort +-d $lat +-e $loc +-f $max_clutch_size +-i $min_clutch_size +-j $nymph_mort +-k $old_nymph_accum +-o $output +-p $oviposition +-q $photoperiod +-s $replications +-t $se_plot +-u $year +-v '$temperature_data' +-y $young_nymph_accum + ]]></command> + <inputs> + <param name="location" type="select" label="Location"> + <options from_file="locations.txt"> + <column name="name" index="0"/> + <column name="value" index="1"/> + </options> + </param> + <param name="temperature_data" type="data" format="csv" label="Temperature data" /> + <param name="year" type="select" label="Temperature data year"> + <options from_file="years.txt"> + <column name="name" index="0"/> + <column name="value" index="1"/> + </options> + </param> + <param name="replications" type="integer" value="10" min="1" label="Number of replications" /> + <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination" /> + <param name="egg_mort" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" /> + <param name="nymph_mort" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality" /> + <param name="adult_mort" type="integer" value="1" min="0" label="Adjustment rate for adult mortality" /> + <param name="oviposition" type="integer" value="1" min="0" label="Adjustment oviposition rate" /> + <param name="min_clutch_size" type="integer" value="0" min="0" label="Adjustment of minimum clutch size" /> + <param name="max_clutch_size" type="integer" value="0" min="0" label="Adjustment of maximum clutch size" /> + <param name="young_nymph_accum" type="integer" value="0" min="0" label="Adjustment of DD accumulation (egg->young nymph)" /> + <param name="old_nymph_accum" type="integer" value="0" min="0" label="Adjustment of DD accumulation (young nymph->old nymph)" /> + <param name="adult_accum" type="integer" value="0" min="0" label="Adjustment of DD accumulation (old nymph->adult)" /> + <param name="se_plot" type="select" label="Plot SE?"> + <option value="1" selected="True">Yes</option> + <option value="0">No</option> + </param> + </inputs> + <outputs> + <data name="output" format="pdf" label="${tool.name} ${str($location).split(':')[0]}, ${year} 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" /> + <output name="output" file="output.pdf" ftype="pdf" compare="contains" /> + </test> + </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. + +----- + +**Required options** + + * **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. + * **Adjustment rate for nymph mortality** - adjustment rate for nymph mortality. + * **Adjustment rate for adult mortality** - adjustment rate for adult mortality. + * **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. + + </help> + <citations> + <citation type="doi">10.3389/fphys.2016.00165</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 244c373f2a34 test-data/asheville2014.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/asheville2014.csv Tue Aug 08 13:14:39 2017 -0400 |
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| @@ -0,0 +1,366 @@ +"","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 +"100790",0.6,-3.3 +"100791",12.8,-2.2 +"100792",5,-3.3 +"100793",11.1,-3.9 +"100794",8.9,-1.1 +"100795",17.2,2.2 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| b |
| diff -r 000000000000 -r 244c373f2a34 test-data/output.pdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.pdf Tue Aug 08 13:14:39 2017 -0400 |
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| b |
| diff -r 000000000000 -r 244c373f2a34 tool-data/locations.txt.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/locations.txt.sample Tue Aug 08 13:14:39 2017 -0400 |
| b |
| @@ -0,0 +1,8 @@ +Asheville NC asheville:35.58 +Bridgeton NJ bridgeton:39.43 +Davis CA davis:38.55 +Geneva NY geneva:42.88 +Homestead FL homestead:25.47 +Riverside CA riverside:33.95 +Salem OR salem:44.93 +Wenatchee WA wneatchee:47.42 |
| b |
| diff -r 000000000000 -r 244c373f2a34 tool-data/years.txt.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/years.txt.sample Tue Aug 08 13:14:39 2017 -0400 |
| b |
| @@ -0,0 +1,31 @@ +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 |