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1 #!/usr/bin/env Rscript
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2
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3 suppressPackageStartupMessages(library("optparse"))
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4
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5 option_list <- list(
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6 make_option(c("-a", "--adult_mort"), action="store", dest="adult_mort", type="integer", help="Adjustment rate for adult mortality"),
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7 make_option(c("-b", "--adult_accum"), action="store", dest="adult_accum", type="integer", help="Adjustment of DD accumulation (old nymph->adult)"),
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8 make_option(c("-c", "--egg_mort"), action="store", dest="egg_mort", type="integer", help="Adjustment rate for egg mortality"),
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9 make_option(c("-e", "--location"), action="store", dest="location", help="Selected location"),
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10 make_option(c("-f", "--min_clutch_size"), action="store", dest="min_clutch_size", type="integer", help="Adjustment of minimum clutch size"),
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11 make_option(c("-i", "--max_clutch_size"), action="store", dest="max_clutch_size", type="integer", help="Adjustment of maximum clutch size"),
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12 make_option(c("-j", "--nymph_mort"), action="store", dest="nymph_mort", type="integer", help="Adjustment rate for nymph mortality"),
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13 make_option(c("-k", "--old_nymph_accum"), action="store", dest="old_nymph_accum", type="integer", help="Adjustment of DD accumulation (young nymph->old nymph)"),
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64
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14 make_option(c("-m", "--num_columns"), action="store", dest="num_columns", type="integer", help="Total number of columns in the temperature dataset"),
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13
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15 make_option(c("-n", "--num_days"), action="store", dest="num_days", type="integer", help="Total number of days in the temperature dataset"),
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16 make_option(c("-o", "--output"), action="store", dest="output", help="Output dataset"),
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17 make_option(c("-p", "--oviposition"), action="store", dest="oviposition", type="integer", help="Adjustment for oviposition rate"),
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18 make_option(c("-q", "--photoperiod"), action="store", dest="photoperiod", type="double", help="Critical photoperiod for diapause induction/termination"),
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19 make_option(c("-s", "--replications"), action="store", dest="replications", type="integer", help="Number of replications"),
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20 make_option(c("-t", "--se_plot"), action="store", dest="se_plot", help="Plot SE"),
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22
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21 make_option(c("-v", "--input"), action="store", dest="input", help="Temperature data for selected location"),
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22 make_option(c("-y", "--young_nymph_accum"), action="store", dest="young_nymph_accum", type="integer", help="Adjustment of DD accumulation (egg->young nymph)")
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23 )
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24
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25 parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
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26 args <- parse_args(parser, positional_arguments=TRUE)
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27 opt <- args$options
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28
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64
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29 add_daylight_length = function(latitude, temperature_data_matrix, num_days) {
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46
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30 # Return a vector of daylight length (photoperido profile) for
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31 # the number of days specified in the input temperature data
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32 # (from Forsythe 1995).
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33 p = 0.8333
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34 daylight_length_vector <- NULL
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35 for (i in 1:num_days) {
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36 # Get the day of the year from the current row
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37 # of the temperature data for computation.
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64
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38 doy <- temperature_data_matrix[i, 4]
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46
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39 theta <- 0.2163108 + 2 * atan(0.9671396 * tan(0.00860 * (doy - 186)))
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40 phi <- asin(0.39795 * cos(theta))
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41 # Compute the length of daylight for the day of the year.
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42 daylight_length_vector[i] <- 24 - (24 / pi * acos((sin(p * pi / 180) + sin(latitude * pi / 180) * sin(phi)) / (cos(latitude * pi / 180) * cos(phi))))
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43 }
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64
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44 # Append daylight_length_vector as a new column to temperature_data_matrix.
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45 temperature_data_matrix <- cbind(temperature_data_matrix, daylight_length_vector)
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46 }
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47
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64
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48 get_temperature_at_hour = function(latitude, temperature_data_matrix, row, num_days) {
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26
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49 # Base development threshold for Brown Marmolated Stink Bug
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50 # insect phenology model.
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46
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51 # TODO: Pass insect on the command line to accomodate more
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52 # the just the Brown Marmolated Stink Bub.
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53 threshold <- 14.17
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54
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55 # Input temperature currently has the following columns.
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56 # # LATITUDE, LONGITUDE, DATE, DOY, TMIN, TMAX
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57 # Minimum temperature for current row.
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64
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58 dnp <- temperature_data_matrix[row, 5]
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59 # Maximum temperature for current row.
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64
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60 dxp <- temperature_data_matrix[row, 6]
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61 # Mean temperature for current row.
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62 dmean <- 0.5 * (dnp + dxp)
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47
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63 # Initialize degree day accumulation
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64 dd <- 0
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65 if (dxp < threshold) {
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66 dd <- 0
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67 }
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68 else {
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26
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69 # Initialize hourly temperature.
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70 T <- NULL
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71 # Initialize degree hour vector.
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72 dh <- NULL
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46
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73 # Daylight length for current row.
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64
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74 y <- temperature_data_matrix[row, 7]
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75 # Darkness length.
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76 z <- 24 - y
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77 # Lag coefficient.
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78 a <- 1.86
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79 # Darkness coefficient.
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80 b <- 2.20
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26
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81 # Sunrise time.
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82 risetime <- 12 - y / 2
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26
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83 # Sunset time.
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84 settime <- 12 + y / 2
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85 ts <- (dxp - dnp) * sin(pi * (settime - 5) / (y + 2 * a)) + dnp
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86 for (i in 1:24) {
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87 if (i > risetime && i < settime) {
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88 # Number of hours after Tmin until sunset.
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89 m <- i - 5
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90 T[i] = (dxp - dnp) * sin(pi * m / (y + 2 * a)) + dnp
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91 if (T[i] < 8.4) {
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92 dh[i] <- 0
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93 }
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94 else {
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95 dh[i] <- T[i] - 8.4
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96 }
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97 }
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98 else if (i > settime) {
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99 n <- i - settime
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100 T[i] = dnp + (ts - dnp) * exp( - b * n / z)
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101 if (T[i] < 8.4) {
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102 dh[i] <- 0
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103 }
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104 else {
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105 dh[i] <- T[i] - 8.4
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106 }
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107 }
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108 else {
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109 n <- i + 24 - settime
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110 T[i]=dnp + (ts - dnp) * exp( - b * n / z)
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111 if (T[i] < 8.4) {
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112 dh[i] <- 0
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113 }
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114 else {
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115 dh[i] <- T[i] - 8.4
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116 }
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117 }
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118 }
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119 dd <- sum(dh) / 24
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120 }
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121 return=c(dmean, dd)
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122 return
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123 }
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124
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125 dev.egg = function(temperature) {
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126 dev.rate= -0.9843 * temperature + 33.438
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127 return = dev.rate
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128 return
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129 }
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130
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131 dev.young = function(temperature) {
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132 n12 <- -0.3728 * temperature + 14.68
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133 n23 <- -0.6119 * temperature + 25.249
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134 dev.rate = mean(n12 + n23)
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135 return = dev.rate
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136 return
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137 }
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138
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139 dev.old = function(temperature) {
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140 n34 <- -0.6119 * temperature + 17.602
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141 n45 <- -0.4408 * temperature + 19.036
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142 dev.rate = mean(n34 + n45)
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143 return = dev.rate
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144 return
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145 }
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146
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147 dev.emerg = function(temperature) {
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148 emerg.rate <- -0.5332 * temperature + 24.147
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149 return = emerg.rate
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150 return
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151 }
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152
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64
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153 mortality.egg = function(temperature) {
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154 if (temperature < 12.7) {
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155 mort.prob = 0.8
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156 }
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157 else {
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158 mort.prob = 0.8 - temperature / 40.0
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159 if (mort.prob < 0) {
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160 mort.prob = 0.01
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161 }
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162 }
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163 return = mort.prob
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164 return
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165 }
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166
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167 mortality.nymph = function(temperature) {
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168 if (temperature < 12.7) {
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169 mort.prob = 0.03
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170 }
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171 else {
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172 mort.prob = temperature * 0.0008 + 0.03
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173 }
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174 return = mort.prob
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175 return
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176 }
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177
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178 mortality.adult = function(temperature) {
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179 if (temperature < 12.7) {
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180 mort.prob = 0.002
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181 }
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182 else {
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183 mort.prob = temperature * 0.0005 + 0.02
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184 }
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185 return = mort.prob
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186 return
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187 }
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188
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22
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189 # Read in the input temperature datafile into a Data Frame object.
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44
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190 # The input data currently must have 6 columns:
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191 # LATITUDE, LONGITUDE, DATE, DOY, TMIN, TMAX
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64
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192 temperature_data_matrix <- read.csv(file=opt$input, header=T, strip.white=TRUE, sep=",")
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193 start_date <- temperature_data_matrix[1, 3]
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194 end_date <- temperature_data_matrix[opt$num_days, 3]
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195 latitude <- temperature_data_matrix[1, 1]
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196 add_daylight_length(latitude, temperature_data_matrix, opt$num_days)
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197
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198 cat("Number of days: ", opt$num_days, "\n")
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199
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200 # Initialize matrix for results from all replications.
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201 S0.rep <- S1.rep <- S2.rep <- S3.rep <- S4.rep <- S5.rep <- matrix(rep(0, opt$num_days * opt$replications), ncol = opt$replications)
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202 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$replications)
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203
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204 # loop through replications
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205 for (N.rep in 1:opt$replications) {
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206 # During each replication start with 1000 individuals.
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207 # TODO: user definable as well?
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208 n <- 1000
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26
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209 # Generation, Stage, DD, T, Diapause.
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210 vec.ini <- c(0, 3, 0, 0, 0)
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211 # Overwintering, previttelogenic, DD=0, T=0, no-diapause.
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212 vec.mat <- rep(vec.ini, n)
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213 # Complete matrix for the population.
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214 vec.mat <- base::t(matrix(vec.mat, nrow=5))
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215 # Time series of population size.
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216 tot.pop <- NULL
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217 gen0.pop <- rep(0, opt$num_days)
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218 gen1.pop <- rep(0, opt$num_days)
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219 gen2.pop <- rep(0, opt$num_days)
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220 S0 <- S1 <- S2 <- S3 <- S4 <- S5 <- rep(0, opt$num_days)
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221 g0.adult <- g1.adult <- g2.adult <- rep(0, opt$num_days)
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222 N.newborn <- N.death <- N.adult <- rep(0, opt$num_days)
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223 dd.day <- rep(0, opt$num_days)
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224
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22
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225 # All the days included in the input temperature dataset.
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226 for (row in 1:opt$num_days) {
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227 # Get the integer day of the year for the current row.
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228 doy <- temperature_data_matrix[row, 4]
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229 # Photoperiod in the day.
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230 photoperiod <- temperature_data_matrix[row, 7]
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231 temp.profile <- get_temperature_at_hour(latitude, temperature_data_matrix, row, opt$num_days)
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232 mean.temp <- temp.profile[1]
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233 dd.temp <- temp.profile[2]
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234 dd.day[row] <- dd.temp
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235 # Trash bin for death.
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236 death.vec <- NULL
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26
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237 # Newborn.
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238 birth.vec <- NULL
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239
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240 # All individuals.
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241 for (i in 1:n) {
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242 # Find individual record.
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243 vec.ind <- vec.mat[i,]
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244 # First of all, still alive?
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245 # Adjustment for late season mortality rate.
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22
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246 if (latitude < 40.0) {
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247 post.mort <- 1
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248 day.kill <- 300
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249 }
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250 else {
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251 post.mort <- 2
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252 day.kill <- 250
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253 }
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254 if (vec.ind[2] == 0) {
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255 # Egg.
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256 death.prob = opt$egg_mort * mortality.egg(mean.temp)
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257 }
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258 else if (vec.ind[2] == 1 | vec.ind[2] == 2) {
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259 death.prob = opt$nymph_mort * mortality.nymph(mean.temp)
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260 }
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261 else if (vec.ind[2] == 3 | vec.ind[2] == 4 | vec.ind[2] == 5) {
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26
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262 # For adult.
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263 if (doy < day.kill) {
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264 death.prob = opt$adult_mort * mortality.adult(mean.temp)
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265 }
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266 else {
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26
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267 # Increase adult mortality after fall equinox.
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268 death.prob = opt$adult_mort * post.mort * mortality.adult(mean.temp)
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269 }
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270 }
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271 # (or dependent on temperature and life stage?)
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272 u.d <- runif(1)
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273 if (u.d < death.prob) {
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274 death.vec <- c(death.vec, i)
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275 }
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276 else {
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277 # Aggregrate index of dead bug.
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278 # Event 1 end of diapause.
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279 if (vec.ind[1] == 0 && vec.ind[2] == 3) {
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280 # Overwintering adult (previttelogenic).
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281 if (photoperiod > opt$photoperiod && vec.ind[3] > 68 && doy < 180) {
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282 # Add 68C to become fully reproductively matured.
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283 # Transfer to vittelogenic.
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284 vec.ind <- c(0, 4, 0, 0, 0)
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285 vec.mat[i,] <- vec.ind
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286 }
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287 else {
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288 # Add to dd.
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289 vec.ind[3] <- vec.ind[3] + dd.temp
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290 # Add 1 day in current stage.
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291 vec.ind[4] <- vec.ind[4] + 1
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292 vec.mat[i,] <- vec.ind
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293 }
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294 }
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295 if (vec.ind[1] != 0 && vec.ind[2] == 3) {
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296 # Not overwintering adult (previttelogenic).
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297 current.gen <- vec.ind[1]
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298 if (vec.ind[3] > 68) {
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299 # Add 68C to become fully reproductively matured.
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300 # Transfer to vittelogenic.
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301 vec.ind <- c(current.gen, 4, 0, 0, 0)
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302 vec.mat[i,] <- vec.ind
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303 }
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304 else {
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26
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305 # Add to dd.
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306 vec.ind[3] <- vec.ind[3] + dd.temp
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26
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307 # Add 1 day in current stage.
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308 vec.ind[4] <- vec.ind[4] + 1
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309 vec.mat[i,] <- vec.ind
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310 }
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311 }
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312
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313 # Event 2 oviposition -- where population dynamics comes from.
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314 if (vec.ind[2] == 4 && vec.ind[1] == 0 && mean.temp > 10) {
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315 # Vittelogenic stage, overwintering generation.
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316 if (vec.ind[4] == 0) {
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317 # Just turned in vittelogenic stage.
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318 n.birth=round(runif(1, 2 + opt$min_clutch_size, 8 + opt$max_clutch_size))
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319 }
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320 else {
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321 # Daily probability of birth.
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322 p.birth = opt$oviposition * 0.01
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323 u1 <- runif(1)
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324 if (u1 < p.birth) {
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325 n.birth=round(runif(1, 2, 8))
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326 }
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327 }
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26
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328 # Add to dd.
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329 vec.ind[3] <- vec.ind[3] + dd.temp
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26
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330 # Add 1 day in current stage.
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331 vec.ind[4] <- vec.ind[4] + 1
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332 vec.mat[i,] <- vec.ind
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333 if (n.birth > 0) {
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26
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334 # Add new birth -- might be in different generations.
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335 new.gen <- vec.ind[1] + 1
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26
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336 # Egg profile.
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337 new.ind <- c(new.gen, 0, 0, 0, 0)
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338 new.vec <- rep(new.ind, n.birth)
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26
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339 # Update batch of egg profile.
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340 new.vec <- t(matrix(new.vec, nrow=5))
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26
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341 # Group with total eggs laid in that day.
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342 birth.vec <- rbind(birth.vec, new.vec)
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343 }
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344 }
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|
345
|
|
26
|
346 # Event 2 oviposition -- for gen 1.
|
|
47
|
347 if (vec.ind[2] == 4 && vec.ind[1] == 1 && mean.temp > 12.5 && doy < 222) {
|
|
26
|
348 # Vittelogenic stage, 1st generation
|
|
0
|
349 if (vec.ind[4] == 0) {
|
|
26
|
350 # Just turned in vittelogenic stage.
|
|
0
|
351 n.birth=round(runif(1, 2 + opt$min_clutch_size, 8 + opt$max_clutch_size))
|
|
|
352 }
|
|
|
353 else {
|
|
26
|
354 # Daily probability of birth.
|
|
0
|
355 p.birth = opt$oviposition * 0.01
|
|
|
356 u1 <- runif(1)
|
|
|
357 if (u1 < p.birth) {
|
|
|
358 n.birth = round(runif(1, 2, 8))
|
|
|
359 }
|
|
|
360 }
|
|
26
|
361 # Add to dd.
|
|
0
|
362 vec.ind[3] <- vec.ind[3] + dd.temp
|
|
26
|
363 # Add 1 day in current stage.
|
|
0
|
364 vec.ind[4] <- vec.ind[4] + 1
|
|
|
365 vec.mat[i,] <- vec.ind
|
|
|
366 if (n.birth > 0) {
|
|
26
|
367 # Add new birth -- might be in different generations.
|
|
0
|
368 new.gen <- vec.ind[1] + 1
|
|
26
|
369 # Egg profile.
|
|
0
|
370 new.ind <- c(new.gen, 0, 0, 0, 0)
|
|
|
371 new.vec <- rep(new.ind, n.birth)
|
|
26
|
372 # Update batch of egg profile.
|
|
0
|
373 new.vec <- t(matrix(new.vec, nrow=5))
|
|
26
|
374 # Group with total eggs laid in that day.
|
|
0
|
375 birth.vec <- rbind(birth.vec, new.vec)
|
|
|
376 }
|
|
|
377 }
|
|
|
378
|
|
26
|
379 # Event 3 development (with diapause determination).
|
|
|
380 # Event 3.1 egg development to young nymph (vec.ind[2]=0 -> egg).
|
|
0
|
381 if (vec.ind[2] == 0) {
|
|
26
|
382 # Egg stage.
|
|
|
383 # Add to dd.
|
|
0
|
384 vec.ind[3] <- vec.ind[3] + dd.temp
|
|
|
385 if (vec.ind[3] >= (68 + opt$young_nymph_accum)) {
|
|
26
|
386 # From egg to young nymph, DD requirement met.
|
|
0
|
387 current.gen <- vec.ind[1]
|
|
26
|
388 # Transfer to young nymph stage.
|
|
0
|
389 vec.ind <- c(current.gen, 1, 0, 0, 0)
|
|
|
390 }
|
|
|
391 else {
|
|
26
|
392 # Add 1 day in current stage.
|
|
0
|
393 vec.ind[4] <- vec.ind[4] + 1
|
|
|
394 }
|
|
|
395 vec.mat[i,] <- vec.ind
|
|
|
396 }
|
|
|
397
|
|
26
|
398 # Event 3.2 young nymph to old nymph (vec.ind[2]=1 -> young nymph: determines diapause).
|
|
0
|
399 if (vec.ind[2] == 1) {
|
|
26
|
400 # young nymph stage.
|
|
|
401 # add to dd.
|
|
0
|
402 vec.ind[3] <- vec.ind[3] + dd.temp
|
|
|
403 if (vec.ind[3] >= (250 + opt$old_nymph_accum)) {
|
|
26
|
404 # From young to old nymph, dd requirement met.
|
|
0
|
405 current.gen <- vec.ind[1]
|
|
26
|
406 # Transfer to old nym stage.
|
|
0
|
407 vec.ind <- c(current.gen, 2, 0, 0, 0)
|
|
47
|
408 if (photoperiod < opt$photoperiod && doy > 180) {
|
|
0
|
409 vec.ind[5] <- 1
|
|
26
|
410 } # Prepare for diapausing.
|
|
0
|
411 }
|
|
|
412 else {
|
|
26
|
413 # Add 1 day in current stage.
|
|
0
|
414 vec.ind[4] <- vec.ind[4] + 1
|
|
|
415 }
|
|
|
416 vec.mat[i,] <- vec.ind
|
|
|
417 }
|
|
|
418
|
|
26
|
419 # Event 3.3 old nymph to adult: previttelogenic or diapausing?
|
|
0
|
420 if (vec.ind[2] == 2) {
|
|
26
|
421 # Old nymph stage.
|
|
|
422 # add to dd.
|
|
0
|
423 vec.ind[3] <- vec.ind[3] + dd.temp
|
|
|
424 if (vec.ind[3] >= (200 + opt$adult_accum)) {
|
|
26
|
425 # From old to adult, dd requirement met.
|
|
0
|
426 current.gen <- vec.ind[1]
|
|
|
427 if (vec.ind[5] == 0) {
|
|
26
|
428 # Non-diapausing adult -- previttelogenic.
|
|
0
|
429 vec.ind <- c(current.gen, 3, 0, 0, 0)
|
|
|
430 }
|
|
|
431 else {
|
|
26
|
432 # Diapausing.
|
|
0
|
433 vec.ind <- c(current.gen, 5, 0, 0, 1)
|
|
|
434 }
|
|
|
435 }
|
|
|
436 else {
|
|
26
|
437 # Add 1 day in current stage.
|
|
0
|
438 vec.ind[4] <- vec.ind[4] + 1
|
|
|
439 }
|
|
|
440 vec.mat[i,] <- vec.ind
|
|
|
441 }
|
|
|
442
|
|
26
|
443 # Event 4 growing of diapausing adult (unimportant, but still necessary).
|
|
0
|
444 if (vec.ind[2] == 5) {
|
|
|
445 vec.ind[3] <- vec.ind[3] + dd.temp
|
|
|
446 vec.ind[4] <- vec.ind[4] + 1
|
|
|
447 vec.mat[i,] <- vec.ind
|
|
|
448 }
|
|
26
|
449 } # Else if it is still alive.
|
|
|
450 } # End of the individual bug loop.
|
|
0
|
451
|
|
26
|
452 # Find how many died.
|
|
0
|
453 n.death <- length(death.vec)
|
|
|
454 if (n.death > 0) {
|
|
|
455 vec.mat <- vec.mat[-death.vec, ]
|
|
|
456 }
|
|
26
|
457 # Remove record of dead.
|
|
|
458 # Find how many new born.
|
|
0
|
459 n.newborn <- length(birth.vec[,1])
|
|
|
460 vec.mat <- rbind(vec.mat, birth.vec)
|
|
26
|
461 # Update population size for the next day.
|
|
0
|
462 n <- n - n.death + n.newborn
|
|
|
463
|
|
26
|
464 # Aggregate results by day.
|
|
0
|
465 tot.pop <- c(tot.pop, n)
|
|
26
|
466 # Egg.
|
|
0
|
467 s0 <- sum(vec.mat[,2] == 0)
|
|
26
|
468 # Young nymph.
|
|
0
|
469 s1 <- sum(vec.mat[,2] == 1)
|
|
26
|
470 # Old nymph.
|
|
0
|
471 s2 <- sum(vec.mat[,2] == 2)
|
|
26
|
472 # Previtellogenic.
|
|
0
|
473 s3 <- sum(vec.mat[,2] == 3)
|
|
26
|
474 # Vitellogenic.
|
|
0
|
475 s4 <- sum(vec.mat[,2] == 4)
|
|
26
|
476 # Diapausing.
|
|
0
|
477 s5 <- sum(vec.mat[,2] == 5)
|
|
26
|
478 # Overwintering adult.
|
|
0
|
479 gen0 <- sum(vec.mat[,1] == 0)
|
|
26
|
480 # First generation.
|
|
0
|
481 gen1 <- sum(vec.mat[,1] == 1)
|
|
26
|
482 # Second generation.
|
|
0
|
483 gen2 <- sum(vec.mat[,1] == 2)
|
|
26
|
484 # Sum of all adults.
|
|
0
|
485 n.adult <- sum(vec.mat[,2] == 3) + sum(vec.mat[,2] == 4) + sum(vec.mat[,2] == 5)
|
|
47
|
486
|
|
|
487 # Generation 0 pop size.
|
|
|
488 gen0.pop[row] <- gen0
|
|
|
489 gen1.pop[row] <- gen1
|
|
|
490 gen2.pop[row] <- gen2
|
|
0
|
491
|
|
47
|
492 S0[row] <- s0
|
|
|
493 S1[row] <- s1
|
|
|
494 S2[row] <- s2
|
|
|
495 S3[row] <- s3
|
|
|
496 S4[row] <- s4
|
|
|
497 S5[row] <- s5
|
|
|
498
|
|
|
499 g0.adult[row] <- sum(vec.mat[,1] == 0)
|
|
|
500 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))
|
|
|
501 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))
|
|
|
502
|
|
|
503 N.newborn[row] <- n.newborn
|
|
|
504 N.death[row] <- n.death
|
|
|
505 N.adult[row] <- n.adult
|
|
13
|
506 } # end of days specified in the input temperature data
|
|
0
|
507
|
|
|
508 dd.cum <- cumsum(dd.day)
|
|
47
|
509
|
|
26
|
510 # Collect all the outputs.
|
|
0
|
511 S0.rep[,N.rep] <- S0
|
|
|
512 S1.rep[,N.rep] <- S1
|
|
|
513 S2.rep[,N.rep] <- S2
|
|
|
514 S3.rep[,N.rep] <- S3
|
|
|
515 S4.rep[,N.rep] <- S4
|
|
|
516 S5.rep[,N.rep] <- S5
|
|
|
517 newborn.rep[,N.rep] <- N.newborn
|
|
|
518 death.rep[,N.rep] <- N.death
|
|
|
519 adult.rep[,N.rep] <- N.adult
|
|
|
520 pop.rep[,N.rep] <- tot.pop
|
|
|
521 g0.rep[,N.rep] <- gen0.pop
|
|
|
522 g1.rep[,N.rep] <- gen1.pop
|
|
|
523 g2.rep[,N.rep] <- gen2.pop
|
|
|
524 g0a.rep[,N.rep] <- g0.adult
|
|
|
525 g1a.rep[,N.rep] <- g1.adult
|
|
|
526 g2a.rep[,N.rep] <- g2.adult
|
|
|
527 }
|
|
|
528
|
|
44
|
529 # Data analysis and visualization can currently
|
|
46
|
530 # plot only within a single calendar year.
|
|
|
531 # TODO: enhance this to accomodate multiple calendar years.
|
|
|
532 n.yr <- 1
|
|
|
533 day.all <- c(1:opt$num_days * n.yr)
|
|
0
|
534
|
|
|
535 # mean value for adults
|
|
|
536 sa <- apply((S3.rep + S4.rep + S5.rep), 1, mean)
|
|
|
537 # mean value for nymphs
|
|
|
538 sn <- apply((S1.rep + S2.rep), 1,mean)
|
|
|
539 # mean value for eggs
|
|
|
540 se <- apply(S0.rep, 1, mean)
|
|
|
541 # mean value for P
|
|
|
542 g0 <- apply(g0.rep, 1, mean)
|
|
|
543 # mean value for F1
|
|
|
544 g1 <- apply(g1.rep, 1, mean)
|
|
|
545 # mean value for F2
|
|
|
546 g2 <- apply(g2.rep, 1, mean)
|
|
|
547 # mean value for P adult
|
|
|
548 g0a <- apply(g0a.rep, 1, mean)
|
|
|
549 # mean value for F1 adult
|
|
|
550 g1a <- apply(g1a.rep, 1, mean)
|
|
|
551 # mean value for F2 adult
|
|
|
552 g2a <- apply(g2a.rep, 1, mean)
|
|
|
553
|
|
|
554 # SE for adults
|
|
|
555 sa.se <- apply((S3.rep + S4.rep + S5.rep), 1, sd) / sqrt(opt$replications)
|
|
|
556 # SE for nymphs
|
|
|
557 sn.se <- apply((S1.rep + S2.rep) / sqrt(opt$replications), 1, sd)
|
|
|
558 # SE for eggs
|
|
|
559 se.se <- apply(S0.rep, 1, sd) / sqrt(opt$replications)
|
|
|
560 # SE value for P
|
|
|
561 g0.se <- apply(g0.rep, 1, sd) / sqrt(opt$replications)
|
|
|
562 # SE for F1
|
|
|
563 g1.se <- apply(g1.rep, 1, sd) / sqrt(opt$replications)
|
|
|
564 # SE for F2
|
|
|
565 g2.se <- apply(g2.rep, 1, sd) / sqrt(opt$replications)
|
|
|
566 # SE for P adult
|
|
|
567 g0a.se <- apply(g0a.rep, 1, sd) / sqrt(opt$replications)
|
|
|
568 # SE for F1 adult
|
|
|
569 g1a.se <- apply(g1a.rep, 1, sd) / sqrt(opt$replications)
|
|
|
570 # SE for F2 adult
|
|
|
571 g2a.se <- apply(g2a.rep, 1, sd) / sqrt(opt$replications)
|
|
|
572
|
|
48
|
573 dev.new(width=20, height=30)
|
|
0
|
574
|
|
|
575 # Start PDF device driver to save charts to output.
|
|
48
|
576 pdf(file=opt$output, width=20, height=30, bg="white")
|
|
0
|
577
|
|
|
578 par(mar = c(5, 6, 4, 4), mfrow=c(3, 1))
|
|
|
579
|
|
54
|
580 # Subfigure 1: population size by life stage
|
|
|
581 title <- paste("BSMB total population by life stage :", opt$location, ": Lat:", latitude, ":", start_date, "to", end_date, sep=" ")
|
|
55
|
582 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)
|
|
31
|
583 # Young and old nymphs.
|
|
|
584 lines(day.all, sn, lwd=2, lty=1, col=2)
|
|
0
|
585 # Eggs
|
|
31
|
586 lines(day.all, se, lwd=2, lty=1, col=4)
|
|
54
|
587 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"))
|
|
|
588 axis(2, cex.axis=3)
|
|
0
|
589 leg.text <- c("Egg", "Nymph", "Adult")
|
|
48
|
590 legend("topleft", leg.text, lty=c(1, 1, 1), col=c(4, 2, 1), cex=3)
|
|
0
|
591 if (opt$se_plot == 1) {
|
|
48
|
592 # Add SE lines to plot
|
|
0
|
593 # SE for adults
|
|
31
|
594 lines (day.all, sa + sa.se, lty=2)
|
|
|
595 lines (day.all, sa - sa.se, lty=2)
|
|
0
|
596 # SE for nymphs
|
|
31
|
597 lines (day.all, sn + sn.se, col=2, lty=2)
|
|
48
|
598 lines (day.all, sn - sn.se, col=2, lty=2)
|
|
0
|
599 # SE for eggs
|
|
31
|
600 lines (day.all, se + se.se, col=4, lty=2)
|
|
48
|
601 lines (day.all, se - se.se, col=4, lty=2)
|
|
0
|
602 }
|
|
|
603
|
|
54
|
604 # Subfigure 2: population size by generation
|
|
|
605 title <- paste("BSMB total population by generation :", opt$location, ": Lat:", latitude, ":", start_date, "to", end_date, sep=" ")
|
|
55
|
606 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)
|
|
56
|
607 lines(day.all, g1, lwd = 2, lty = 1, col=2)
|
|
|
608 lines(day.all, g2, lwd = 2, lty = 1, col=4)
|
|
54
|
609 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"))
|
|
|
610 axis(2, cex.axis=3)
|
|
0
|
611 leg.text <- c("P", "F1", "F2")
|
|
54
|
612 legend("topleft", leg.text, lty=c(1, 1, 1), col=c(1, 2, 4), cex=3)
|
|
0
|
613 if (opt$se_plot == 1) {
|
|
48
|
614 # Add SE lines to plot
|
|
0
|
615 # SE for adults
|
|
56
|
616 lines (day.all, g0+g0.se, lty=2)
|
|
|
617 lines (day.all, g0-g0.se, lty=2)
|
|
0
|
618 # SE for nymphs
|
|
56
|
619 lines (day.all, g1+g1.se, col=2, lty=2)
|
|
|
620 lines (day.all, g1-g1.se, col=2, lty=2)
|
|
0
|
621 # SE for eggs
|
|
56
|
622 lines (day.all, g2+g2.se, col=4, lty=2)
|
|
|
623 lines (day.all, g2-g2.se, col=4, lty=2)
|
|
0
|
624 }
|
|
|
625
|
|
54
|
626 # Subfigure 3: adult population size by generation
|
|
|
627 title <- paste("BSMB adult population by generation :", opt$location, ": Lat:", latitude, ":", start_date, "to", end_date, sep=" ")
|
|
55
|
628 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)
|
|
56
|
629 lines(day.all, g1a, lwd = 2, lty = 1, col=2)
|
|
|
630 lines(day.all, g2a, lwd = 2, lty = 1, col=4)
|
|
54
|
631 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"))
|
|
|
632 axis(2, cex.axis=3)
|
|
0
|
633 leg.text <- c("P", "F1", "F2")
|
|
54
|
634 legend("topleft", leg.text, lty=c(1, 1, 1), col=c(1, 2, 4), cex=3)
|
|
0
|
635 if (opt$se_plot == 1) {
|
|
48
|
636 # Add SE lines to plot
|
|
0
|
637 # SE for adults
|
|
56
|
638 lines (day.all, g0a+g0a.se, lty=2)
|
|
|
639 lines (day.all, g0a-g0a.se, lty=2)
|
|
0
|
640 # SE for nymphs
|
|
56
|
641 lines (day.all, g1a+g1a.se, col=2, lty=2)
|
|
|
642 lines (day.all, g1a-g1a.se, col=2, lty=2)
|
|
0
|
643 # SE for eggs
|
|
56
|
644 lines (day.all, g2a+g2a.se, col=4, lty=2)
|
|
|
645 lines (day.all, g2a-g2a.se, col=4, lty=2)
|
|
0
|
646 }
|
|
|
647
|
|
|
648 # Turn off device driver to flush output.
|
|
|
649 dev.off()
|
