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0
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1 #!/usr/bin/env Rscript
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2
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3 get_file_path = function(life_stage, base_name, life_stage_nymph=NULL, life_stage_adult=NULL) {
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4 if (!is.null(life_stage_nymph)) {
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5 lsi = get_life_stage_index(life_stage, life_stage_nymph=life_stage_nymph);
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6 file_name = paste(lsi, tolower(life_stage_nymph), base_name, sep="_");
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7 } else if (!is.null(life_stage_adult)) {
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8 lsi = get_life_stage_index(life_stage, life_stage_adult=life_stage_adult);
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9 file_name = paste(lsi, tolower(life_stage_adult), base_name, sep="_");
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10 } else {
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11 lsi = get_life_stage_index(life_stage);
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12 file_name = paste(lsi, base_name, sep="_");
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13 }
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14 file_path = paste("output_plots_dir", file_name, sep="/");
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15 return(file_path);
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16 }
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17
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18 get_life_stage_index = function(life_stage, life_stage_nymph=NULL, life_stage_adult=NULL) {
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19 # Name collection elements so that they
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20 # are displayed in logical order.
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21 if (life_stage=="Egg") {
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22 lsi = "01";
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23 } else if (life_stage=="Nymph") {
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24 if (life_stage_nymph=="Young") {
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25 lsi = "02";
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26 } else if (life_stage_nymph=="Old") {
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27 lsi = "03";
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28 } else if (life_stage_nymph=="Total") {
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29 lsi="04";
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30 }
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31 } else if (life_stage=="Adult") {
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32 if (life_stage_adult=="Pre-vittelogenic") {
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33 lsi = "05";
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34 } else if (life_stage_adult=="Vittelogenic") {
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35 lsi = "06";
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36 } else if (life_stage_adult=="Diapausing") {
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37 lsi = "07";
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38 } else if (life_stage_adult=="Total") {
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39 lsi = "08";
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40 }
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41 } else if (life_stage=="Total") {
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42 lsi = "09";
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43 }
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44 return(lsi);
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45 }
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46
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47 get_mean_and_std_error = function(p_replications, f1_replications, f2_replications) {
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48 # P mean.
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49 p_m = apply(p_replications, 1, mean);
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50 # P standard error.
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51 p_se = apply(p_replications, 1, sd) / sqrt(opt$replications);
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52 # F1 mean.
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53 f1_m = apply(f1_replications, 1, mean);
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54 # F1 standard error.
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55 f1_se = apply(f1_replications, 1, sd) / sqrt(opt$replications);
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56 # F2 mean.
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57 f2_m = apply(f2_replications, 1, mean);
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58 # F2 standard error.
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59 f2_se = apply(f2_replications, 1, sd) / sqrt(opt$replications);
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60 return(list(p_m, p_se, f1_m, f1_se, f2_m, f2_se))
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61 }
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62
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63 get_tick_index = function(index, last_tick, ticks, tick_labels, tick_sep) {
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64 # The R code tries hard not to draw overlapping tick labels, and so
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65 # will omit labels where they would abut or overlap previously drawn
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66 # labels. This can result in, for example, every other tick being
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67 # labelled. We'll keep track of the last tick to make sure all of
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68 # the month labels are displayed, and missing ticks are restricted
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69 # to Sundays which have no labels anyway.
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70 if (last_tick==0) {
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71 return(length(ticks)+1);
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72 }
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73 last_saved_tick = ticks[[length(ticks)]];
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74 if (index-last_saved_tick<tick_sep) {
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75 last_saved_month = tick_labels[[length(tick_labels)]];
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76 if (last_saved_month=="") {
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77 # We're safe overwriting a tick
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78 # with no label (i.e., a Sunday tick).
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79 return(length(ticks));
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80 } else {
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81 # Don't eliminate a Month label.
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82 return(NULL);
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83 }
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84 }
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85 return(length(ticks)+1);
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86 }
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87
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88 get_total_days = function(is_leap_year) {
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89 # Get the total number of days in the current year.
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90 if (is_leap_year) {
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91 return(366);
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92 } else {
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93 return(365);
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94 }
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95 }
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96
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97 get_x_axis_ticks_and_labels = function(temperature_data_frame, prepend_end_doy_norm, append_start_doy_norm, date_interval=FALSE) {
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98 # Generate a list of ticks and labels for plotting the x axis.
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99 if (prepend_end_doy_norm > 0) {
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100 prepend_end_norm_row = which(temperature_data_frame$DOY==prepend_end_doy_norm);
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101 } else {
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102 prepend_end_norm_row = 0;
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103 }
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104 if (append_start_doy_norm > 0) {
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105 append_start_norm_row = which(temperature_data_frame$DOY==append_start_doy_norm);
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106 } else {
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107 append_start_norm_row = 0;
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108 }
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109 num_rows = dim(temperature_data_frame)[1];
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110 tick_labels = list();
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111 ticks = list();
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112 current_month_label = NULL;
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113 last_tick = 0;
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114 if (date_interval) {
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115 tick_sep = 0;
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116 } else {
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117 tick_sep = 3;
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118 }
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119 for (i in 1:num_rows) {
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120 # Get the year and month from the date which
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121 # has the format YYYY-MM-DD.
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122 date = format(temperature_data_frame$DATE[i]);
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123 # Get the month label.
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124 items = strsplit(date, "-")[[1]];
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125 month = items[2];
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126 month_label = month.abb[as.integer(month)];
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127 day = as.integer(items[3]);
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128 doy = as.integer(temperature_data_frame$DOY[i]);
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129 # We're plotting the entire year, so ticks will
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130 # occur on Sundays and the first of each month.
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131 if (i == prepend_end_norm_row) {
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132 # Add a tick for the end of the 30 year normnals data
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133 # that was prepended to the year-to-date data.
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134 label_str = "End prepended 30 year normals";
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135 tick_index = get_tick_index(i, last_tick, ticks, tick_labels, tick_sep)
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136 ticks[tick_index] = i;
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137 if (date_interval) {
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138 # Append the day to label_str
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139 tick_labels[tick_index] = paste(label_str, day, sep=" ");
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140 } else {
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141 tick_labels[tick_index] = label_str;
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142 }
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143 last_tick = i;
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144 } else if (doy == append_start_doy_norm) {
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145 # Add a tick for the start of the 30 year normnals data
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146 # that was appended to the year-to-date data.
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147 label_str = "Start appended 30 year normals";
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148 tick_index = get_tick_index(i, last_tick, ticks, tick_labels, tick_sep)
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149 ticks[tick_index] = i;
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150 if (!identical(current_month_label, month_label)) {
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151 # Append the month to label_str.
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152 label_str = paste(label_str, month_label, spe=" ");
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153 current_month_label = month_label;
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154 }
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155 if (date_interval) {
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156 # Append the day to label_str
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157 label_str = paste(label_str, day, sep=" ");
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158 }
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159 tick_labels[tick_index] = label_str;
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160 last_tick = i;
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161 } else if (i==num_rows) {
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162 # Add a tick for the last day of the year.
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163 label_str = "";
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164 tick_index = get_tick_index(i, last_tick, ticks, tick_labels, tick_sep)
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165 ticks[tick_index] = i;
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166 if (!identical(current_month_label, month_label)) {
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167 # Append the month to label_str.
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168 label_str = month_label;
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169 current_month_label = month_label;
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170 }
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171 if (date_interval) {
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172 # Append the day to label_str
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173 label_str = paste(label_str, day, sep=" ");
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174 }
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175 tick_labels[tick_index] = label_str;
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176 } else {
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177 if (!identical(current_month_label, month_label)) {
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178 # Add a tick for the month.
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179 tick_index = get_tick_index(i, last_tick, ticks, tick_labels, tick_sep)
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180 ticks[tick_index] = i;
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181 if (date_interval) {
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182 # Append the day to the month.
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183 tick_labels[tick_index] = paste(month_label, day, sep=" ");
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184 } else {
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185 tick_labels[tick_index] = month_label;
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186 }
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187 current_month_label = month_label;
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188 last_tick = i;
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189 }
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190 tick_index = get_tick_index(i, last_tick, ticks, tick_labels, tick_sep)
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191 if (!is.null(tick_index)) {
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192 if (date_interval) {
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193 # Add a tick for every day. The first tick is the
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194 # month label, so add a tick only if i is not 1
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195 if (i>1 & day>1) {
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196 tick_index = get_tick_index(i, last_tick, ticks, tick_labels, tick_sep)
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197 ticks[tick_index] = i;
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198 # Add the day as the label.
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199 tick_labels[tick_index] = day;
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200 last_tick = i;
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201 }
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202 } else {
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203 # Get the day.
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204 day = weekdays(as.Date(date));
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205 if (day=="Sunday") {
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206 # Add a tick if we're on a Sunday.
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207 ticks[tick_index] = i;
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208 # Add a blank month label so it is not displayed.
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209 tick_labels[tick_index] = "";
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210 last_tick = i;
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211 }
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212 }
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213 }
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214 }
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215 }
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216 return(list(ticks, tick_labels));
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217 }
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218
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219 render_chart = function(ticks, date_labels, chart_type, plot_std_error, insect, location, latitude, start_date, end_date, days, maxval,
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220 replications, life_stage, group, group_std_error, group2=NULL, group2_std_error=NULL, group3=NULL, group3_std_error=NULL,
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221 life_stages_adult=NULL, life_stages_nymph=NULL) {
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222 if (chart_type=="pop_size_by_life_stage") {
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223 if (life_stage=="Total") {
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224 title = paste(insect, ": Reps", replications, ":", life_stage, "Pop :", location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
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225 legend_text = c("Egg", "Nymph", "Adult");
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226 columns = c(4, 2, 1);
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227 plot(days, group, main=title, type="l", ylim=c(0, maxval), axes=FALSE, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3);
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228 legend("topleft", legend_text, lty=c(1, 1, 1), col=columns, cex=3);
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229 lines(days, group2, lwd=2, lty=1, col=2);
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230 lines(days, group3, lwd=2, lty=1, col=4);
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231 axis(side=1, at=ticks, labels=date_labels, las=2, font.axis=3, xpd=TRUE, cex=3, cex.lab=3, cex.axis=3, cex.main=3);
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232 axis(side=2, font.axis=3, xpd=TRUE, cex=3, cex.lab=3, cex.axis=3, cex.main=3);
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233 if (plot_std_error=="yes") {
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234 # Standard error for group.
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235 lines(days, group+group_std_error, lty=2);
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236 lines(days, group-group_std_error, lty=2);
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237 # Standard error for group2.
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238 lines(days, group2+group2_std_error, col=2, lty=2);
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239 lines(days, group2-group2_std_error, col=2, lty=2);
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240 # Standard error for group3.
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241 lines(days, group3+group3_std_error, col=4, lty=2);
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242 lines(days, group3-group3_std_error, col=4, lty=2);
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243 }
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244 } else {
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245 if (life_stage=="Egg") {
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246 title = paste(insect, ": Reps", replications, ":", life_stage, "Pop :", location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
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247 legend_text = c(life_stage);
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248 columns = c(4);
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249 } else if (life_stage=="Nymph") {
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250 stage = paste(life_stages_nymph, "Nymph Pop :", sep=" ");
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251 title = paste(insect, ": Reps", replications, ":", stage, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
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252 legend_text = c(paste(life_stages_nymph, life_stage, sep=" "));
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253 columns = c(2);
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254 } else if (life_stage=="Adult") {
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255 stage = paste(life_stages_adult, "Adult Pop", sep=" ");
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256 title = paste(insect, ": Reps", replications, ":", stage, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
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257 legend_text = c(paste(life_stages_adult, life_stage, sep=" "));
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258 columns = c(1);
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259 }
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260 plot(days, group, main=title, type="l", ylim=c(0, maxval), axes=FALSE, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3);
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261 legend("topleft", legend_text, lty=c(1), col="black", cex=3);
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262 axis(side=1, at=ticks, labels=date_labels, las=2, font.axis=3, xpd=TRUE, cex=3, cex.lab=3, cex.axis=3, cex.main=3);
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263 axis(side=2, font.axis=3, xpd=TRUE, cex=3, cex.lab=3, cex.axis=3, cex.main=3);
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264 if (plot_std_error=="yes") {
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265 # Standard error for group.
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266 lines(days, group+group_std_error, lty=2);
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267 lines(days, group-group_std_error, lty=2);
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268 }
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269 }
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270 } else if (chart_type=="pop_size_by_generation") {
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271 if (life_stage=="Total") {
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272 title_str = ": Total Pop by Gen :";
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273 } else if (life_stage=="Egg") {
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274 title_str = ": Egg Pop by Gen :";
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275 } else if (life_stage=="Nymph") {
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276 title_str = paste(":", life_stages_nymph, "Nymph Pop by Gen", ":", sep=" ");
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277 } else if (life_stage=="Adult") {
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278 title_str = paste(":", life_stages_adult, "Adult Pop by Gen", ":", sep=" ");
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279 }
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280 title = paste(insect, ": Reps", replications, title_str, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" ");
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281 legend_text = c("P", "F1", "F2");
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282 columns = c(1, 2, 4);
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283 plot(days, group, main=title, type="l", ylim=c(0, maxval), axes=FALSE, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3);
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284 legend("topleft", legend_text, lty=c(1, 1, 1), col=columns, cex=3);
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285 lines(days, group2, lwd=2, lty=1, col=2);
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286 lines(days, group3, lwd=2, lty=1, col=4);
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287 axis(side=1, at=ticks, labels=date_labels, las=2, font.axis=3, xpd=TRUE, cex=3, cex.lab=3, cex.axis=3, cex.main=3);
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288 axis(side=2, font.axis=3, xpd=TRUE, cex=3, cex.lab=3, cex.axis=3, cex.main=3);
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289 if (plot_std_error=="yes") {
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290 # Standard error for group.
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291 lines(days, group+group_std_error, lty=2);
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292 lines(days, group-group_std_error, lty=2);
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293 # Standard error for group2.
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294 lines(days, group2+group2_std_error, col=2, lty=2);
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295 lines(days, group2-group2_std_error, col=2, lty=2);
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296 # Standard error for group3.
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297 lines(days, group3+group3_std_error, col=4, lty=2);
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298 lines(days, group3-group3_std_error, col=4, lty=2);
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299 }
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300 }
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301 }
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302
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303 stop_err = function(msg) {
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304 cat(msg, file=stderr());
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305 quit(save="no", status=1);
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306 }
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307
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308 validate_date = function(date_str) {
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309 valid_date = as.Date(date_str, format="%Y-%m-%d");
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310 if( class(valid_date)=="try-error" || is.na(valid_date)) {
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311 msg = paste("Invalid date: ", date_str, ", valid date format is yyyy-mm-dd.", sep="");
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312 stop_err(msg);
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313 }
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314 return(valid_date);
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315 }
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