Mercurial > repos > greg > insect_phenology_model
comparison insect_phenology_model.R @ 28:afe6d8bac0c0 draft
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| author | greg |
|---|---|
| date | Mon, 12 Mar 2018 09:15:16 -0400 |
| parents | 452e0e189e84 |
| children | ef6aa8c21729 |
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| 27:452e0e189e84 | 28:afe6d8bac0c0 |
|---|---|
| 1055 temperature_data_frame = append_vector(temperature_data_frame, eggs.std_error, "EGGSE"); | 1055 temperature_data_frame = append_vector(temperature_data_frame, eggs.std_error, "EGGSE"); |
| 1056 } | 1056 } |
| 1057 if (process_nymphs) { | 1057 if (process_nymphs) { |
| 1058 # Calculate nymph populations for selected life stage. | 1058 # Calculate nymph populations for selected life stage. |
| 1059 for (life_stage_nymph in life_stages_nymph) { | 1059 for (life_stage_nymph in life_stages_nymph) { |
| 1060 if (life_stage_nymph=="Total") { | 1060 if (life_stage_nymph=="Young") { |
| 1061 # Mean value for all nymphs. | |
| 1062 total_nymphs = apply((YoungNymphs.replications+OldNymphs.replications), 1, mean); | |
| 1063 temperature_data_frame = append_vector(temperature_data_frame, total_nymphs, "TOTALNYMPH"); | |
| 1064 # Standard error for all nymphs. | |
| 1065 total_nymphs.std_error = apply((YoungNymphs.replications+OldNymphs.replications) / sqrt(opt$replications), 1, sd); | |
| 1066 temperature_data_frame = append_vector(temperature_data_frame, total_nymphs.std_error, "TOTALNYMPHSE"); | |
| 1067 } else if (life_stage_nymph=="Young") { | |
| 1068 # Mean value for young nymphs. | 1061 # Mean value for young nymphs. |
| 1069 young_nymphs = apply(YoungNymphs.replications, 1, mean); | 1062 young_nymphs = apply(YoungNymphs.replications, 1, mean); |
| 1070 temperature_data_frame = append_vector(temperature_data_frame, young_nymphs, "YOUNGNYMPH"); | 1063 temperature_data_frame = append_vector(temperature_data_frame, young_nymphs, "YOUNGNYMPH"); |
| 1071 # Standard error for young nymphs. | 1064 # Standard error for young nymphs. |
| 1072 young_nymphs.std_error = apply(YoungNymphs.replications / sqrt(opt$replications), 1, sd); | 1065 young_nymphs.std_error = apply(YoungNymphs.replications / sqrt(opt$replications), 1, sd); |
| 1076 old_nymphs = apply(OldNymphs.replications, 1, mean); | 1069 old_nymphs = apply(OldNymphs.replications, 1, mean); |
| 1077 temperature_data_frame = append_vector(temperature_data_frame, old_nymphs, "OLDNYMPH"); | 1070 temperature_data_frame = append_vector(temperature_data_frame, old_nymphs, "OLDNYMPH"); |
| 1078 # Standard error for old nymphs. | 1071 # Standard error for old nymphs. |
| 1079 old_nymphs.std_error = apply(OldNymphs.replications / sqrt(opt$replications), 1, sd); | 1072 old_nymphs.std_error = apply(OldNymphs.replications / sqrt(opt$replications), 1, sd); |
| 1080 temperature_data_frame = append_vector(temperature_data_frame, old_nymphs.std_error, "OLDNYMPHSE"); | 1073 temperature_data_frame = append_vector(temperature_data_frame, old_nymphs.std_error, "OLDNYMPHSE"); |
| 1074 } else if (life_stage_nymph=="Total") { | |
| 1075 # Mean value for all nymphs. | |
| 1076 total_nymphs = apply((YoungNymphs.replications+OldNymphs.replications), 1, mean); | |
| 1077 temperature_data_frame = append_vector(temperature_data_frame, total_nymphs, "TOTALNYMPH"); | |
| 1078 # Standard error for all nymphs. | |
| 1079 total_nymphs.std_error = apply((YoungNymphs.replications+OldNymphs.replications) / sqrt(opt$replications), 1, sd); | |
| 1080 temperature_data_frame = append_vector(temperature_data_frame, total_nymphs.std_error, "TOTALNYMPHSE"); | |
| 1081 } | 1081 } |
| 1082 } | 1082 } |
| 1083 } | 1083 } |
| 1084 if (process_adults) { | 1084 if (process_adults) { |
| 1085 # Calculate adult populations for selected life stage. | 1085 # Calculate adult populations for selected life stage. |
| 1086 for (life_stage_adult in life_stages_adult) { | 1086 for (life_stage_adult in life_stages_adult) { |
| 1087 if (life_stage_adult=="Total") { | 1087 if (life_stage_adult == "Pre-vittelogenic") { |
| 1088 # Mean value for all adults. | |
| 1089 total_adults = apply((Previttelogenic.replications+Vittelogenic.replications+Diapausing.replications), 1, mean); | |
| 1090 temperature_data_frame = append_vector(temperature_data_frame, total_adults, "TOTALADULT"); | |
| 1091 # Standard error for all adults. | |
| 1092 total_adults.std_error = apply((Previttelogenic.replications+Vittelogenic.replications+Diapausing.replications), 1, sd) / sqrt(opt$replications); | |
| 1093 temperature_data_frame = append_vector(temperature_data_frame, total_adults.std_error, "TOTALADULTSE"); | |
| 1094 } else if (life_stage_adult == "Pre-vittelogenic") { | |
| 1095 # Mean value for previttelogenic adults. | 1088 # Mean value for previttelogenic adults. |
| 1096 previttelogenic_adults = apply(Previttelogenic.replications, 1, mean); | 1089 previttelogenic_adults = apply(Previttelogenic.replications, 1, mean); |
| 1097 temperature_data_frame = append_vector(temperature_data_frame, previttelogenic_adults, "PRE-VITADULT"); | 1090 temperature_data_frame = append_vector(temperature_data_frame, previttelogenic_adults, "PRE-VITADULT"); |
| 1098 # Standard error for previttelogenic adults. | 1091 # Standard error for previttelogenic adults. |
| 1099 previttelogenic_adults.std_error = apply(Previttelogenic.replications, 1, sd) / sqrt(opt$replications); | 1092 previttelogenic_adults.std_error = apply(Previttelogenic.replications, 1, sd) / sqrt(opt$replications); |
| 1110 diapausing_adults = apply(Diapausing.replications, 1, mean); | 1103 diapausing_adults = apply(Diapausing.replications, 1, mean); |
| 1111 temperature_data_frame = append_vector(temperature_data_frame, diapausing_adults, "DIAPAUSINGADULT"); | 1104 temperature_data_frame = append_vector(temperature_data_frame, diapausing_adults, "DIAPAUSINGADULT"); |
| 1112 # Standard error for vittelogenic adults. | 1105 # Standard error for vittelogenic adults. |
| 1113 diapausing_adults.std_error = apply(Diapausing.replications, 1, sd) / sqrt(opt$replications); | 1106 diapausing_adults.std_error = apply(Diapausing.replications, 1, sd) / sqrt(opt$replications); |
| 1114 temperature_data_frame = append_vector(temperature_data_frame, diapausing_adults.std_error, "DIAPAUSINGADULTSE"); | 1107 temperature_data_frame = append_vector(temperature_data_frame, diapausing_adults.std_error, "DIAPAUSINGADULTSE"); |
| 1108 } else if (life_stage_adult=="Total") { | |
| 1109 # Mean value for all adults. | |
| 1110 total_adults = apply((Previttelogenic.replications+Vittelogenic.replications+Diapausing.replications), 1, mean); | |
| 1111 temperature_data_frame = append_vector(temperature_data_frame, total_adults, "TOTALADULT"); | |
| 1112 # Standard error for all adults. | |
| 1113 total_adults.std_error = apply((Previttelogenic.replications+Vittelogenic.replications+Diapausing.replications), 1, sd) / sqrt(opt$replications); | |
| 1114 temperature_data_frame = append_vector(temperature_data_frame, total_adults.std_error, "TOTALADULTSE"); | |
| 1115 } | 1115 } |
| 1116 } | 1116 } |
| 1117 } | 1117 } |
| 1118 | 1118 |
| 1119 if (plot_generations_separately) { | 1119 if (plot_generations_separately) { |