Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.R @ 24:b90f9b781a77 draft

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author greg
date Thu, 08 Mar 2018 13:37:50 -0500
parents 36d7bb034285
children 390d89243074
comparison
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23:36d7bb034285 24:b90f9b781a77
397 life_stages_adult_str = as.character(opt$life_stages_adult); 397 life_stages_adult_str = as.character(opt$life_stages_adult);
398 life_stages_adult = strsplit(life_stages_adult_str, ",")[[1]]; 398 life_stages_adult = strsplit(life_stages_adult_str, ",")[[1]];
399 for (life_stage_adult in life_stages_adult) { 399 for (life_stage_adult in life_stages_adult) {
400 if (life_stage_adult=="Pre-vittelogenic") { 400 if (life_stage_adult=="Pre-vittelogenic") {
401 process_previttelogenic_adults = TRUE; 401 process_previttelogenic_adults = TRUE;
402 } else if (life_stage_adult=="Vitelogenic") { 402 } else if (life_stage_adult=="Vittelogenic") {
403 process_vittelogenic_adults = TRUE; 403 process_vittelogenic_adults = TRUE;
404 } else if (life_stage_adult=="Diapausing") { 404 } else if (life_stage_adult=="Diapausing") {
405 process_diapausing_adults = TRUE; 405 process_diapausing_adults = TRUE;
406 } else if (life_stage_adult=="Total") { 406 } else if (life_stage_adult=="Total") {
407 process_total_adults = TRUE; 407 process_total_adults = TRUE;
420 } 420 }
421 if (process_previttelogenic_adults | process_total_adults) { 421 if (process_previttelogenic_adults | process_total_adults) {
422 Previttelogenic.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); 422 Previttelogenic.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
423 } 423 }
424 if (process_vittelogenic_adults | process_total_adults) { 424 if (process_vittelogenic_adults | process_total_adults) {
425 Vitelogenic.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); 425 Vittelogenic.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
426 } 426 }
427 if (process_diapausing_adults | process_total_adults) { 427 if (process_diapausing_adults | process_total_adults) {
428 Diapausing.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); 428 Diapausing.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
429 } 429 }
430 newborn.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); 430 newborn.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
506 } 506 }
507 if (process_previttelogenic_adults | process_total_adults) { 507 if (process_previttelogenic_adults | process_total_adults) {
508 Previttelogenic = rep(0, opt$num_days); 508 Previttelogenic = rep(0, opt$num_days);
509 } 509 }
510 if (process_vittelogenic_adults | process_total_adults) { 510 if (process_vittelogenic_adults | process_total_adults) {
511 Vitelogenic = rep(0, opt$num_days); 511 Vittelogenic = rep(0, opt$num_days);
512 } 512 }
513 if (process_diapausing_adults | process_total_adults) { 513 if (process_diapausing_adults | process_total_adults) {
514 Diapausing = rep(0, opt$num_days); 514 Diapausing = rep(0, opt$num_days);
515 } 515 }
516 N.newborn = rep(0, opt$num_days); 516 N.newborn = rep(0, opt$num_days);
812 # For pre-vittelogenic population size, column 2 (Stage) must be 3. 812 # For pre-vittelogenic population size, column 2 (Stage) must be 3.
813 Previttelogenic[row] = sum(vector.matrix[,2]==3); 813 Previttelogenic[row] = sum(vector.matrix[,2]==3);
814 } 814 }
815 if (process_vittelogenic_adults | process_total_adults) { 815 if (process_vittelogenic_adults | process_total_adults) {
816 # For vittelogenic population size, column 2 (Stage) must be 4. 816 # For vittelogenic population size, column 2 (Stage) must be 4.
817 Vitelogenic[row] = sum(vector.matrix[,2]==4); 817 Vittelogenic[row] = sum(vector.matrix[,2]==4);
818 } 818 }
819 if (process_diapausing_adults | process_total_adults) { 819 if (process_diapausing_adults | process_total_adults) {
820 # For diapausing population size, column 2 (Stage) must be 5. 820 # For diapausing population size, column 2 (Stage) must be 5.
821 Diapausing[row] = sum(vector.matrix[,2]==5); 821 Diapausing[row] = sum(vector.matrix[,2]==5);
822 } 822 }
912 F2.previttelogenic_adult[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==3); 912 F2.previttelogenic_adult[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==3);
913 } 913 }
914 if (process_vittelogenic_adults) { 914 if (process_vittelogenic_adults) {
915 # For vittelogenic adult life stage of generation P population 915 # For vittelogenic adult life stage of generation P population
916 # size, the following combination is required: 916 # size, the following combination is required:
917 # - column 1 (Generation) is 0 and column 2 (Stage) is 4 (Vitelogenic) 917 # - column 1 (Generation) is 0 and column 2 (Stage) is 4 (Vittelogenic)
918 P.vittelogenic_adult[row] = sum(vector.matrix[,1]==0 & vector.matrix[,2]==4); 918 P.vittelogenic_adult[row] = sum(vector.matrix[,1]==0 & vector.matrix[,2]==4);
919 # For vittelogenic adult life stage of generation F1 population 919 # For vittelogenic adult life stage of generation F1 population
920 # size, the following combination is required: 920 # size, the following combination is required:
921 # - column 1 (Generation) is 1 and column 2 (Stage) is 4 (Vitelogenic) 921 # - column 1 (Generation) is 1 and column 2 (Stage) is 4 (Vittelogenic)
922 F1.vittelogenic_adult[row] = sum(vector.matrix[,1]==1 & vector.matrix[,2]==4); 922 F1.vittelogenic_adult[row] = sum(vector.matrix[,1]==1 & vector.matrix[,2]==4);
923 # For vittelogenic adult life stage of generation F2 population 923 # For vittelogenic adult life stage of generation F2 population
924 # size, the following combination is required: 924 # size, the following combination is required:
925 # - column 1 (Generation) is 2 and column 2 (Stage) is 4 (Vitelogenic) 925 # - column 1 (Generation) is 2 and column 2 (Stage) is 4 (Vittelogenic)
926 F2.vittelogenic_adult[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==4); 926 F2.vittelogenic_adult[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==4);
927 } 927 }
928 if (process_diapausing_adults) { 928 if (process_diapausing_adults) {
929 # For diapausing adult life stage of generation P population 929 # For diapausing adult life stage of generation P population
930 # size, the following combination is required: 930 # size, the following combination is required:
941 } 941 }
942 if (process_total_adults) { 942 if (process_total_adults) {
943 # For total adult life stage of generation P population 943 # For total adult life stage of generation P population
944 # size, one of the following combinations is required: 944 # size, one of the following combinations is required:
945 # - column 1 (Generation) is 0 and column 2 (Stage) is 3 (Pre-vittelogenic) 945 # - column 1 (Generation) is 0 and column 2 (Stage) is 3 (Pre-vittelogenic)
946 # - column 1 (Generation) is 0 and column 2 (Stage) is 4 (Vitelogenic) 946 # - column 1 (Generation) is 0 and column 2 (Stage) is 4 (Vittelogenic)
947 # - column 1 (Generation) is 0 and column 2 (Stage) is 5 (Diapausing) 947 # - column 1 (Generation) is 0 and column 2 (Stage) is 5 (Diapausing)
948 P.total_adult[row] = sum((vector.matrix[,1]==0 & vector.matrix[,2]==3) | (vector.matrix[,1]==0 & vector.matrix[,2]==4) | (vector.matrix[,1]==0 & vector.matrix[,2]==5)); 948 P.total_adult[row] = sum((vector.matrix[,1]==0 & vector.matrix[,2]==3) | (vector.matrix[,1]==0 & vector.matrix[,2]==4) | (vector.matrix[,1]==0 & vector.matrix[,2]==5));
949 # For total adult life stage of generation F1 population 949 # For total adult life stage of generation F1 population
950 # size, one of the following combinations is required: 950 # size, one of the following combinations is required:
951 # - column 1 (Generation) is 1 and column 2 (Stage) is 3 (Pre-vittelogenic) 951 # - column 1 (Generation) is 1 and column 2 (Stage) is 3 (Pre-vittelogenic)
952 # - column 1 (Generation) is 1 and column 2 (Stage) is 4 (Vitelogenic) 952 # - column 1 (Generation) is 1 and column 2 (Stage) is 4 (Vittelogenic)
953 # - column 1 (Generation) is 1 and column 2 (Stage) is 5 (Diapausing) 953 # - column 1 (Generation) is 1 and column 2 (Stage) is 5 (Diapausing)
954 F1.total_adult[row] = sum((vector.matrix[,1]==1 & vector.matrix[,2]==3) | (vector.matrix[,1]==1 & vector.matrix[,2]==4) | (vector.matrix[,1]==1 & vector.matrix[,2]==5)); 954 F1.total_adult[row] = sum((vector.matrix[,1]==1 & vector.matrix[,2]==3) | (vector.matrix[,1]==1 & vector.matrix[,2]==4) | (vector.matrix[,1]==1 & vector.matrix[,2]==5));
955 # For total adult life stage of generation F2 population 955 # For total adult life stage of generation F2 population
956 # size, one of the following combinations is required: 956 # size, one of the following combinations is required:
957 # - column 1 (Generation) is 2 and column 2 (Stage) is 3 (Pre-vittelogenic) 957 # - column 1 (Generation) is 2 and column 2 (Stage) is 3 (Pre-vittelogenic)
958 # - column 1 (Generation) is 2 and column 2 (Stage) is 4 (Vitelogenic) 958 # - column 1 (Generation) is 2 and column 2 (Stage) is 4 (Vittelogenic)
959 # - column 1 (Generation) is 2 and column 2 (Stage) is 5 (Diapausing) 959 # - column 1 (Generation) is 2 and column 2 (Stage) is 5 (Diapausing)
960 F2.total_adult[row] = sum((vector.matrix[,1]==2 & vector.matrix[,2]==3) | (vector.matrix[,1]==2 & vector.matrix[,2]==4) | (vector.matrix[,1]==2 & vector.matrix[,2]==5)); 960 F2.total_adult[row] = sum((vector.matrix[,1]==2 & vector.matrix[,2]==3) | (vector.matrix[,1]==2 & vector.matrix[,2]==4) | (vector.matrix[,1]==2 & vector.matrix[,2]==5));
961 } 961 }
962 } 962 }
963 } # End of days specified in the input temperature data. 963 } # End of days specified in the input temperature data.
976 } 976 }
977 if (process_previttelogenic_adults | process_total_adults) { 977 if (process_previttelogenic_adults | process_total_adults) {
978 Previttelogenic.replications[,current_replication] = Previttelogenic; 978 Previttelogenic.replications[,current_replication] = Previttelogenic;
979 } 979 }
980 if (process_vittelogenic_adults | process_total_adults) { 980 if (process_vittelogenic_adults | process_total_adults) {
981 Vitelogenic.replications[,current_replication] = Vitelogenic; 981 Vittelogenic.replications[,current_replication] = Vittelogenic;
982 } 982 }
983 if (process_diapausing_adults | process_total_adults) { 983 if (process_diapausing_adults | process_total_adults) {
984 Diapausing.replications[,current_replication] = Diapausing; 984 Diapausing.replications[,current_replication] = Diapausing;
985 } 985 }
986 newborn.replications[,current_replication] = N.newborn; 986 newborn.replications[,current_replication] = N.newborn;
1068 if (process_adults) { 1068 if (process_adults) {
1069 # Calculate adult populations for selected life stage. 1069 # Calculate adult populations for selected life stage.
1070 for (life_stage_adult in life_stages_adult) { 1070 for (life_stage_adult in life_stages_adult) {
1071 if (life_stage_adult=="Total") { 1071 if (life_stage_adult=="Total") {
1072 # Mean value for all adults. 1072 # Mean value for all adults.
1073 total_adults = apply((Previttelogenic.replications+Vitelogenic.replications+Diapausing.replications), 1, mean); 1073 total_adults = apply((Previttelogenic.replications+Vittelogenic.replications+Diapausing.replications), 1, mean);
1074 # Standard error for all adults. 1074 # Standard error for all adults.
1075 total_adults.std_error = apply((Previttelogenic.replications+Vitelogenic.replications+Diapausing.replications), 1, sd) / sqrt(opt$replications); 1075 total_adults.std_error = apply((Previttelogenic.replications+Vittelogenic.replications+Diapausing.replications), 1, sd) / sqrt(opt$replications);
1076 } else if (life_stage_adult == "Pre-vittelogenic") { 1076 } else if (life_stage_adult == "Pre-vittelogenic") {
1077 # Mean value for previttelogenic adults. 1077 # Mean value for previttelogenic adults.
1078 previttelogenic_adults = apply(Previttelogenic.replications, 1, mean); 1078 previttelogenic_adults = apply(Previttelogenic.replications, 1, mean);
1079 # Standard error for previttelogenic adults. 1079 # Standard error for previttelogenic adults.
1080 previttelogenic_adults.std_error = apply(Previttelogenic.replications, 1, sd) / sqrt(opt$replications); 1080 previttelogenic_adults.std_error = apply(Previttelogenic.replications, 1, sd) / sqrt(opt$replications);
1081 } else if (life_stage_adult == "Vittelogenic") { 1081 } else if (life_stage_adult == "Vittelogenic") {
1082 # Mean value for vittelogenic adults. 1082 # Mean value for vittelogenic adults.
1083 vittelogenic_adults = apply(Vitelogenic.replications, 1, mean); 1083 vittelogenic_adults = apply(Vittelogenic.replications, 1, mean);
1084 # Standard error for vittelogenic adults. 1084 # Standard error for vittelogenic adults.
1085 vittelogenic_adults.std_error = apply(Vitelogenic.replications, 1, sd) / sqrt(opt$replications); 1085 vittelogenic_adults.std_error = apply(Vittelogenic.replications, 1, sd) / sqrt(opt$replications);
1086 } else if (life_stage_adult == "Diapausing") { 1086 } else if (life_stage_adult == "Diapausing") {
1087 # Mean value for vittelogenic adults. 1087 # Mean value for vittelogenic adults.
1088 diapausing_adults = apply(Diapausing.replications, 1, mean); 1088 diapausing_adults = apply(Diapausing.replications, 1, mean);
1089 # Standard error for vittelogenic adults. 1089 # Standard error for vittelogenic adults.
1090 diapausing_adults.std_error = apply(Diapausing.replications, 1, sd) / sqrt(opt$replications); 1090 diapausing_adults.std_error = apply(Diapausing.replications, 1, sd) / sqrt(opt$replications);