comparison insect_phenology_model.R @ 24:b90f9b781a77 draft

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23:36d7bb034285

    life_stages_adult_str = as.character(opt$life_stages_adult);
    life_stages_adult = strsplit(life_stages_adult_str, ",")[[1]];
    for (life_stage_adult in life_stages_adult) {
        if (life_stage_adult=="Pre-vittelogenic") {
            process_previttelogenic_adults = TRUE;
        } else if (life_stage_adult=="Vitelogenic") {
            process_vittelogenic_adults = TRUE;
        } else if (life_stage_adult=="Diapausing") {
            process_diapausing_adults = TRUE;
        } else if (life_stage_adult=="Total") {
            process_total_adults = TRUE;

}
if (process_previttelogenic_adults | process_total_adults) {
    Previttelogenic.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
}
if (process_vittelogenic_adults | process_total_adults) {
    Vitelogenic.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
}
if (process_diapausing_adults | process_total_adults) {
    Diapausing.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
}
newborn.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);

    }
    if (process_previttelogenic_adults | process_total_adults) {
        Previttelogenic = rep(0, opt$num_days);
    }
    if (process_vittelogenic_adults | process_total_adults) {
        Vitelogenic = rep(0, opt$num_days);
    }
    if (process_diapausing_adults | process_total_adults) {
        Diapausing = rep(0, opt$num_days);
    }
    N.newborn = rep(0, opt$num_days);

            # For pre-vittelogenic population size, column 2 (Stage) must be 3.
            Previttelogenic[row] = sum(vector.matrix[,2]==3);
        }
        if (process_vittelogenic_adults | process_total_adults) {
            # For vittelogenic population size, column 2 (Stage) must be 4.
            Vitelogenic[row] = sum(vector.matrix[,2]==4);
        }
        if (process_diapausing_adults | process_total_adults) {
            # For diapausing population size, column 2 (Stage) must be 5.
            Diapausing[row] = sum(vector.matrix[,2]==5);
        }

                F2.previttelogenic_adult[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==3);
            }
            if (process_vittelogenic_adults) {
                # For vittelogenic adult life stage of generation P population
                # size, the following combination is required:
                # - column 1 (Generation) is 0 and column 2 (Stage) is 4 (Vitelogenic)
                P.vittelogenic_adult[row] = sum(vector.matrix[,1]==0 & vector.matrix[,2]==4);
                # For vittelogenic adult life stage of generation F1 population
                # size, the following combination is required:
                # - column 1 (Generation) is 1 and column 2 (Stage) is 4 (Vitelogenic)
                F1.vittelogenic_adult[row] = sum(vector.matrix[,1]==1 & vector.matrix[,2]==4);
                # For vittelogenic adult life stage of generation F2 population
                # size, the following combination is required:
                # - column 1 (Generation) is 2 and column 2 (Stage) is 4 (Vitelogenic)
                F2.vittelogenic_adult[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==4);
            }
            if (process_diapausing_adults) {
                # For diapausing adult life stage of generation P population
                # size, the following combination is required:

            }
            if (process_total_adults) {
                # For total adult life stage of generation P population
                # size, one of the following combinations is required:
                # - column 1 (Generation) is 0 and column 2 (Stage) is 3 (Pre-vittelogenic)
                # - column 1 (Generation) is 0 and column 2 (Stage) is 4 (Vitelogenic)
                # - column 1 (Generation) is 0 and column 2 (Stage) is 5 (Diapausing)
                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));
                # For total adult life stage of generation F1 population
                # size, one of the following combinations is required:
                # - column 1 (Generation) is 1 and column 2 (Stage) is 3 (Pre-vittelogenic)
                # - column 1 (Generation) is 1 and column 2 (Stage) is 4 (Vitelogenic)
                # - column 1 (Generation) is 1 and column 2 (Stage) is 5 (Diapausing)
                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));
                # For total adult life stage of generation F2 population
                # size, one of the following combinations is required:
                # - column 1 (Generation) is 2 and column 2 (Stage) is 3 (Pre-vittelogenic)
                # - column 1 (Generation) is 2 and column 2 (Stage) is 4 (Vitelogenic)
                # - column 1 (Generation) is 2 and column 2 (Stage) is 5 (Diapausing)
                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));
            }
        }
    }   # End of days specified in the input temperature data.

    }
    if (process_previttelogenic_adults | process_total_adults) {
        Previttelogenic.replications[,current_replication] = Previttelogenic;
    }
    if (process_vittelogenic_adults | process_total_adults) {
        Vitelogenic.replications[,current_replication] = Vitelogenic;
    }
    if (process_diapausing_adults | process_total_adults) {
        Diapausing.replications[,current_replication] = Diapausing;
    }
    newborn.replications[,current_replication] = N.newborn;

if (process_adults) {
    # Calculate adult populations for selected life stage.
    for (life_stage_adult in life_stages_adult) {
        if (life_stage_adult=="Total") {
            # Mean value for all adults.
            total_adults = apply((Previttelogenic.replications+Vitelogenic.replications+Diapausing.replications), 1, mean);
            # Standard error for all adults.
            total_adults.std_error = apply((Previttelogenic.replications+Vitelogenic.replications+Diapausing.replications), 1, sd) / sqrt(opt$replications);
        } else if (life_stage_adult == "Pre-vittelogenic") {
            # Mean value for previttelogenic adults.
            previttelogenic_adults = apply(Previttelogenic.replications, 1, mean);
            # Standard error for previttelogenic adults.
            previttelogenic_adults.std_error = apply(Previttelogenic.replications, 1, sd) / sqrt(opt$replications);
        } else if (life_stage_adult == "Vittelogenic") {
            # Mean value for vittelogenic adults.
            vittelogenic_adults = apply(Vitelogenic.replications, 1, mean);
            # Standard error for vittelogenic adults.
            vittelogenic_adults.std_error = apply(Vitelogenic.replications, 1, sd) / sqrt(opt$replications);
        } else if (life_stage_adult == "Diapausing") {
            # Mean value for vittelogenic adults.
            diapausing_adults = apply(Diapausing.replications, 1, mean);
            # Standard error for vittelogenic adults.
            diapausing_adults.std_error = apply(Diapausing.replications, 1, sd) / sqrt(opt$replications);

24:b90f9b781a77

    life_stages_adult_str = as.character(opt$life_stages_adult);
    life_stages_adult = strsplit(life_stages_adult_str, ",")[[1]];
    for (life_stage_adult in life_stages_adult) {
        if (life_stage_adult=="Pre-vittelogenic") {
            process_previttelogenic_adults = TRUE;
        } else if (life_stage_adult=="Vittelogenic") {
            process_vittelogenic_adults = TRUE;
        } else if (life_stage_adult=="Diapausing") {
            process_diapausing_adults = TRUE;
        } else if (life_stage_adult=="Total") {
            process_total_adults = TRUE;

}
if (process_previttelogenic_adults | process_total_adults) {
    Previttelogenic.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
}
if (process_vittelogenic_adults | process_total_adults) {
    Vittelogenic.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
}
if (process_diapausing_adults | process_total_adults) {
    Diapausing.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);
}
newborn.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);

    }
    if (process_previttelogenic_adults | process_total_adults) {
        Previttelogenic = rep(0, opt$num_days);
    }
    if (process_vittelogenic_adults | process_total_adults) {
        Vittelogenic = rep(0, opt$num_days);
    }
    if (process_diapausing_adults | process_total_adults) {
        Diapausing = rep(0, opt$num_days);
    }
    N.newborn = rep(0, opt$num_days);

            # For pre-vittelogenic population size, column 2 (Stage) must be 3.
            Previttelogenic[row] = sum(vector.matrix[,2]==3);
        }
        if (process_vittelogenic_adults | process_total_adults) {
            # For vittelogenic population size, column 2 (Stage) must be 4.
            Vittelogenic[row] = sum(vector.matrix[,2]==4);
        }
        if (process_diapausing_adults | process_total_adults) {
            # For diapausing population size, column 2 (Stage) must be 5.
            Diapausing[row] = sum(vector.matrix[,2]==5);
        }

                F2.previttelogenic_adult[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==3);
            }
            if (process_vittelogenic_adults) {
                # For vittelogenic adult life stage of generation P population
                # size, the following combination is required:
                # - column 1 (Generation) is 0 and column 2 (Stage) is 4 (Vittelogenic)
                P.vittelogenic_adult[row] = sum(vector.matrix[,1]==0 & vector.matrix[,2]==4);
                # For vittelogenic adult life stage of generation F1 population
                # size, the following combination is required:
                # - column 1 (Generation) is 1 and column 2 (Stage) is 4 (Vittelogenic)
                F1.vittelogenic_adult[row] = sum(vector.matrix[,1]==1 & vector.matrix[,2]==4);
                # For vittelogenic adult life stage of generation F2 population
                # size, the following combination is required:
                # - column 1 (Generation) is 2 and column 2 (Stage) is 4 (Vittelogenic)
                F2.vittelogenic_adult[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==4);
            }
            if (process_diapausing_adults) {
                # For diapausing adult life stage of generation P population
                # size, the following combination is required:

            }
            if (process_total_adults) {
                # For total adult life stage of generation P population
                # size, one of the following combinations is required:
                # - column 1 (Generation) is 0 and column 2 (Stage) is 3 (Pre-vittelogenic)
                # - column 1 (Generation) is 0 and column 2 (Stage) is 4 (Vittelogenic)
                # - column 1 (Generation) is 0 and column 2 (Stage) is 5 (Diapausing)
                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));
                # For total adult life stage of generation F1 population
                # size, one of the following combinations is required:
                # - column 1 (Generation) is 1 and column 2 (Stage) is 3 (Pre-vittelogenic)
                # - column 1 (Generation) is 1 and column 2 (Stage) is 4 (Vittelogenic)
                # - column 1 (Generation) is 1 and column 2 (Stage) is 5 (Diapausing)
                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));
                # For total adult life stage of generation F2 population
                # size, one of the following combinations is required:
                # - column 1 (Generation) is 2 and column 2 (Stage) is 3 (Pre-vittelogenic)
                # - column 1 (Generation) is 2 and column 2 (Stage) is 4 (Vittelogenic)
                # - column 1 (Generation) is 2 and column 2 (Stage) is 5 (Diapausing)
                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));
            }
        }
    }   # End of days specified in the input temperature data.

    }
    if (process_previttelogenic_adults | process_total_adults) {
        Previttelogenic.replications[,current_replication] = Previttelogenic;
    }
    if (process_vittelogenic_adults | process_total_adults) {
        Vittelogenic.replications[,current_replication] = Vittelogenic;
    }
    if (process_diapausing_adults | process_total_adults) {
        Diapausing.replications[,current_replication] = Diapausing;
    }
    newborn.replications[,current_replication] = N.newborn;

if (process_adults) {
    # Calculate adult populations for selected life stage.
    for (life_stage_adult in life_stages_adult) {
        if (life_stage_adult=="Total") {
            # Mean value for all adults.
            total_adults = apply((Previttelogenic.replications+Vittelogenic.replications+Diapausing.replications), 1, mean);
            # Standard error for all adults.
            total_adults.std_error = apply((Previttelogenic.replications+Vittelogenic.replications+Diapausing.replications), 1, sd) / sqrt(opt$replications);
        } else if (life_stage_adult == "Pre-vittelogenic") {
            # Mean value for previttelogenic adults.
            previttelogenic_adults = apply(Previttelogenic.replications, 1, mean);
            # Standard error for previttelogenic adults.
            previttelogenic_adults.std_error = apply(Previttelogenic.replications, 1, sd) / sqrt(opt$replications);
        } else if (life_stage_adult == "Vittelogenic") {
            # Mean value for vittelogenic adults.
            vittelogenic_adults = apply(Vittelogenic.replications, 1, mean);
            # Standard error for vittelogenic adults.
            vittelogenic_adults.std_error = apply(Vittelogenic.replications, 1, sd) / sqrt(opt$replications);
        } else if (life_stage_adult == "Diapausing") {
            # Mean value for vittelogenic adults.
            diapausing_adults = apply(Diapausing.replications, 1, mean);
            # Standard error for vittelogenic adults.
            diapausing_adults.std_error = apply(Diapausing.replications, 1, sd) / sqrt(opt$replications);