comparison insect_phenology_model.R @ 63:c5df0777fa31 draft

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62:3116ddd4c26d

    }
    return(mortality.probability)
}

mortality.egg = function(temperature, adj=0) {
    if (adj == 0) {
        # If no input from adjustment, default
        # value is 0 (data from Nielsen, 2008).
        T.mortality = c(15, 17, 20, 25, 27, 30, 33, 35);
        egg.mortality = c(50, 2, 1, 0, 0, 0, 5, 100);
        # Calculates slopes and intercepts for lines.
        slopes = NULL;
        intercepts = NULL;
        for (i in 1:length(T.mortality)) {
            slopes[i] = (egg.mortality[i+1] - egg.mortality[i]) / (T.mortality[i+1] - T.mortality[i]);
            intercepts[i] = -slopes[i] * T.mortality[i] + egg.mortality[i];
        }
        # Calculates mortality based on temperature.
        mortality.probability = NULL;
        for (j in 1:length(temperature)) {
            mortality.probability[j] = if(temperature[j] <= T.mortality[2]) {
                                           temperature[j] * slopes[1] + intercepts[1];
                                       } else if (temperature[j] > T.mortality[2] && temperature[j] <= T.mortality[3]) {
                                           temperature[j] * slopes[2] + intercepts[2];
                                       } else if (temperature[j] > T.mortality[3] && temperature[j] <= T.mortality[4]) {
                                           temperature[j] * slopes[3] + intercepts[3];
                                       } else if (temperature[j] > T.mortality[4] && temperature[j] <= T.mortality[5]) {
                                           temperature[j] * slopes[4] + intercepts[4];
                                       } else if (temperature[j] > T.mortality[5] && temperature[j] <= T.mortality[6]) {
                                           temperature[j] * slopes[5] + intercepts[5];
                                       } else if (temperature[j] > T.mortality[6] && temperature[j] <= T.mortality[7]) {
                                           temperature[j] * slopes[6] + intercepts[6];
                                       } else if (temperature[j] > T.mortality[7]) {
                                           temperature[j] * slopes[7] + intercepts[7];
                                       }
            # If mortality > 100, make it equal to 100.
            mortality.probability[mortality.probability>100] = 100;
            # If mortality <0, make equal to 0.
            mortality.probability[mortality.probability<0] = 0;
        }
    } else {
        # Make mortality adjustments based on adj parameter.
        mortality.probability = (100 - mortality.probability) * adj + mortality.probability;
        # if mortality > 100, make it equal to 100.
        mortality.probability[mortality.probability>100] = 100;
        # If mortality <0, make equal to 0.
        mortality.probability[mortality.probability<0] = 0;
        # Change percent to proportion.
        mortality.probability = mortality.probability / 100;
    }
    return(mortality.probability)
}

mortality.nymph = function(temperature) {
    if (temperature < 12.7) {

63:c5df0777fa31

    }
    return(mortality.probability)
}

mortality.egg = function(temperature, adj=0) {
    # If no input from adjustment, default
    # value is 0 (data from Nielsen, 2008).
    T.mortality = c(15, 17, 20, 25, 27, 30, 33, 35);
    egg.mortality = c(50, 2, 1, 0, 0, 0, 5, 100);
    # Calculates slopes and intercepts for lines.
    slopes = NULL;
    intercepts = NULL;
    for (i in 1:length(T.mortality)) {
        slopes[i] = (egg.mortality[i+1] - egg.mortality[i]) / (T.mortality[i+1] - T.mortality[i]);
        intercepts[i] = -slopes[i] * T.mortality[i] + egg.mortality[i];
    }
    # Calculates mortality based on temperature.
    mortality.probability = NULL;
    for (j in 1:length(temperature)) {
        mortality.probability[j] = if(temperature[j] <= T.mortality[2]) {
                                       temperature[j] * slopes[1] + intercepts[1];
                                   } else if (temperature[j] > T.mortality[2] && temperature[j] <= T.mortality[3]) {
                                       temperature[j] * slopes[2] + intercepts[2];
                                   } else if (temperature[j] > T.mortality[3] && temperature[j] <= T.mortality[4]) {
                                       temperature[j] * slopes[3] + intercepts[3];
                                   } else if (temperature[j] > T.mortality[4] && temperature[j] <= T.mortality[5]) {
                                       temperature[j] * slopes[4] + intercepts[4];
                                   } else if (temperature[j] > T.mortality[5] && temperature[j] <= T.mortality[6]) {
                                       temperature[j] * slopes[5] + intercepts[5];
                                   } else if (temperature[j] > T.mortality[6] && temperature[j] <= T.mortality[7]) {
                                       temperature[j] * slopes[6] + intercepts[6];
                                   } else if (temperature[j] > T.mortality[7]) {
                                       temperature[j] * slopes[7] + intercepts[7];
                                   }
        # If mortality > 100, make it equal to 100.
        mortality.probability[mortality.probability>100] = 100;
        # If mortality <0, make equal to 0.
        mortality.probability[mortality.probability<0] = 0;
    }
    # Make mortality adjustments based on adj parameter.
    mortality.probability = (100 - mortality.probability) * adj + mortality.probability;
    # if mortality > 100, make it equal to 100.
    mortality.probability[mortality.probability>100] = 100;
    # If mortality <0, make equal to 0.
    mortality.probability[mortality.probability<0] = 0;
    # Change percent to proportion.
    mortality.probability = mortality.probability / 100;
}
    return(mortality.probability)
}

mortality.nymph = function(temperature) {
    if (temperature < 12.7) {