comparison insect_phenology_model.R @ 54:5bb1d76c29ca draft

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53:b7c9837047d9

        mortality.probability = temperature * 0.0005 + 0.02;
    }
    return(mortality.probability)
}

mortality.egg = function(temperature) {
    if (temperature < 12.7) {
        mortality.probability = 0.8;
    }
    else {
        mortality.probability = 0.8 - temperature / 40.0;
        if (mortality.probability < 0) {
            mortality.probability = 0.01;
        }
    }
    return(mortality.probability)
}

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

                post.mortality = 2;
                day.kill = 250;
            }
            if (vector.individual[2] == 0) {
                # Egg.
                death.probability = opt$egg_mortality * mortality.egg(mean.temp);
            }
            else if (vector.individual[2] == 1 | vector.individual[2] == 2) {
                # Nymph.
                death.probability = opt$nymph_mortality * mortality.nymph(mean.temp);
            }

54:5bb1d76c29ca

        mortality.probability = temperature * 0.0005 + 0.02;
    }
    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) {

                post.mortality = 2;
                day.kill = 250;
            }
            if (vector.individual[2] == 0) {
                # Egg.
                death.probability = opt$egg_mortality * mortality.egg(mean.temp, adj=opt$egg_mortality);
            }
            else if (vector.individual[2] == 1 | vector.individual[2] == 2) {
                # Nymph.
                death.probability = opt$nymph_mortality * mortality.nymph(mean.temp);
            }