calculatorD.js

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//////////////////////////////// CALCULATOR D /////////////////////////////////
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// calculator type D inputs
var calculatorTypeDInputs = {
    population:1,
    surveillanceScale:'National',
    confidenceLevel1:95,
    fluSampleSize2:1,
    detectionThreshold3:5,
    confidenceInterval3:80,
    falseNegativeTolerance3:10,
    falsePositiveTolerance3:25,
    fluSampleSize4:1,
    detectionThreshold4:5,
    confidenceInterval4:80,
};

// tooltip text
var tooltipTypeDTotalPopulation = "This is the total population size under surveillance. For labs representing entire states, simply select the name of the state. This will automatically provide the 2012 census projection of the state population. For labs collecting specimens from subsets of state populations or populations that cross multiple states, choose 'Other' and enter the estimated size of the entire population under consideration.";
var tooltipTypeDConfidenceLevel = "The desired confidence that the sample will contain at least one AVR+ when the prevalence of an antiviral resistant influenza reaches the specified limit of detection. For example, if the PHL choose a confidence level of 95% and a detection threshold of 1/700, then the resulting minimum sample size should be sufficient to detect an antiviral resistant influenza when it reaches a prevalence of 1/700 AVR+/Flu+, 95% of the time. Intuitively, a high confidence level and a low detection threshold requires many samples, while low confidence and a high detection threshold results in fewer samples.";
var tooltipTypeDDetectionThreshold = "The detection threshold for an antiviral resistant influenza is the prevalence of the antiviral resistant influenza (out of all Flu+ cases) at which the first antiviral resistant influenza specimens are expected to appear in the lab. For example, a detection threshold of 1/700 means that antiviral resistant influenza should be detected by the lab when it rises to a prevalence of one out of every 700 cases of influenza.";
var tooltipTypeDMinimumFluSampleSize = "The minimum number of Flu+ specimens required to detect an antiviral resistant influenza when its prevalence (AVR+/Flu+) reaches the specified detection threshold, with the specified level of confidence.";
var tooltipTypeDFluSampleSize = "The number of Flu+ specimens to be tested.";
var tooltipTypeDSurveillanceScale = "This is the scale of the surveillance effort. The default is national, meaning that all states are contributing to a national surveillance effort proportional to their population size.  The number of samples that a state PHL needs to test is apportioned based on population size. The calculator also provides the option for states to calculate the number of specimens to test for detection of an antiviral resistant influenza event at a specific threshold within their state; however, the sample size for an individual state at the same threshold (e.g. 1/500 or 1/700) will be significantly larger than that needed for the national threshold.";

// type D2 tooltips, for investigation:
var tooltipTypeD2FluSampleSize = "Flu+ sample size tooltip";
var tooltipTypeD2DetectionThreshold = "detection threshold tooltip";
var tooltipTypeD2ConfidenceInterval = "confidence interval tooltip";
var tooltipTypeD2FalseNegativeTolerance = "false negative tolerance tooltip";
var tooltipTypeD2FalsePositiveTolerance = "false positive tolerance tooltip";

// active tab index
var calculatorTypeDActiveTabIndex = 0;

function evaluateTypeD_FluSampleSize_vs_detectionThreshold(detectionThreshold)
{
    // this object contains parameter values

    var sampleSize = Math.log(1. - this.confidenceLevel/100.) / Math.log(1. - detectionThreshold/100.);

    if(this.surveillanceScale == "State")
    {
        // finite population correction
        sampleSize = sampleSize * Math.sqrt((this.population - sampleSize) / (this.population - 1.));
    }

    if(this.surveillanceScale == "National")
    {
        sampleSize = sampleSize * this.population / nationalPopulation;
    }

    return Math.ceil(sampleSize);
}

// draw chart and table given labels, x series, y series
function drawTypeDTab1()
{
    var labels = ['Detection Threshold (AVR+/Flu+)', 'Minimum Flu+ Sample Size'];
    var x = [];
    var xChartLabelMap = {};
    var xTableLabelMap = {};
    var y;

    // range: detection threshhold (increments of 0.1)
    var min = 0.1;
    var max = 5;
    var numValues = 50;

    for(var i=0; i<numValues; i++)
    {
        // round to the nearest 100th
        var value = Math.round((min + i/(numValues-1)*(max-min)) * 100) / 100;

        // we need the 1/165 case
        if(value == 0.6)
        {
            value = 0.606;
        }

        x.push(value);

        // labels
        xChartLabelMap[value] = "Detection Threshhold: " + value + "% (1/" + Math.round(100. / value) + ")";
        xTableLabelMap[value] = value + "% (1/" + Math.round(100. / value) + ")";

        if(value == 0.1)
        {
            // also get other special cases...
            // the label code is identical to above
            value = 0.1429;
            x.push(value);
            xChartLabelMap[value] = "Detection Threshhold: " + value + "% (1/" + Math.round(100. / value) + ")";
            xTableLabelMap[value] = value + "% (1/" + Math.round(100. / value) + ")";

            value = 0.1667;
            x.push(value);
            xChartLabelMap[value] = "Detection Threshhold: " + value + "% (1/" + Math.round(100. / value) + ")";
            xTableLabelMap[value] = value + "% (1/" + Math.round(100. / value) + ")";
        }
    }

    // use a parameters object to pass in any other input parameters to the evaluation function
    var parameters = new Object();
    parameters.population = calculatorTypeDInputs.population;
    parameters.surveillanceScale = calculatorTypeDInputs.surveillanceScale;
    parameters.confidenceLevel = calculatorTypeDInputs.confidenceLevel1;

    // evaluation for each x
    y = x.map(evaluateTypeD_FluSampleSize_vs_detectionThreshold, parameters);

    // separate DataTable objects for chart / table to allow for formatting
    var dataChart = arraysToDataTable(labels, [x, y]);
    var dataTable = dataChart.clone();

    // chart: use xChartLabelMap as the x label
    var formatterChart = new labelFormatter(xChartLabelMap);
    formatterChart.format(dataChart, 0);

    // table: use xTableLabelMap as the x label
    var formatterChart = new labelFormatter(xTableLabelMap);
    formatterChart.format(dataTable, 0);

    var optionsChart = {
        title: '',
        hAxis : { title: labels[0], format: "#.##'%'" },
        vAxis : { title: labels[1] },
        legend : { position: 'none' },
        fontSize : chartFontSize
    };

    // need to specify width here (rather than in CSS) for IE
    var optionsTable = {
        width: '225px'
    };

    $("#calculatorD1_chart_table_description_div").html("<span class='calculatorTooltip' title='" + tooltipTypeDMinimumFluSampleSize + "'>Minimum sample size (of Flu+ specimens)</span> required to detect an antiviral resistant (AVR+) influenza at a specified <span class='calculatorTooltip' title='" + tooltipTypeDDetectionThreshold + "'>detection threshold (AVR+/Flu+)</span>, with a confidence of " + formatTextParameter(parameters.confidenceLevel + "%") + ". These calculations assume a total population of " + formatTextParameter(numberWithCommas(parameters.population)) + ". Use the mouse to view values in the sample size graph and scroll through sample size table.");

    var chart = new google.visualization.LineChart(document.getElementById('calculatorD1_chart_div'));
    chart.draw(dataChart, optionsChart);

    var table = new google.visualization.Table(document.getElementById('calculatorD1_table_div'));
    table.draw(dataTable, optionsTable);

    // selection handling
    var thisObj = drawTypeDTab1;

    google.visualization.events.addListener(chart, 'select', chartSelectHandler);
    google.visualization.events.addListener(table, 'select', tableSelectHandler);

    function chartSelectHandler(e) { thisObj.selectHandler(chart.getSelection()); }
    function tableSelectHandler(e) { thisObj.selectHandler(table.getSelection()); }

    thisObj.selectHandler = function(selectionArray)
    {
        if(selectionArray.length > 0 && selectionArray[0].row != null)
        {
            thisObj.selectedRow = selectionArray[0].row;

            // make sure row is valid
            if(thisObj.selectedRow >= x.length)
            {
                thisObj.selectedRow = 0;
            }

            // form new array with only this entry (to avoid multiple selections)
            var newSelectionArray = [{row:selectionArray[0].row}];

            // select element in chart and table
            chart.setSelection(newSelectionArray);
            table.setSelection(newSelectionArray);

            var noteText = "Note: Historical PHL data suggest that a 1/700 AVR+/Flu+ threshold is appropriate during the peak of the season, a 1/55 threshold during moderate periods of influenza activity, and 1/3.5 during out-of-season (summer) months to achieve detection with 85-95% confidence.";

            if(parameters.surveillanceScale == "National")
            {
                $("#calculatorD1_chart_table_report_div").html("To be " + formatTextParameter(parameters.confidenceLevel + "%") + " confident of detecting 1 or more antiviral resistant influenza events at a prevalence of " + formatTextParameter(xTableLabelMap[x[thisObj.selectedRow]]) + " at a national level, the PHL must test " + formatTextParameter(numberWithCommas(y[thisObj.selectedRow])) + " Flu+ specimens." + "<p>" + noteText + "</p>");
            }
            else
            {
                $("#calculatorD1_chart_table_report_div").html("To be " + formatTextParameter(parameters.confidenceLevel + "%") + " confident of detecting 1 or more antiviral resistant influenza events at a prevalence of " + formatTextParameter(xTableLabelMap[x[thisObj.selectedRow]]) + " (within the population under surveillance), the PHL must test " + formatTextParameter(numberWithCommas(y[thisObj.selectedRow])) + " Flu+ specimens." + "<p>" + noteText + "</p>");
            }
        }
    }

    thisObj.selectHandler([{row:thisObj.selectedRow ? thisObj.selectedRow : 0}]);
}

function calculatorTypeDInitialize()
{
    // initialize UI elements and events

    // tooltips
    $(".tooltipTypeDTotalPopulation").attr("title", tooltipTypeDTotalPopulation);
    $(".tooltipTypeDConfidenceLevel").attr("title", tooltipTypeDConfidenceLevel);
    $(".tooltipTypeDDetectionThreshold").attr("title", tooltipTypeDDetectionThreshold);
    $(".tooltipTypeDMinimumFluSampleSize").attr("title", tooltipTypeDMinimumFluSampleSize);
    $(".tooltipTypeDFluSampleSize").attr("title", tooltipTypeDFluSampleSize);
    $(".tooltipTypeDSurveillanceScale").attr("title", tooltipTypeDSurveillanceScale);

    $(".tooltipTypeD2FluSampleSize").attr("title", tooltipTypeD2FluSampleSize);
    $(".tooltipTypeD2DetectionThreshold").attr("title", tooltipTypeD2DetectionThreshold);
    $(".tooltipTypeD2ConfidenceInterval").attr("title", tooltipTypeD2ConfidenceInterval);
    $(".tooltipTypeD2FalseNegativeTolerance").attr("title", tooltipTypeD2FalseNegativeTolerance);
    $(".tooltipTypeD2FalsePositiveTolerance").attr("title", tooltipTypeD2FalsePositiveTolerance);

    // population options
    var populationOptions = $("#calculatorD_select_population");

    $.each(statePopulations, function(key, value) {
        populationOptions.append($("<option />").val(key).text(key));
    });

    populationOptions.append($("<option />").val("Other").text("Other"));

    // population selection
    $("#calculatorD_select_population, #calculatorD_input_population").bind('keyup mouseup change', function(e) {
        // selected state and population for that state
        var state = $("#calculatorD_select_population :selected").val();
        var population = 0;

        if(state == "Other")
        {
            // hide number label and show number input
            $("#calculatorD_select_population_number_label").hide();
            $("#calculatorD_input_population").show();

            population = $("#calculatorD_input_population").val();
        }
        else
        {
            // show number label and hide number input
            $("#calculatorD_select_population_number_label").show();
            $("#calculatorD_input_population").hide();

            population = statePopulations[state];

            // update the number label
            $("#calculatorD_select_population_number_label").html(numberWithCommas(population));
        }

        // save the value
        calculatorTypeDInputs.population = population;

        // update the surveillane scale "state" option text
        $("#calculatorD_select_surveillance_scale option:last-child").text($("#calculatorD_select_population :selected").val());

        // refresh
        calculatorTypeDRefresh();
    });

    // force an initial update event (since we have no current value for population)
    $("#calculatorD_select_population").change();

    // surveillance scale selection
    $("#calculatorD_select_surveillance_scale").bind('keyup mouseup change', function(e) {
        // make sure we have a valid value
        var value = $("#calculatorD_select_surveillance_scale :selected").val();

        if(value != "National" && value != "State")
        {
            alert("invalid surveillance scale value");
            return;
        }

        // save the value
        calculatorTypeDInputs.surveillanceScale = value;

        // refresh
        calculatorTypeDRefresh();
    });

    // force an initial update event (since we have no current value for population)
    $("#calculatorD_select_surveillance_scale").change();

    // tab 1: confidence level slider
    $("#calculatorD1_input_confidence_level_slider").slider({
        value:calculatorTypeDInputs.confidenceLevel1,
        min: 80,
        max: 99,
        step: 1,
        slide: function(event, ui) {
            $("#calculatorD1_input_confidence_level").val(ui.value + "%");
            calculatorTypeDInputs.confidenceLevel1 = parseFloat($("#calculatorD1_input_confidence_level").val());
            calculatorTypeDRefresh();
        }
    });

    $("#calculatorD1_input_confidence_level").val($("#calculatorD1_input_confidence_level_slider").slider("value") + "%");
}

function calculatorTypeDRefresh()
{
    if(calculatorTypeDActiveTabIndex == 0)
    {
        drawTypeDTab1();
    }
    else
    {
        alert("error, unknown tab index " + calculatorTypeDActiveTabIndex);
    }
}