@sjcrh/proteinpaint-shared 2.145.1-0 → 2.146.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/package.json +1 -1
- package/src/compute.percentile.js +3 -2
- package/src/index.js +0 -1
- package/src/descriptive.stats.js +0 -95
package/package.json
CHANGED
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@@ -1,7 +1,8 @@
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// compute the percentile value from an array of values
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// sorted parameter allows to skip sorting if array is pre-sorted
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// source: https://www.dummies.com/article/academics-the-arts/math/statistics/how-to-calculate-percentiles-in-statistics-169783/
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export default function computePercentile(values, percentile) {
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values.sort((a, b) => a - b)
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export default function computePercentile(values, percentile, sorted = false) {
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if (!sorted) values.sort((a, b) => a - b)
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const index = Math.abs((percentile / 100) * values.length - 1)
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const value = Number.isInteger(index) ? (values[index] + values[index + 1]) / 2 : values[Math.ceil(index)]
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return value
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package/src/index.js
CHANGED
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@@ -3,7 +3,6 @@ export * from './bulk.js'
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export * from './clustering.js'
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export * from './common.js'
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export * from './compute.percentile.js'
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export * from './descriptive.stats.js'
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export * from './fetch-helpers.js'
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export * from './fileSize.js'
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export * from './filter.js'
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package/src/descriptive.stats.js
DELETED
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@@ -1,95 +0,0 @@
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import { roundValueAuto } from './roundValue.js'
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/* This file generates summary statistics on any given array of numbers*/
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export function getDescriptiveStats(array) {
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//console.log("array:",array)
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let arr = array
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if (typeof array[0] == 'string') {
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// somehow the values can be string but not numbers
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// must cast to numbers to properly compute values
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arr = array.map(Number)
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}
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//compute total
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const sorted_arr = arr.sort((a, b) => a - b)
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const n = arr.length
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//compute median
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const median = computePercentile(sorted_arr, 50)
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//compute mean
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const mean = getMean(arr)
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// compute variance
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const variance = getVariance(sorted_arr)
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// compute standard deviation
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const stdDev = Math.sqrt(variance)
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//compute percentile ranges
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const p25 = computePercentile(sorted_arr, 25)
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const p75 = computePercentile(sorted_arr, 75)
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//compute IQR
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const IQR = p75 - p25
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const min = sorted_arr[0]
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const max = sorted_arr[sorted_arr.length - 1]
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// Calculate fences
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const lowerFence = p25 - 1.5 * IQR //p25 is same as q1
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const upperFence = p75 + 1.5 * IQR //p75 is same as q3
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// Identify outliers
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const outlierRange = { min: lowerFence, max: upperFence }
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return {
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total: n,
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min,
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max,
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p25,
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p75,
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median,
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mean,
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variance,
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stdDev,
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IQR,
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outlierRange
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}
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}
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export function summaryStats(array) {
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const stats = getDescriptiveStats(array)
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return {
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values: [
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{ id: 'total', label: 'Total', value: stats.total },
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{ id: 'min', label: 'Minimum', value: roundValueAuto(stats.min, true) },
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{ id: 'p25', label: '1st quartile', value: roundValueAuto(stats.p25, true) },
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{ id: 'median', label: 'Median', value: roundValueAuto(stats.median, true) },
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{ id: 'mean', label: 'Mean', value: roundValueAuto(stats.mean, true) },
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{ id: 'p75', label: '3rd quartile', value: roundValueAuto(stats.p75, true) },
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{ id: 'max', label: 'Maximum', value: roundValueAuto(stats.max, true) },
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{ id: 'SD', label: 'Standard deviation', value: roundValueAuto(stats.stdDev, true) },
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{ id: 'variance', label: 'Variance', value: roundValueAuto(stats.variance, true) },
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{ id: 'IQR', label: 'Inter-quartile range', value: roundValueAuto(stats.IQR, true) }
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]
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}
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}
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function computePercentile(values, percentile) {
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const index = Math.abs((percentile / 100) * values.length - 1)
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const value = Number.isInteger(index) ? (values[index] + values[index + 1]) / 2 : values[Math.ceil(index)]
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return value
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}
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export function getMean(data) {
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return data.reduce((sum, value) => sum + value, 0) / data.length
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}
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export function getVariance(data) {
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const meanValue = getMean(data)
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const squaredDifferences = data.map(value => Math.pow(value - meanValue, 2))
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return squaredDifferences.reduce((sum, value) => sum + value, 0) / data.length
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}
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export function getStdDev(data) {
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const variance = getVariance(data)
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return Math.sqrt(variance)
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}
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