@sjcrh/proteinpaint-shared 2.145.2 → 2.146.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-shared",
-  "version": "2.145.2",
+  "version": "2.146.2",
   "description": "ProteinPaint code that is shared between server and client-side workspaces",
   "type": "module",
   "main": "src/index.js",

package/src/compute.percentile.js

@@ -1,7 +1,8 @@
 // compute the percentile value from an array of values
+// sorted parameter allows to skip sorting if array is pre-sorted
 // source: https://www.dummies.com/article/academics-the-arts/math/statistics/how-to-calculate-percentiles-in-statistics-169783/
-export default function computePercentile(values, percentile) {
-	values.sort((a, b) => a - b)
+export default function computePercentile(values, percentile, sorted = false) {
+	if (!sorted) values.sort((a, b) => a - b)
 	const index = Math.abs((percentile / 100) * values.length - 1)
 	const value = Number.isInteger(index) ? (values[index] + values[index + 1]) / 2 : values[Math.ceil(index)]
 	return value

package/src/index.js

@@ -3,7 +3,6 @@ export * from './bulk.js'
 export * from './clustering.js'
 export * from './common.js'
 export * from './compute.percentile.js'
-export * from './descriptive.stats.js'
 export * from './fetch-helpers.js'
 export * from './fileSize.js'
 export * from './filter.js'

package/src/descriptive.stats.js

@@ -1,107 +0,0 @@
-import { roundValueAuto } from './roundValue.js'
-
-/* This file generates summary statistics on any given array of numbers*/
-
-export function getDescriptiveStats(array) {
-	//console.log("array:",array)
-	let arr = array
-	if (typeof array[0] == 'string') {
-		// somehow the values can be string but not numbers
-		// must cast to numbers to properly compute values
-		arr = array.map(Number)
-	}
-	//compute total
-	const sorted_arr = arr.sort((a, b) => a - b)
-	const n = arr.length
-
-	//compute median
-	const median = computePercentile(sorted_arr, 50)
-	//compute mean
-	const mean = getMean(arr)
-	// compute variance
-	const variance = getVariance(sorted_arr)
-	// compute standard deviation
-	const stdDev = Math.sqrt(variance)
-
-	//compute percentile ranges
-	const p25 = computePercentile(sorted_arr, 25)
-	const p75 = computePercentile(sorted_arr, 75)
-
-	//compute IQR
-	const IQR = p75 - p25
-	const min = sorted_arr[0]
-	const max = sorted_arr[sorted_arr.length - 1]
-
-	// Calculate outlier boundaries
-	const outlierMin = p25 - 1.5 * IQR //p25 is same as q1
-	const outlierMax = p75 + 1.5 * IQR //p75 is same as q3
-
-	return {
-		total: n,
-		min,
-		max,
-		p25,
-		p75,
-		median,
-		mean,
-		variance,
-		stdDev,
-		IQR,
-		outlierMin,
-		outlierMax
-	}
-}
-
-export function summaryStats(array, showOutlierRange = false) {
-	const stats = getDescriptiveStats(array)
-	return summaryStatsFromStats(stats, showOutlierRange)
-}
-
-export function summaryStatsFromStats(stats, showOutlierRange = false) {
-	const result = {
-		values: [
-			{ id: 'total', label: 'Total', value: stats.total },
-			{ id: 'min', label: 'Minimum', value: roundValueAuto(stats.min, true) },
-			{ id: 'p25', label: '1st quartile', value: roundValueAuto(stats.p25, true) },
-			{ id: 'median', label: 'Median', value: roundValueAuto(stats.median, true) },
-			{ id: 'mean', label: 'Mean', value: roundValueAuto(stats.mean, true) },
-			{ id: 'p75', label: '3rd quartile', value: roundValueAuto(stats.p75, true) },
-			{ id: 'max', label: 'Maximum', value: roundValueAuto(stats.max, true) },
-			{ id: 'SD', label: 'Standard deviation', value: roundValueAuto(stats.stdDev, true) },
-			{ id: 'variance', label: 'Variance', value: roundValueAuto(stats.variance, true) },
-			{ id: 'IQR', label: 'Inter-quartile range', value: roundValueAuto(stats.IQR, true) }
-		]
-	}
-	if (showOutlierRange) {
-		result.values.push(
-			{ id: 'outlierMin', label: 'Outlier min', value: roundValueAuto(stats.outlierMin, true) },
-			{ id: 'outlierMax', label: 'Outlier max', value: roundValueAuto(stats.outlierMax, true) }
-		)
-	}
-	return result
-}
-
-function computePercentile(values, percentile) {
-	const index = Math.abs((percentile / 100) * values.length - 1)
-	const value = Number.isInteger(index) ? (values[index] + values[index + 1]) / 2 : values[Math.ceil(index)]
-	return value
-}
-
-export function getMean(data) {
-	return data.reduce((sum, value) => sum + value, 0) / data.length
-}
-
-export function getVariance(data) {
-	const meanValue = getMean(data)
-	const squaredDifferences = data.map(value => Math.pow(value - meanValue, 2))
-	//Using n−1 compensates for the fact that we're basing variance on a sample mean,
-	// which tends to underestimate true variability. The correction is especially important with small sample sizes,
-	// where dividing by n would significantly distort the variance estimate.
-	// For more details see https://en.wikipedia.org/wiki/Bessel%27s_correction
-	return squaredDifferences.reduce((sum, value) => sum + value, 0) / (data.length - 1)
-}
-
-export function getStdDev(data) {
-	const variance = getVariance(data)
-	return Math.sqrt(variance)
-}