@stdlib/stats-padjust 0.0.7 → 0.2.0

package/LICENSE

@@ -175,307 +175,3 @@
       of your accepting any such warranty or additional liability.
 
    END OF TERMS AND CONDITIONS
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-Boost Software License - Version 1.0 - August 17th, 2003
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-Permission is hereby granted, free of charge, to any person or organization
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-* OpenBLAS <https://raw.githubusercontent.com/xianyi/OpenBLAS/
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-* Boost <http://www.boost.org/LICENSE_1_0.txt>
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-Boost Software License - Version 1.0 - August 17th, 2003
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-Permission is hereby granted, free of charge, to any person or organization
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-DEALINGS IN THE SOFTWARE.
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-* Cephes <http://www.netlib.org/cephes/readme>
-
-Copyright (c) 1984-2000 Stephen L. Moshier
-
-Some software in this archive may be from the book _Methods and Programs for
-Mathematical Functions_ (Prentice-Hall or Simon & Schuster International, 1989)
-or from the Cephes Mathematical Library, a commercial product. In either event,
-it is copyrighted by the author. What you see here may be used freely but it
-comes with no support or guarantee.
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-Stephen L. Moshier
-moshier@na-net.ornl.gov
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-ATTRIBUTION
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-The library contains implementations from the following external libraries,
-which have their own licenses:
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-* FreeBSD <https://svnweb.freebsd.org/>
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-Copyright (C) 1993-2004 by Sun Microsystems, Inc. All rights reserved.
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-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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-* SLATEC Common Mathematical Library <http://www.netlib.no/netlib/slatec/>
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-e66dd973650c375bc1739c820e5b96bb5bd000a8/LICENSE.md>
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-Copyright (c) 2015: Dahua Lin.
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-SpecialFunctions.jl/02a173fbe24a61c4b392aec17a9764ac5727feb1/LICENSE>
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-* MT19937 <http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/MT2002/CODES/
-mt19937ar.c>
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-Copyright (C) 1997 - 2002, Makoto Matsumoto and Takuji Nishimura,
-All rights reserved.
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-Redistribution and use in source and binary forms, with or without
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-are met:
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- 1. Redistributions of source code must retain the above copyright
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-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

package/NOTICE

@@ -1 +1 @@
-Copyright (c) 2016-2022 The Stdlib Authors.
+Copyright (c) 2016-2024 The Stdlib Authors.

package/README.md

@@ -18,6 +18,17 @@ limitations under the License.
 
 -->
 
+
+<details>
+  <summary>
+    About stdlib...
+  </summary>
+  <p>We believe in a future in which the web is a preferred environment for numerical computation. To help realize this future, we've built stdlib. stdlib is a standard library, with an emphasis on numerical and scientific computation, written in JavaScript (and C) for execution in browsers and in Node.js.</p>
+  <p>The library is fully decomposable, being architected in such a way that you can swap out and mix and match APIs and functionality to cater to your exact preferences and use cases.</p>
+  <p>When you use stdlib, you can be absolutely certain that you are using the most thorough, rigorous, well-written, studied, documented, tested, measured, and high-quality code out there.</p>
+  <p>To join us in bringing numerical computing to the web, get started by checking us out on <a href="https://github.com/stdlib-js/stdlib">GitHub</a>, and please consider <a href="https://opencollective.com/stdlib">financially supporting stdlib</a>. We greatly appreciate your continued support!</p>
+</details>
+
 # padjust
 
 [![NPM version][npm-image]][npm-url] [![Build Status][test-image]][test-url] [![Coverage Status][coverage-image]][coverage-url] <!-- [![dependencies][dependencies-image]][dependencies-url] -->
@@ -156,7 +167,7 @@ See [LICENSE][stdlib-license].
 
 ## Copyright
 
-Copyright &copy; 2016-2022. The Stdlib [Authors][stdlib-authors].
+Copyright &copy; 2016-2024. The Stdlib [Authors][stdlib-authors].
 
 </section>
 
@@ -169,8 +180,8 @@ Copyright &copy; 2016-2022. The Stdlib [Authors][stdlib-authors].
 [npm-image]: http://img.shields.io/npm/v/@stdlib/stats-padjust.svg
 [npm-url]: https://npmjs.org/package/@stdlib/stats-padjust
 
-[test-image]: https://github.com/stdlib-js/stats-padjust/actions/workflows/test.yml/badge.svg
-[test-url]: https://github.com/stdlib-js/stats-padjust/actions/workflows/test.yml
+[test-image]: https://github.com/stdlib-js/stats-padjust/actions/workflows/test.yml/badge.svg?branch=v0.2.0
+[test-url]: https://github.com/stdlib-js/stats-padjust/actions/workflows/test.yml?query=branch:v0.2.0
 
 [coverage-image]: https://img.shields.io/codecov/c/github/stdlib-js/stats-padjust/main.svg
 [coverage-url]: https://codecov.io/github/stdlib-js/stats-padjust?branch=main
@@ -182,19 +193,23 @@ Copyright &copy; 2016-2022. The Stdlib [Authors][stdlib-authors].
 
 -->
 
+[chat-image]: https://img.shields.io/gitter/room/stdlib-js/stdlib.svg
+[chat-url]: https://app.gitter.im/#/room/#stdlib-js_stdlib:gitter.im
+
+[stdlib]: https://github.com/stdlib-js/stdlib
+
+[stdlib-authors]: https://github.com/stdlib-js/stdlib/graphs/contributors
+
 [umd]: https://github.com/umdjs/umd
 [es-module]: https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Modules
 
 [deno-url]: https://github.com/stdlib-js/stats-padjust/tree/deno
+[deno-readme]: https://github.com/stdlib-js/stats-padjust/blob/deno/README.md
 [umd-url]: https://github.com/stdlib-js/stats-padjust/tree/umd
+[umd-readme]: https://github.com/stdlib-js/stats-padjust/blob/umd/README.md
 [esm-url]: https://github.com/stdlib-js/stats-padjust/tree/esm
-
-[chat-image]: https://img.shields.io/gitter/room/stdlib-js/stdlib.svg
-[chat-url]: https://gitter.im/stdlib-js/stdlib/
-
-[stdlib]: https://github.com/stdlib-js/stdlib
-
-[stdlib-authors]: https://github.com/stdlib-js/stdlib/graphs/contributors
+[esm-readme]: https://github.com/stdlib-js/stats-padjust/blob/esm/README.md
+[branches-url]: https://github.com/stdlib-js/stats-padjust/blob/main/branches.md
 
 [stdlib-license]: https://raw.githubusercontent.com/stdlib-js/stats-padjust/main/LICENSE
 

package/SECURITY.md

@@ -0,0 +1,5 @@
+# Security
+
+> Policy for reporting security vulnerabilities.
+
+See the security policy [in the main project repository](https://github.com/stdlib-js/stdlib/security).

package/dist/index.d.ts

@@ -0,0 +1,3 @@
+/// <reference path="../docs/types/index.d.ts" />
+import padjust from '../docs/types/index';
+export = padjust;

package/dist/index.js

@@ -0,0 +1,17 @@
+"use strict";var g=function(r,t){return function(){return t||r((t={exports:{}}).exports,t),t.exports}};var c=g(function(br,m){
+function N(r,t){var i,n;for(n=0;n<r.length;n++)i=r[n],r[n]=t*i>1?1:t*i;return r}m.exports=N
+});var l=g(function(yr,A){
+var O=require('@stdlib/array-int32/dist');function R(r,t){return r<t?-1:r>t?1:0}function z(r,t){return r<t?1:r>t?-1:0}function B(r,t){var i,n,u;for(i=t?z:R,n=new O(r.length),u=0;u<r.length;u++)n[u]=u;return n.sort(f);function f(e,v){return i(r[e],r[v])}}A.exports=B
+});var j=g(function(mr,T){
+var C=require('@stdlib/math-base-special-min/dist'),x=require('@stdlib/math-base-special-max/dist'),E=require('@stdlib/array-float64/dist'),F=require('@stdlib/constants-float64-pinf/dist'),G=l(),J=Array.prototype.slice;function K(r,t){var i,n,u,f,e,v,b,y,a,o,h,d,q;if(e=r.length,n=t-e,n>0)for(r=J.call(r);n>0;)r.push(1),n-=1;for(i=G(r),y=F,a=0;a<t;a++)q=t*r[a]/(a+1),q<y&&(y=q);for(d=new E(t),u=new E(t),a=t-1;a>1;a--){for(b=F,h=t-a+1;h<=t;h++)q=a*r[i[h]]/(2+h-t+a-1),q<b&&(b=q);for(o=0;o<t-a+1;o++)d[o]=C(a*r[i[o]],b);for(h=t-a+1;h<=t;h++)d[h]=d[t-a];for(o=0;o<u.length;o++)u[o]=x(d[o],u[o])}for(v=new Array(e),a=0;a<e;a++)f=i[a],q=x(u[a],r[f]),v[f]=q;return v}T.exports=K
+});var P=g(function(cr,V){
+var L=require('@stdlib/math-base-special-min/dist'),Q=require('@stdlib/stats-base-cumax/dist'),U=require('@stdlib/array-float64/dist'),W=l();function X(r,t){var i,n,u,f,e;for(u=r.length,i=W(r),n=new U(u),e=0;e<u;e++)n[e]=(t-e)*r[i[e]];for(n=Q(u,n,1,n,1),f=new Array(u),e=0;e<u;e++)f[i[e]]=L(n[e],1);return f}V.exports=X
+});var I=g(function(Ar,S){
+var Y=require('@stdlib/math-base-special-min/dist'),Z=require('@stdlib/stats-base-cumin/dist'),_=require('@stdlib/array-float64/dist'),$=l();function s(r,t){var i,n,u,f,e;for(u=r.length,i=$(r,!0),n=new _(u),e=0;e<u;e++)n[e]=t/(u-e)*r[i[e]];for(n=Z(u,n,1,n,1),f=new Array(u),e=0;e<u;e++)f[i[e]]=Y(n[e],1);return f}S.exports=s
+});var D=g(function(xr,k){
+var p=require('@stdlib/math-base-special-min/dist'),rr=require('@stdlib/stats-base-cumin/dist'),er=require('@stdlib/array-float64/dist'),tr=l();function ir(r,t){var i,n,u,f,e,v;for(u=r.length,i=tr(r,!0),v=0,e=0;e<t;e++)v+=1/(1+e);for(n=new er(u),e=0;e<u;e++)n[e]=v*t/(u-e)*r[i[e]];for(n=rr(u,n,1,n,1),f=new Array(u),e=0;e<u;e++)f[i[e]]=p(n[e],1);return f}k.exports=ir
+});var M=g(function(Er,H){
+var nr=require('@stdlib/assert-is-probability-array/dist'),ur=require('@stdlib/assert-is-integer/dist').isPrimitive,ar=require('@stdlib/assert-is-string/dist').isPrimitive,w=require('@stdlib/error-tools-fmtprodmsg/dist'),fr=c(),or=j(),vr=P(),hr=I(),qr=D(),gr=["bh","bonferroni","by","holm","hommel"];function dr(r,t,i){if(!nr(r))throw new TypeError(w('1Ll9x',r));if(!ar(t))throw new TypeError(w('1Ll39',t));if(arguments.length>2){if(!ur(i))throw new TypeError(w('1Ll2z',i));if(i<r.length)throw new RangeError(w('1LlDP',i))}switch(i=i||r.length,t){case"bonferroni":return fr(r,i);case"by":return qr(r,i);case"bh":return hr(r,i);case"holm":return vr(r,i);case"hommel":return or(r,i);default:throw new Error(w('1LlDQ',gr.join('", "'),t))}}H.exports=dr
+});var lr=M();module.exports=lr;
+/** @license Apache-2.0 */
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../lib/bonferroni.js", "../lib/order.js", "../lib/hommel.js", "../lib/holm.js", "../lib/bh.js", "../lib/by.js", "../lib/main.js", "../lib/index.js"],
+  "sourcesContent": ["/**\n* @license Apache-2.0\n*\n* Copyright (c) 2020 The Stdlib Authors.\n*\n* Licensed under the Apache License, Version 2.0 (the \"License\");\n* you may not use this file except in compliance with the License.\n* You may obtain a copy of the License at\n*\n*    http://www.apache.org/licenses/LICENSE-2.0\n*\n* Unless required by applicable law or agreed to in writing, software\n* distributed under the License is distributed on an \"AS IS\" BASIS,\n* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n* See the License for the specific language governing permissions and\n* limitations under the License.\n*/\n\n'use strict';\n\n// MAIN //\n\n/**\n* Adjusts the p-values via the Bonferroni method.\n*\n* @private\n* @param {ProbabilityArray} pvalues - p-values to be adjusted\n* @param {PositiveInteger} comparisons - number of comparisons\n* @returns {ProbabilityArray} adjusted p-values\n*/\nfunction bonferroni( pvalues, comparisons ) {\n\tvar pval;\n\tvar i;\n\tfor ( i = 0; i < pvalues.length; i++ ) {\n\t\tpval = pvalues[ i ];\n\t\tpvalues[ i ] = ( comparisons * pval > 1 ) ? 1 : comparisons * pval;\n\t}\n\treturn pvalues;\n}\n\n\n// EXPORTS //\n\nmodule.exports = bonferroni;\n", "/**\n* @license Apache-2.0\n*\n* Copyright (c) 2020 The Stdlib Authors.\n*\n* Licensed under the Apache License, Version 2.0 (the \"License\");\n* you may not use this file except in compliance with the License.\n* You may obtain a copy of the License at\n*\n*    http://www.apache.org/licenses/LICENSE-2.0\n*\n* Unless required by applicable law or agreed to in writing, software\n* distributed under the License is distributed on an \"AS IS\" BASIS,\n* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n* See the License for the specific language governing permissions and\n* limitations under the License.\n*/\n\n'use strict';\n\n// MODULES //\n\nvar Int32Array = require( '@stdlib/array-int32' );\n\n\n// FUNCTIONS //\n\n/**\n* Returns a comparison result. If `-1`, `a` comes before `b`. If `1`, `b` comes before `a`. If `0`, the order stays the same.\n*\n* @private\n* @param {number} a - first number\n* @param {number} b - second number\n* @returns {boolean} comparison result\n*/\nfunction ascending( a, b ) {\n\tif ( a < b ) {\n\t\treturn -1;\n\t}\n\tif ( a > b ) {\n\t\treturn 1;\n\t}\n\treturn 0;\n}\n\n/**\n* Returns a comparison result. If `-1`, `a` comes before `b`. If `1`, `b` comes before `a`. If `0`, the order stays the same.\n*\n* @private\n* @param {number} a - first number\n* @param {number} b - second number\n* @returns {boolean} comparison result\n*/\nfunction descending( a, b ) {\n\tif ( a < b ) {\n\t\treturn 1;\n\t}\n\tif ( a > b ) {\n\t\treturn -1;\n\t}\n\treturn 0;\n}\n\n\n// MAIN //\n\n/**\n* Returns a permutation which rearranges input array.\n*\n* @private\n* @param {ArrayLike} x - input array-like object\n* @param {boolean} invert - controls whether to permutation that sorts input array in descending order\n* @returns {Array} permutation array\n*/\nfunction order( x, invert ) {\n\tvar comparator;\n\tvar arr;\n\tvar i;\n\n\tcomparator = ( invert ) ? descending : ascending;\n\tarr = new Int32Array( x.length );\n\tfor ( i = 0; i < x.length; i++ ) {\n\t\tarr[ i ] = i;\n\t}\n\treturn arr.sort( compare );\n\n\t/**\n\t* Compare the elements of the input array.\n\t*\n\t* @private\n\t* @param {number} a - first number\n\t* @param {number} b - second number\n\t* @returns {boolean} comparison result\n\t*/\n\tfunction compare( a, b ) {\n\t\treturn comparator( x[a], x[b] );\n\t}\n}\n\n\n// EXPORTS //\n\nmodule.exports = order;\n", "/**\n* @license Apache-2.0\n*\n* Copyright (c) 2020 The Stdlib Authors.\n*\n* Licensed under the Apache License, Version 2.0 (the \"License\");\n* you may not use this file except in compliance with the License.\n* You may obtain a copy of the License at\n*\n*    http://www.apache.org/licenses/LICENSE-2.0\n*\n* Unless required by applicable law or agreed to in writing, software\n* distributed under the License is distributed on an \"AS IS\" BASIS,\n* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n* See the License for the specific language governing permissions and\n* limitations under the License.\n*/\n\n'use strict';\n\n// MODULES //\n\nvar min = require( '@stdlib/math-base-special-min' );\nvar max = require( '@stdlib/math-base-special-max' );\nvar Float64Array = require( '@stdlib/array-float64' );\nvar PINF = require( '@stdlib/constants-float64-pinf' );\nvar order = require( './order.js' );\n\n\n// VARIABLES //\n\nvar slice = Array.prototype.slice;\n\n\n// MAIN //\n\n/**\n* Adjusts the p-values via Hommel's method.\n*\n* @private\n* @param {ProbabilityArray} pvalues - p-values to be adjusted\n* @param {PositiveInteger} comparisons - number of comparisons\n* @returns {ProbabilityArray} adjusted p-values\n*/\nfunction hommel( pvalues, comparisons ) {\n\tvar indices;\n\tvar diff;\n\tvar adj;\n\tvar idx;\n\tvar len;\n\tvar out;\n\tvar mq;\n\tvar m;\n\tvar i;\n\tvar j;\n\tvar k;\n\tvar q;\n\tvar v;\n\n\tlen = pvalues.length;\n\tdiff = comparisons - len;\n\tif ( diff > 0 ) {\n\t\tpvalues = slice.call( pvalues );\n\t\twhile ( diff > 0 ) {\n\t\t\tpvalues.push( 1.0 );\n\t\t\tdiff -= 1;\n\t\t}\n\t}\n\tindices = order( pvalues );\n\tm = PINF;\n\tfor ( i = 0; i < comparisons; i++ ) {\n\t\tv = comparisons * pvalues[ i ] / ( i+1 );\n\t\tif ( v < m ) {\n\t\t\tm = v;\n\t\t}\n\t}\n\tq = new Float64Array( comparisons );\n\tadj = new Float64Array( comparisons );\n\tfor ( i = comparisons - 1; i > 1; i-- ) {\n\t\tmq = PINF;\n\t\tfor ( k = comparisons - i + 1; k <= comparisons; k++ ) {\n\t\t\tv = i * pvalues[ indices[ k ] ] / ( 2 + k - comparisons + i - 1 );\n\t\t\tif ( v < mq ) {\n\t\t\t\tmq = v;\n\t\t\t}\n\t\t}\n\t\tfor ( j = 0; j < comparisons - i + 1; j++ ) {\n\t\t\tq[ j ] = min( i * pvalues[ indices[ j ] ], mq );\n\t\t}\n\t\tfor ( k = comparisons - i + 1; k <= comparisons; k++ ) {\n\t\t\tq[ k ] = q[ comparisons - i ];\n\t\t}\n\t\tfor ( j = 0; j < adj.length; j++ ) {\n\t\t\tadj[ j ] = max( q[ j ], adj[ j ] );\n\t\t}\n\t}\n\tout = new Array( len );\n\tfor ( i = 0; i < len; i++ ) {\n\t\tidx = indices[ i ];\n\t\tv = max( adj[ i ], pvalues[ idx ] );\n\t\tout[ idx ] = v;\n\t}\n\treturn out;\n}\n\n\n// EXPORTS //\n\nmodule.exports = hommel;\n", "/**\n* @license Apache-2.0\n*\n* Copyright (c) 2020 The Stdlib Authors.\n*\n* Licensed under the Apache License, Version 2.0 (the \"License\");\n* you may not use this file except in compliance with the License.\n* You may obtain a copy of the License at\n*\n*    http://www.apache.org/licenses/LICENSE-2.0\n*\n* Unless required by applicable law or agreed to in writing, software\n* distributed under the License is distributed on an \"AS IS\" BASIS,\n* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n* See the License for the specific language governing permissions and\n* limitations under the License.\n*/\n\n'use strict';\n\n// MODULES //\n\nvar min = require( '@stdlib/math-base-special-min' );\nvar cumax = require( '@stdlib/stats-base-cumax' );\nvar Float64Array = require( '@stdlib/array-float64' );\nvar order = require( './order.js' );\n\n\n// MAIN //\n\n/**\n* Adjusts the p-values via the Bonferroni\u2013Holm method.\n*\n* @private\n* @param {ProbabilityArray} pvalues - p-values to be adjusted\n* @param {PositiveInteger} comparisons - number of comparisons\n* @returns {ProbabilityArray} adjusted p-values\n*/\nfunction holm( pvalues, comparisons ) {\n\tvar indices;\n\tvar sorted;\n\tvar len;\n\tvar out;\n\tvar i;\n\n\tlen = pvalues.length;\n\tindices = order( pvalues );\n\tsorted = new Float64Array( len );\n\tfor ( i = 0; i < len; i++ ) {\n\t\tsorted[ i ] = ( comparisons - i ) * pvalues[ indices[ i ] ];\n\t}\n\tsorted = cumax( len, sorted, 1, sorted, 1 );\n\tout = new Array( len );\n\tfor ( i = 0; i < len; i++ ) {\n\t\tout[ indices[ i ] ] = min( sorted[ i ], 1.0 );\n\t}\n\treturn out;\n}\n\n\n// EXPORTS //\n\nmodule.exports = holm;\n", "/**\n* @license Apache-2.0\n*\n* Copyright (c) 2020 The Stdlib Authors.\n*\n* Licensed under the Apache License, Version 2.0 (the \"License\");\n* you may not use this file except in compliance with the License.\n* You may obtain a copy of the License at\n*\n*    http://www.apache.org/licenses/LICENSE-2.0\n*\n* Unless required by applicable law or agreed to in writing, software\n* distributed under the License is distributed on an \"AS IS\" BASIS,\n* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n* See the License for the specific language governing permissions and\n* limitations under the License.\n*/\n\n'use strict';\n\n// MODULES //\n\nvar min = require( '@stdlib/math-base-special-min' );\nvar cumin = require( '@stdlib/stats-base-cumin' );\nvar Float64Array = require( '@stdlib/array-float64' );\nvar order = require( './order.js' );\n\n\n// MAIN //\n\n/**\n* Adjusts the p-values via the Benjamini-Hochberg procedure.\n*\n* @private\n* @param {ProbabilityArray} pvalues - p-values to be adjusted\n* @param {PositiveInteger} comparisons - number of comparisons\n* @returns {ProbabilityArray} adjusted p-values\n*/\nfunction bh( pvalues, comparisons ) {\n\tvar indices;\n\tvar sorted;\n\tvar len;\n\tvar out;\n\tvar i;\n\n\tlen = pvalues.length;\n\tindices = order( pvalues, true );\n\tsorted = new Float64Array( len );\n\tfor ( i = 0; i < len; i++ ) {\n\t\tsorted[ i ] = comparisons / ( len - i ) * pvalues[ indices[ i ] ];\n\t}\n\tsorted = cumin( len, sorted, 1, sorted, 1 );\n\tout = new Array( len );\n\tfor ( i = 0; i < len; i++ ) {\n\t\tout[ indices[ i ] ] = min( sorted[ i ], 1.0 );\n\t}\n\treturn out;\n}\n\n\n// EXPORTS //\n\nmodule.exports = bh;\n", "/**\n* @license Apache-2.0\n*\n* Copyright (c) 2020 The Stdlib Authors.\n*\n* Licensed under the Apache License, Version 2.0 (the \"License\");\n* you may not use this file except in compliance with the License.\n* You may obtain a copy of the License at\n*\n*    http://www.apache.org/licenses/LICENSE-2.0\n*\n* Unless required by applicable law or agreed to in writing, software\n* distributed under the License is distributed on an \"AS IS\" BASIS,\n* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n* See the License for the specific language governing permissions and\n* limitations under the License.\n*/\n\n'use strict';\n\n// MODULES //\n\nvar min = require( '@stdlib/math-base-special-min' );\nvar cumin = require( '@stdlib/stats-base-cumin' );\nvar Float64Array = require( '@stdlib/array-float64' );\nvar order = require( './order.js' );\n\n\n// MAIN //\n\n/**\n* Adjusts the p-values via the Benjamini & Yekutieli method.\n*\n* @private\n* @param {ProbabilityArray} pvalues - p-values to be adjusted\n* @param {PositiveInteger} comparisons - number of comparisons\n* @returns {ProbabilityArray} adjusted p-values\n*/\nfunction by( pvalues, comparisons ) {\n\tvar indices;\n\tvar sorted;\n\tvar len;\n\tvar out;\n\tvar i;\n\tvar q;\n\n\tlen = pvalues.length;\n\tindices = order( pvalues, true );\n\tq = 0;\n\tfor ( i = 0; i < comparisons; i++ ) {\n\t\tq += 1 / ( 1 + i );\n\t}\n\tsorted = new Float64Array( len );\n\tfor ( i = 0; i < len; i++ ) {\n\t\tsorted[ i ] = q * comparisons / ( len - i ) * pvalues[ indices[ i ] ];\n\t}\n\tsorted = cumin( len, sorted, 1, sorted, 1 );\n\tout = new Array( len );\n\tfor ( i = 0; i < len; i++ ) {\n\t\tout[ indices[ i ] ] = min( sorted[ i ], 1.0 );\n\t}\n\treturn out;\n}\n\n\n// EXPORTS //\n\nmodule.exports = by;\n", "/**\n* @license Apache-2.0\n*\n* Copyright (c) 2020 The Stdlib Authors.\n*\n* Licensed under the Apache License, Version 2.0 (the \"License\");\n* you may not use this file except in compliance with the License.\n* You may obtain a copy of the License at\n*\n*    http://www.apache.org/licenses/LICENSE-2.0\n*\n* Unless required by applicable law or agreed to in writing, software\n* distributed under the License is distributed on an \"AS IS\" BASIS,\n* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n* See the License for the specific language governing permissions and\n* limitations under the License.\n*/\n\n'use strict';\n\n// MODULES //\n\nvar isProbabilityArray = require( '@stdlib/assert-is-probability-array' );\nvar isInteger = require( '@stdlib/assert-is-integer' ).isPrimitive;\nvar isString = require( '@stdlib/assert-is-string' ).isPrimitive;\nvar format = require( '@stdlib/string-format' );\nvar bonferroni = require( './bonferroni.js' );\nvar hommel = require( './hommel.js' );\nvar holm = require( './holm.js' );\nvar bh = require( './bh.js' );\nvar by = require( './by.js' );\n\n\n// VARIABLES //\n\nvar METHODS = [ 'bh', 'bonferroni', 'by', 'holm', 'hommel' ];\n\n\n// MAIN //\n\n/**\n* Adjusts supplied p-values for multiple comparisons via a specified method.\n*\n* @param {ProbabilityArray} pvals - p-values to be adjusted\n* @param {string} method - correction method\n* @param {PositiveInteger} [comparisons=pvals.length] - number of comparisons\n* @throws {TypeError} first argument has to be an array-like object\n* @throws {TypeError} second argument must be a string\n* @throws {Error} second argument must be `bh`, `bonferroni`, `by`, `holm`, or `hommel`\n* @throws {RangeError} comparisons must be greater or equal to the number of p-values to be adjusted\n* @returns {ProbabilityArray} array containing the corrected p-values\n*\n* @example\n* var pvalues = [ 0.008, 0.03, 0.123, 0.6, 0.2 ];\n* var out = padjust( pvalues, 'bonferroni' );\n* // returns [ 0.04, 0.15, ..., 1, 1 ]\n*\n* @example\n* var pvalues = [ 0.008, 0.03, 0.123, 0.6, 0.2 ];\n* var out = padjust( pvalues, 'by' );\n* // returns [ ~0.091, ~0.171, ..., 1, ~0.571 ]\n*\n* @example\n* var pvalues = [ 0.008, 0.03, 0.123, 0.6, 0.2 ];\n* var out = padjust( pvalues, 'bh' );\n* // returns [ 0.04, 0.075, ..., 0.6, 0.25 ]\n*\n* @example\n* var pvalues = [ 0.008, 0.03, 0.123, 0.6, 0.2 ];\n* var out = padjust( pvalues, 'holm' );\n* // returns [ 0.04, 0.12, ..., 0.6, 0.4 ]\n*\n* @example\n* var pvalues = [ 0.008, 0.03, 0.123, 0.6, 0.2 ];\n* var out = padjust( pvalues, 'hommel' );\n* // returns [ 0.032, 0.12, ..., 0.6, 0.4 ]\n*/\nfunction padjust( pvals, method, comparisons ) {\n\tif ( !isProbabilityArray( pvals ) ) {\n\t\tthrow new TypeError( format( 'invalid argument. First argument must be an array of probabilities. Value: `%s`.', pvals ) );\n\t}\n\tif ( !isString( method ) ) {\n\t\tthrow new TypeError( format( 'invalid argument. Second argument must be a string. Value: `%s`.', method ) );\n\t}\n\tif ( arguments.length > 2 ) {\n\t\tif ( !isInteger( comparisons ) ) {\n\t\t\tthrow new TypeError( format( 'invalid argument. Third argument must be an integer. Value: `%s`.', comparisons ) );\n\t\t}\n\t\tif ( comparisons < pvals.length ) {\n\t\t\tthrow new RangeError( format( 'invalid argument. The number of comparisons must be greater or equal to the number of p-values to be adjusted. Value: `%u`.', comparisons ) );\n\t\t}\n\t}\n\tcomparisons = comparisons || pvals.length;\n\tswitch ( method ) {\n\tcase 'bonferroni':\n\t\treturn bonferroni( pvals, comparisons );\n\tcase 'by':\n\t\treturn by( pvals, comparisons );\n\tcase 'bh':\n\t\treturn bh( pvals, comparisons );\n\tcase 'holm':\n\t\treturn holm( pvals, comparisons );\n\tcase 'hommel':\n\t\treturn hommel( pvals, comparisons );\n\tdefault:\n\t\tthrow new Error( format( 'invalid argument. Second argument must be one of the following: \"%s\". Value: `%s`.', METHODS.join( '\", \"' ), method ) );\n\t}\n}\n\n\n// EXPORTS //\n\nmodule.exports = padjust;\n", "/**\n* @license Apache-2.0\n*\n* Copyright (c) 2020 The Stdlib Authors.\n*\n* Licensed under the Apache License, Version 2.0 (the \"License\");\n* you may not use this file except in compliance with the License.\n* You may obtain a copy of the License at\n*\n*    http://www.apache.org/licenses/LICENSE-2.0\n*\n* Unless required by applicable law or agreed to in writing, software\n* distributed under the License is distributed on an \"AS IS\" BASIS,\n* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n* See the License for the specific language governing permissions and\n* limitations under the License.\n*/\n\n'use strict';\n\n/**\n* Adjust supplied p-values for multiple comparisons via a specified method.\n*\n* @module @stdlib/stats-padjust\n*\n* @example\n* var padjust = require( '@stdlib/stats-padjust' );\n*\n* var pvalues = [ 0.008, 0.03, 0.123, 0.6, 0.2 ];\n* var out = padjust( pvalues, 'bh' );\n* // returns [ 0.04, 0.075, ~0.205, 0.6, 0.25 ]\n*/\n\n// MODULES //\n\nvar main = require( './main.js' );\n\n\n// EXPORTS //\n\nmodule.exports = main;\n"],
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+  "names": ["require_bonferroni", "__commonJSMin", "exports", "module", "bonferroni", "pvalues", "comparisons", "pval", "i", "require_order", "__commonJSMin", "exports", "module", "Int32Array", "ascending", "a", "b", "descending", "order", "x", "invert", "comparator", "arr", "i", "compare", "require_hommel", "__commonJSMin", "exports", "module", "min", "max", "Float64Array", "PINF", "order", "slice", "hommel", "pvalues", "comparisons", "indices", "diff", "adj", "idx", "len", "out", "mq", "m", "i", "j", "k", "q", "v", "require_holm", "__commonJSMin", "exports", "module", "min", "cumax", "Float64Array", "order", "holm", "pvalues", "comparisons", "indices", "sorted", "len", "out", "i", "require_bh", "__commonJSMin", "exports", "module", "min", "cumin", "Float64Array", "order", "bh", "pvalues", "comparisons", "indices", "sorted", "len", "out", "i", "require_by", "__commonJSMin", "exports", "module", "min", "cumin", "Float64Array", "order", "by", "pvalues", "comparisons", "indices", "sorted", "len", "out", "i", "q", "require_main", "__commonJSMin", "exports", "module", "isProbabilityArray", "isInteger", "isString", "format", "bonferroni", "hommel", "holm", "bh", "by", "METHODS", "padjust", "pvals", "method", "comparisons", "main"]
+}

package/docs/types/index.d.ts

@@ -16,7 +16,7 @@
 * limitations under the License.
 */
 
-// TypeScript Version: 2.0
+// TypeScript Version: 4.1
 
 /**
 * Correction method.
@@ -69,7 +69,7 @@ type Method = 'bh' | 'bonferroni' | 'by' | 'holm' | 'hommel';
 * var out = padjust( pvalues, 'hommel' );
 * // returns [ 0.032, 0.12, ..., 0.6, 0.4 ]
 */
-declare function padjust( x: Array<number>, method: Method, comparisons?: number ): Array<number>; // tslint-disable-line max-line-length
+declare function padjust( x: Array<number>, method: Method, comparisons?: number ): Array<number>;
 
 
 // EXPORTS //

package/lib/index.js

@@ -33,9 +33,9 @@
 
 // MODULES //
 
-var padjust = require( './main.js' );
+var main = require( './main.js' );
 
 
 // EXPORTS //
 
-module.exports = padjust;
+module.exports = main;

package/lib/main.js

@@ -23,6 +23,7 @@
 var isProbabilityArray = require( '@stdlib/assert-is-probability-array' );
 var isInteger = require( '@stdlib/assert-is-integer' ).isPrimitive;
 var isString = require( '@stdlib/assert-is-string' ).isPrimitive;
+var format = require( '@stdlib/string-format' );
 var bonferroni = require( './bonferroni.js' );
 var hommel = require( './hommel.js' );
 var holm = require( './holm.js' );
@@ -44,9 +45,9 @@ var METHODS = [ 'bh', 'bonferroni', 'by', 'holm', 'hommel' ];
 * @param {string} method - correction method
 * @param {PositiveInteger} [comparisons=pvals.length] - number of comparisons
 * @throws {TypeError} first argument has to be an array-like object
-* @throws {TypeError} second argument must be a string primitive
+* @throws {TypeError} second argument must be a string
 * @throws {Error} second argument must be `bh`, `bonferroni`, `by`, `holm`, or `hommel`
-* @throws {RangeError} comparisons must be greater or equal to the number of elements in `pvals`
+* @throws {RangeError} comparisons must be greater or equal to the number of p-values to be adjusted
 * @returns {ProbabilityArray} array containing the corrected p-values
 *
 * @example
@@ -76,17 +77,17 @@ var METHODS = [ 'bh', 'bonferroni', 'by', 'holm', 'hommel' ];
 */
 function padjust( pvals, method, comparisons ) {
 	if ( !isProbabilityArray( pvals ) ) {
-		throw new TypeError( 'invalid argument. First argument must be an array of probabilities. Value: `' + pvals + '`.' );
+		throw new TypeError( format( 'invalid argument. First argument must be an array of probabilities. Value: `%s`.', pvals ) );
 	}
 	if ( !isString( method ) ) {
-		throw new TypeError( 'invalid argument. Second argument must be a string primitive. Value: `' + method + '`.' );
+		throw new TypeError( format( 'invalid argument. Second argument must be a string. Value: `%s`.', method ) );
 	}
 	if ( arguments.length > 2 ) {
 		if ( !isInteger( comparisons ) ) {
-			throw new TypeError( 'invalid argument. `comparisons` must be an integer. Value: `' + comparisons + '`.' );
+			throw new TypeError( format( 'invalid argument. Third argument must be an integer. Value: `%s`.', comparisons ) );
 		}
 		if ( comparisons < pvals.length ) {
-			throw new RangeError( 'invalid argument. When specified, `comparisons` arguments must have at least a length of '+pvals.length+'. Value: `' + comparisons + '`.' );
+			throw new RangeError( format( 'invalid argument. The number of comparisons must be greater or equal to the number of p-values to be adjusted. Value: `%u`.', comparisons ) );
 		}
 	}
 	comparisons = comparisons || pvals.length;
@@ -102,7 +103,7 @@ function padjust( pvals, method, comparisons ) {
 	case 'hommel':
 		return hommel( pvals, comparisons );
 	default:
-		throw new Error( 'invalid argument. Second argument must be one of '+METHODS.join( ', ' )+' Value: `' + method + '`.' );
+		throw new Error( format( 'invalid argument. Second argument must be one of the following: "%s". Value: `%s`.', METHODS.join( '", "' ), method ) );
 	}
 }
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@stdlib/stats-padjust",
-  "version": "0.0.7",
+  "version": "0.2.0",
   "description": "Adjust supplied p-values for multiple comparisons via a specified method.",
   "license": "Apache-2.0",
   "author": {
@@ -37,26 +37,28 @@
     "url": "https://github.com/stdlib-js/stdlib/issues"
   },
   "dependencies": {
-    "@stdlib/array-float64": "^0.0.x",
-    "@stdlib/array-int32": "^0.0.x",
-    "@stdlib/assert-is-integer": "^0.0.x",
-    "@stdlib/assert-is-probability-array": "^0.0.x",
-    "@stdlib/assert-is-string": "^0.0.x",
-    "@stdlib/constants-float64-pinf": "^0.0.x",
-    "@stdlib/math-base-special-max": "^0.0.x",
-    "@stdlib/math-base-special-min": "^0.0.x",
-    "@stdlib/stats-base-cumax": "^0.0.x",
-    "@stdlib/stats-base-cumin": "^0.0.x"
+    "@stdlib/array-float64": "^0.2.0",
+    "@stdlib/array-int32": "^0.2.0",
+    "@stdlib/assert-is-integer": "^0.2.0",
+    "@stdlib/assert-is-probability-array": "^0.2.0",
+    "@stdlib/assert-is-string": "^0.2.0",
+    "@stdlib/constants-float64-pinf": "^0.2.0",
+    "@stdlib/math-base-special-max": "^0.2.0",
+    "@stdlib/math-base-special-min": "^0.2.0",
+    "@stdlib/stats-base-cumax": "^0.2.0",
+    "@stdlib/stats-base-cumin": "^0.2.0",
+    "@stdlib/string-format": "^0.2.0",
+    "@stdlib/error-tools-fmtprodmsg": "^0.1.1"
   },
   "devDependencies": {
-    "@stdlib/assert-is-array": "^0.0.x",
-    "@stdlib/bench": "^0.0.x",
-    "@stdlib/constants-float64-eps": "^0.0.x",
-    "@stdlib/math-base-special-abs": "^0.0.x",
-    "@stdlib/random-base-randu": "^0.0.x",
+    "@stdlib/constants-float64-eps": "^0.1.1",
+    "@stdlib/math-base-special-abs": "^0.1.1",
+    "@stdlib/random-base-randu": "^0.1.0",
     "tape": "git+https://github.com/kgryte/tape.git#fix/globby",
     "istanbul": "^0.4.1",
-    "tap-spec": "5.x.x"
+    "tap-min": "git+https://github.com/Planeshifter/tap-min.git",
+    "@stdlib/bench-harness": "^0.1.2",
+    "@stdlib/bench": "^0.3.1"
   },
   "engines": {
     "node": ">=0.10.0",
@@ -94,7 +96,7 @@
     "yekutieli"
   ],
   "funding": {
-    "type": "patreon",
-    "url": "https://www.patreon.com/athan"
+    "type": "opencollective",
+    "url": "https://opencollective.com/stdlib"
   }
 }

package/docs/repl.txt

@@ -1,63 +0,0 @@
-
-{{alias}}( pvals, method[, comparisons] )
-    Adjusts supplied p-values for multiple comparisons via a specified method.
-
-    The `method` parameter can be one of the following values:
-
-    -   **bh**: Benjamini-Hochberg procedure controlling the False Discovery
-    Rate (FDR).
-    -   **bonferroni**: Bonferroni correction fixing the family-wise error rate
-    by multiplying the p-values with the number of comparisons. The Bonferroni
-    correction is usually a too conservative adjustment compared to the others.
-    -   **by**: Procedure by Benjamini & Yekutieli for controlling the False
-    Discovery Rate (FDR) under dependence.
-    -   **holm**: Hommel's method controlling family-wise error rate. It is
-    uniformly more powerful than the Bonferroni correction.
-    -   **hommel**: Hommel's method, which is valid when hypothesis tests are
-    independent. It is more expensive to compute than the other methods.
-
-    By default, the number of comparisons for which the p-values should be
-    corrected is equal to the number of provided p-values. Alternatively, it is
-    possible to set `comparisons` to a number greater than the length of
-    `pvals`. In that case, the methods assume `comparisons - pvals.length`
-    unobserved p-values that are greater than all observed p-values (for Holm's
-    method and the Bonferroni correction) or equal to `1` for the remaining
-    methods.
-
-    Parameters
-    ----------
-    pvals: Array<number>
-        P-values to be adjusted.
-
-    method: string
-        Correction method.
-
-    comparisons: integer (optional)
-        Number of comparisons. Default value: `pvals.length`.
-
-    Returns
-    -------
-    out: Array<number>
-        Array containing the corrected p-values.
-
-    Examples
-    --------
-    > var pvalues = [ 0.008, 0.03, 0.123, 0.6, 0.2 ];
-    > var out = {{alias}}( pvalues, 'bh' )
-    [ 0.04, 0.075, ~0.205, 0.6, 0.25 ]
-
-    > out = {{alias}}( pvalues, 'bonferroni' )
-    [ 0.04, 0.15, 0.615, 1.0, 1.0 ]
-
-    > out = {{alias}}( pvalues, 'by' )
-    [ ~0.457, ~0.856, 1.0, 1.0, 1.0 ]
-
-    > out = {{alias}}( pvalues, 'holm' )
-    [ 0.2, 0.6, 1.0, 1.0, 1.0 ]
-
-    > out = {{alias}}( pvalues, 'hommel' )
-    [ 0.16, 0.6, 1.0, 1.0, 1.0 ]
-
-    See Also
-    --------
-

package/docs/types/test.ts

@@ -1,74 +0,0 @@
-/*
-* @license Apache-2.0
-*
-* Copyright (c) 2021 The Stdlib Authors.
-*
-* Licensed under the Apache License, Version 2.0 (the "License");
-* you may not use this file except in compliance with the License.
-* You may obtain a copy of the License at
-*
-*    http://www.apache.org/licenses/LICENSE-2.0
-*
-* Unless required by applicable law or agreed to in writing, software
-* distributed under the License is distributed on an "AS IS" BASIS,
-* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-* See the License for the specific language governing permissions and
-* limitations under the License.
-*/
-
-import padjust = require( './index' );
-
-
-// TESTS //
-
-// The function returns an array of numbers...
-{
-	const pvalues = [ 0.008, 0.03, 0.123, 0.6, 0.2 ];
-	padjust( pvalues, 'holm' ); // $ExpectType number[]
-	padjust( pvalues, 'hommel', 8 ); // $ExpectType number[]
-}
-
-// The function does not compile if provided a value other than an array of numbers...
-{
-	padjust( 'abc', 'bh' ); // $ExpectError
-	padjust( true, 'bh' ); // $ExpectError
-	padjust( false, 'bh' ); // $ExpectError
-	padjust( null, 'bh' ); // $ExpectError
-	padjust( undefined, 'bh' ); // $ExpectError
-	padjust( 5, 'bh' ); // $ExpectError
-	padjust( {}, 'bh' ); // $ExpectError
-	padjust( ( x: number ): number => x, 'bh' ); // $ExpectError
-}
-
-// The compiler throws an error if the function is provided a second argument which is not a recognized method...
-{
-	const pvalues = [ 0.008, 0.03, 0.123, 0.6, 0.2 ];
-	padjust( pvalues, 123 ); // $ExpectError
-	padjust( pvalues, 'abc' ); // $ExpectError
-	padjust( pvalues, true ); // $ExpectError
-	padjust( pvalues, false ); // $ExpectError
-	padjust( pvalues, null ); // $ExpectError
-	padjust( pvalues, [] ); // $ExpectError
-	padjust( pvalues, {} ); // $ExpectError
-	padjust( pvalues, ( x: number ): number => x ); // $ExpectError
-}
-
-// The compiler throws an error if the function is provided a third argument which is not a number...
-{
-	const pvalues = [ 0.008, 0.03, 0.123, 0.6, 0.2 ];
-	padjust( pvalues, 'bh', 'abc' ); // $ExpectError
-	padjust( pvalues, 'bh', true ); // $ExpectError
-	padjust( pvalues, 'bh', false ); // $ExpectError
-	padjust( pvalues, 'bh', null ); // $ExpectError
-	padjust( pvalues, 'bh', [] ); // $ExpectError
-	padjust( pvalues, 'bh', {} ); // $ExpectError
-	padjust( pvalues, 'bh', ( x: number ): number => x ); // $ExpectError
-}
-
-// The function does not compile if provided an invalid number of arguments...
-{
-	const pvalues = [ 0.008, 0.03, 0.123, 0.6, 0.2 ];
-	padjust(); // $ExpectError
-	padjust( pvalues ); // $ExpectError
-	padjust( pvalues, 'bonferroni', 5, {} ); // $ExpectError
-}