ANOVA Functionality #148

frank113 · 2018-01-30T19:41:39Z

Resolves # .

This pull request will add ANOVA functionality.

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Description

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This pull request:

Creates an anova function to perform one-way ANOVA given an array of continuous values and an array of factors. Support for other input methods will be added.
b
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@stdlib-js/reviewers

Planeshifter

Awesome, Frank! Thanks for all your work. I left some comments on things we should resolve before merging in this pull request.

Planeshifter · 2018-02-04T00:40:16Z

lib/node_modules/@stdlib/math/stats/anova1/README.md

+<!-- /.examples -->
+
+<section class="links">
+


Please add

[mdn-array]: https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Array [mdn-typed-array]: https://developer.mozilla.org/en-US/docs/Web/JavaScript/Typed_arrays

so that the Markdown reference links are not missing their definitions and are rendered correctly.

Planeshifter · 2018-02-04T00:42:50Z

lib/node_modules/@stdlib/math/stats/anova1/README.md

@@ -0,0 +1,140 @@
+# One Way ANOVA
+
+> Perform One-Way ANOVA on given data


Let's change the description to Perform a one-way analysis of variance.

Planeshifter · 2018-02-04T00:43:26Z

lib/node_modules/@stdlib/math/stats/anova1/README.md

+
+### anova1( x, factor\[, ...params]\[, opts] )
+
+For an [array][mdn-array] or [typed array][mdn-typed-array] of numeric values `x` and an [array][mdn-array] of classifications `factor`, one-way anova1 is performed. The hypotheses are given as follows:


Let's revert this undesired change that was introduced when renaming the package: s/anova1/anova.

I am unsure what you mean here. I am taking this to mean the removal of the optional parameters that we discussed after the 200 staff meeting on Tuesday. I will ask about this when we meet tomorrow.

I believe @Planeshifter is referring to the description:

... classifications factor, one-way anova is performed.

Planeshifter · 2018-02-04T00:49:21Z

lib/node_modules/@stdlib/math/stats/anova1/README.md

+
+For an [array][mdn-array] or [typed array][mdn-typed-array] of numeric values `x` and an [array][mdn-array] of classifications `factor`, one-way anova1 is performed. The hypotheses are given as follows:
+
+$$H_{0}: \mu_{1} = \mu_{2} = \dots = \mu_{k}$$


We have a special way of writing formulas so that we can later automatically render the equations using MathJax. For this one, we could do

 

Resolved. Out of curiosity, does the markdown format always revert to MathJax?

Yes, as MathJax is what we use for server-side equation rendering. See

stdlib/lib/node_modules/@stdlib/_tools/utils/tex-equation-to-svg/lib/factory.js

Line 23 in 4b96208

var mathjax = require( 'mathjax-node-sre' );

.

Planeshifter · 2018-02-04T00:52:57Z

lib/node_modules/@stdlib/math/stats/anova1/examples/index.js

@@ -0,0 +1,19 @@
+'use strict';
+
+var ANOVA = require('../lib/make_anova.js');


Let's rename ANOVA to anova1 here.

Planeshifter · 2018-02-04T01:29:46Z

lib/node_modules/@stdlib/math/stats/anova1/lib/mean_table.js

+	var newMean;
+
+
+	if (x.length !== factor.length) {


It's fine to remove this check given since this function is only called inside of make_anova.js (where we have already established that the arrays have the same length) and won't be publicly available.

Ok. This may be useful for future development yet for now I agree with the sentiment. Removed.

Planeshifter · 2018-02-04T01:30:25Z

lib/node_modules/@stdlib/math/stats/anova1/lib/mean_table.js

+function meanTable(x, factor) {
+	var treatments;
+	var factorCount;
+	var meanTable;


Can we rename the meanTable variable? As-is, it has the same name as the function, which can be confusing.

tableOfMeans

You probably don't have to be as descriptive. It would be enough to name the variable out. The meaning of the variable is readily available from the function docs, and, as it stands now, one has to read until function end to know what value is returned from the function.

Planeshifter · 2018-02-04T01:31:42Z

lib/node_modules/@stdlib/math/stats/anova1/lib/index.js

+'use strict';
+
+/**
+* One-Way Analysis of Variance.


One-way analysis of variance.

Planeshifter · 2018-02-04T01:34:04Z

lib/node_modules/@stdlib/math/stats/anova1/test/test.js

+	f = ['frank', 'philipp', 'nugent', 'frank', 'philipp', 'nugent', 'frank', 'philipp', 'nugent', 'frank'];
+	out = anova1(x, f);
+
+	t.equal(out.treatment_df, 2);


Where do these values come from? We should add a comment, e.g. // Tested against R:. Better yet would be to have a script to generate the R fixtures automatically. But we can add that later.

These values came from R testing side by side, forgot to add the R testing fixtures. Will do at a later date.

Planeshifter · 2018-02-04T01:35:17Z

lib/node_modules/@stdlib/math/stats/anova1/lib/make_anova.js

+
+	// Now to make the out object
+	out = {};
+	setReadOnly(out, 'treatment_df', treats.length - 1);


Can we avoid underscores in property names? We could use names like treatSumSq and errMeanSq? Not so sure about the degrees of freedom. What do you think, @frank113 and @kgryte?

I would take inspiration from MATLAB (https://www.mathworks.com/help/stats/anova1.html), including in terms of the output data structures.

@kgryte The MATLAB looks much cleaner than what I have; far more readable. I will update the naming to mirror it. For Prob>F could we simply replace it with p?

Instead of Prob>F, let's use pValue to be consistent with the other stats packages.

Yes, or pValue, whichever is the convention currently used my @Planeshifter elsewhere.

kgryte added Feature Issue or pull request for adding a new feature. Math Issue or pull request specific to math functionality. labels Jan 30, 2018

Planeshifter requested changes Feb 4, 2018

View reviewed changes

frank113 closed this Feb 19, 2018

		@@ -0,0 +1,140 @@
		# One Way ANOVA

		> Perform One-Way ANOVA on given data


		### anova1( x, factor\[, ...params]\[, opts] )

		For an [array][mdn-array] or [typed array][mdn-typed-array] of numeric values `x` and an [array][mdn-array] of classifications `factor`, one-way anova1 is performed. The hypotheses are given as follows:


		For an [array][mdn-array] or [typed array][mdn-typed-array] of numeric values `x` and an [array][mdn-array] of classifications `factor`, one-way anova1 is performed. The hypotheses are given as follows:

		$$H_{0}: \mu_{1} = \mu_{2} = \dots = \mu_{k}$$

		@@ -0,0 +1,19 @@
		'use strict';

		var ANOVA = require('../lib/make_anova.js');

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ANOVA Functionality #148

ANOVA Functionality #148

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frank113 commented Jan 30, 2018

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