Add Constructor to FisherExactTest #156
Open
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Add constructor to accept a Matrix as argument.
nalimilan
reviewed
May 17, 2019
src/fisher.jl
Outdated
| @@ -41,10 +45,11 @@ The contingency table is structured as: | |||
| |*Y1*| a | b | | |||
| |*Y2*| c | d | | |||
|
|
|||
| !!! note | |||
| !!! Note: | |||
There was a problem hiding this comment.
This is syntax, not text, so please keep it as-is.
src/fisher.jl
Outdated
| The `show` function output contains the conditional maximum likelihood estimate of the | ||
| odds ratio rather than the sample odds ratio; it maximizes the likelihood given by | ||
| Fisher's non-central hypergeometric distribution. | ||
| The entries must be non-negative integers. |
There was a problem hiding this comment.
Say this in the sentence about contingency table rather than in this note, which is about something else.
There was a problem hiding this comment.
I made all the suggested changes.
Add the suggested changes (constructor for vectors and update documentation).
nalimilan
reviewed
May 26, 2019
|
|
||
| Perform Fisher's exact test of the null hypothesis that the success probabilities ``a/c`` | ||
| and ``b/d`` are equal, that is the odds ratio ``(a/c) / (b/d)`` is one, against the | ||
| alternative hypothesis that they are not equal. | ||
|
|
||
| If `x` is a matrix with at least two rows and columns, it is taken as a two-dimensional | ||
| contingency table. Otherwise, `x` and `y` must be vectors of the same length. The contingency | ||
| table is calculated using `counts` function from the `StatsBase` package. |
There was a problem hiding this comment.
Suggested change
| table is calculated using `counts` function from the `StatsBase` package. | |
| table is calculated using the `counts` function from the `StatsBase` package. |
| FisherExactTest(x[1,1], x[1,2], x[2,1], x[2,2]) | ||
| end | ||
|
|
||
| function FisherExactTest(x::AbstractVector{T}, y::AbstractVector{T}) where T<:Integer |
There was a problem hiding this comment.
Suggested change
| function FisherExactTest(x::AbstractVector{T}, y::AbstractVector{T}) where T<:Integer | |
| function FisherExactTest(x::AbstractVector{<:Integer}, y::AbstractVector{<:Integer}) |
| @@ -73,6 +79,15 @@ struct FisherExactTest <: HypothesisTest | |||
| end | |||
| end | |||
|
|
|||
| function FisherExactTest(x::AbstractMatrix{T}) where T<:Integer | |||
There was a problem hiding this comment.
Suggested change
| function FisherExactTest(x::AbstractMatrix{T}) where T<:Integer | |
| function FisherExactTest(x::AbstractMatrix{<:Integer}) |
|
|
||
| d = counts(x,y) | ||
|
|
||
| FisherExactTest(d) |
There was a problem hiding this comment.
Please check that results are the same for both calls, and that they are equal to what you get when passing a, b, c and d manually.
|
Bump. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
I recently reported an issue #154, since fisher's test works with contingency tables it would be expected to accept a matrix as argument, however it is not implemented. This commit resolves this problem.