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Add Constructor to FisherExactTest #156

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Add Constructor to FisherExactTest #156

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3492754
Add Constructor to FisherExactTest
LawrenceMz May 13, 2019
037a393
Update FisherExactTest documentation
LawrenceMz May 13, 2019
87905cb
Constructor for vectors
LawrenceMz May 19, 2019
ce7d35a
Update documentation
LawrenceMz May 19, 2019
150cda6
Test for new constructors
LawrenceMz May 19, 2019
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11 changes: 10 additions & 1 deletion src/fisher.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -26,11 +26,15 @@ export FisherExactTest

"""
FisherExactTest(a::Integer, b::Integer, c::Integer, d::Integer)
FisherExactTest(x)

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.

See [`pvalue(::FisherExactTest)`](@ref) and [`confint(::FisherExactTest)`](@ref) for details
about the computation of the default p-value and confidence interval, respectively.

Expand All @@ -41,10 +45,11 @@ The contingency table is structured as:
|*Y1*| a | b |
|*Y2*| c | d |

!!! note
!!! Note:
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This is syntax, not text, so please keep it as-is.

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.
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Say this in the sentence about contingency table rather than in this note, which is about something else.

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I made all the suggested changes.


Implements: [`pvalue(::FisherExactTest)`](@ref), [`confint(::FisherExactTest)`](@ref)

Expand Down Expand Up @@ -73,6 +78,10 @@ struct FisherExactTest <: HypothesisTest
end
end

function FisherExactTest(x::AbstractMatrix{T}) where T<:Integer
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Suggested change
function FisherExactTest(x::AbstractMatrix{T}) where T<:Integer
function FisherExactTest(x::AbstractMatrix{<:Integer})

FisherExactTest(x[1,1], x[1,2], x[2,1], x[2,2])
end

testname(::FisherExactTest) = "Fisher's exact test"
population_param_of_interest(x::FisherExactTest) = ("Odds ratio", 1.0, x.ω) # parameter of interest: name, value under h0, point estimate
default_tail(test::FisherExactTest) = :both
Expand Down