Allow Real arguments in R functions and use Julia implementations only

Project.toml

@@ -1,6 +1,6 @@
 name = "StatsFuns"
 uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
-version = "0.9.10"
+version = "0.9.11"
 
 [deps]
 ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
@@ -13,7 +13,7 @@ SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 [compat]
 ChainRulesCore = "1"
 IrrationalConstants = "0.1"
-LogExpFunctions = "0.3"
+LogExpFunctions = "0.3.2"
 Reexport = "1"
 Rmath = "0.4, 0.5, 0.6, 0.7"
 SpecialFunctions = "0.8, 0.9, 0.10, 1.0"

README.md

@@ -40,6 +40,7 @@ log4π,      # log(4π)
 # basicfuns
 xlogx,          # x * log(x), or 0 when x is zero
 xlogy,          # x * log(y), or 0 when x is zero
+xlog1py,        # x * log(1 + y) for x > 0, or 0 when x == 0
 logistic,       # 1 / (1 + exp(-x))
 logit,          # log(x / (1 - x))
 log1psq,        # log(1 + x^2)

src/StatsFuns.jl

@@ -35,6 +35,7 @@ import ChainRulesCore
 @reexport using LogExpFunctions:
     xlogx,          # x * log(x) for x > 0, or 0 when x == 0
     xlogy,          # x * log(y) for x > 0, or 0 when x == 0
+    xlog1py,        # x * log(1 + y) for x > 0, or 0 when x == 0
     logistic,       # 1 / (1 + exp(-x))
     logit,          # log(x / (1 - x))
     log1psq,        # log(1 + x^2)

src/chainrules.jl

@@ -12,9 +12,9 @@ ChainRulesCore.@scalar_rule(
     binomlogpdf(n::Real, p::Real, k::Real),
     @setup(z = digamma(n - k + 1)),
     (
-        digamma(n + 2) - z + log1p(-p) - 1 / (1 + n),
+        ChainRulesCore.NoTangent(),
         (k / p - n) / (1 - p),
-        z - digamma(k + 1) + logit(p),
+        ChainRulesCore.NoTangent(),
     ),
 )
 
@@ -59,7 +59,7 @@ ChainRulesCore.@scalar_rule(
 
 ChainRulesCore.@scalar_rule(
     poislogpdf(λ::Number, x::Number),
-    ((iszero(x) && iszero(λ) ? zero(x / λ) : x / λ) - 1, log(λ) - digamma(x + 1)),
+    ((iszero(x) && iszero(λ) ? zero(x / λ) : x / λ) - 1, ChainRulesCore.NoTangent()),
 )
 
 ChainRulesCore.@scalar_rule(

src/distrs/beta.jl

@@ -1,8 +1,8 @@
 # functions related to beta distributions
 
-import .RFunctions:
-    betapdf,
-    betalogpdf,
+# R implementations
+# For pdf and logpdf we use the Julia implementation
+using .RFunctions:
     betacdf,
     betaccdf,
     betalogcdf,
@@ -12,8 +12,13 @@ import .RFunctions:
     betainvlogcdf,
     betainvlogccdf
 
-# pdf for numbers with generic types
-betapdf(α::Real, β::Real, x::Number) = x^(α - 1) * (1 - x)^(β - 1) / beta(α, β)
+# Julia implementations
+betapdf(α::Real, β::Real, x::Real) = exp(betalogpdf(α, β, x))
 
-# logpdf for numbers with generic types
-betalogpdf(α::Real, β::Real, x::Number) = (α - 1) * log(x) + (β - 1) * log1p(-x) - logbeta(α, β)
+betalogpdf(α::Real, β::Real, x::Real) = betalogpdf(promote(α, β, x)...)
+function betalogpdf(α::T, β::T, x::T) where {T<:Real}
+    # we ensure that `log(x)` and `log1p(-x)` do not error
+    y = clamp(x, 0, 1)
+    val = xlogy(α - 1, y) + xlog1py(β - 1, -y) - logbeta(α, β)
+    return x < 0 || x > 1 ? oftype(val, -Inf) : val
+end

src/distrs/binom.jl

@@ -1,8 +1,8 @@
 # functions related to binomial distribution
 
-import .RFunctions:
-    binompdf,
-    binomlogpdf,
+# R implementations
+# For pdf and logpdf we use the Julia implementation
+using .RFunctions:
     binomcdf,
     binomccdf,
     binomlogcdf,
@@ -12,8 +12,13 @@ import .RFunctions:
     binominvlogcdf,
     binominvlogccdf
 
-# pdf for numbers with generic types
+
+# Julia implementations
 binompdf(n::Real, p::Real, k::Real) = exp(binomlogpdf(n, p, k))
 
-# logpdf for numbers with generic types
-binomlogpdf(n::Real, p::Real, k::Real) = -log1p(n) - logbeta(n - k + 1, k + 1) + k * log(p) + (n - k) * log1p(-p)
+binomlogpdf(n::Real, p::Real, k::Real) = binomlogpdf(promote(n, p, k)...)
+function binomlogpdf(n::T, p::T, k::T) where {T<:Real}
+    m = clamp(k, 0, n)
+    val = betalogpdf(m + 1, n - m + 1, p) - log(n + 1)
+    return 0 <= k <= n && isinteger(k) ? val : oftype(val, -Inf)
+end

src/distrs/chisq.jl

@@ -1,8 +1,8 @@
 # functions related to chi-square distribution
 
-import .RFunctions:
-    chisqpdf,
-    chisqlogpdf,
+# R implementations
+# For pdf and logpdf we use the Julia implementation
+using .RFunctions:
     chisqcdf,
     chisqccdf,
     chisqlogcdf,
@@ -12,14 +12,11 @@ import .RFunctions:
     chisqinvlogcdf,
     chisqinvlogccdf
 
-# pdf for numbers with generic types
-function chisqpdf(k::Real, x::Number)
-  hk = k / 2  # half k
-  1 / (2^(hk) * gamma(hk)) * x^(hk - 1) * exp(-x / 2)
-end
+# Julia implementations
+# promotion ensures that we do forward e.g. `chisqpdf(::Int, ::Float32)` to
+# `gammapdf(::Float32, ::Int, ::Float32)` but not `gammapdf(::Float64, ::Int, ::Float32)`
+chisqpdf(k::Real, x::Real) = chisqpdf(promote(k, x)...)
+chisqpdf(k::T, x::T) where {T<:Real} = gammapdf(k / 2, 2, x)
 
-# logpdf for numbers with generic types
-function chisqlogpdf(k::Real, x::Number)
-  hk = k / 2  # half k
-  -hk * logtwo - loggamma(hk) + (hk - 1) * log(x) - x / 2
-end
+chisqlogpdf(k::Real, x::Real) = chisqlogpdf(promote(k, x)...)
+chisqlogpdf(k::T, x::T) where {T<:Real} = gammalogpdf(k / 2, 2, x)

src/distrs/fdist.jl

@@ -1,8 +1,8 @@
 # functions related to F distribution
 
-import .RFunctions:
-    fdistpdf,
-    fdistlogpdf,
+# R implementations
+# For pdf and logpdf we use the Julia implementation
+using .RFunctions:
     fdistcdf,
     fdistccdf,
     fdistlogcdf,
@@ -12,8 +12,14 @@ import .RFunctions:
     fdistinvlogcdf,
     fdistinvlogccdf
 
-# pdf for numbers with generic types
-fdistpdf(ν1::Real, ν2::Real, x::Number) = sqrt((ν1 * x)^ν1 * ν2^ν2 / (ν1 * x + ν2)^(ν1 + ν2)) / (x * beta(ν1 / 2, ν2 / 2))
+# Julia implementations
+fdistpdf(ν1::Real, ν2::Real, x::Real) = exp(fdistlogpdf(ν1, ν2, x))
 
-# logpdf for numbers with generic types
-fdistlogpdf(ν1::Real, ν2::Real, x::Number) = (ν1 * log(ν1 * x) + ν2 * log(ν2) - (ν1 + ν2) * log(ν1 * x + ν2)) / 2 - log(x) - logbeta(ν1 / 2, ν2 / 2)
+fdistlogpdf(ν1::Real, ν2::Real, x::Real) = fdistlogpdf(promote(ν1, ν2, x)...)
+function fdistlogpdf(ν1::T, ν2::T, x::T) where {T<:Real}
+    # we ensure that `log(x)` does not error if `x < 0`
+    ν1ν2 = ν1 / ν2
+    y = max(x, 0)
+    val = (xlogy(ν1, ν1ν2) + xlogy(ν1 - 2, y) - xlogy(ν1 + ν2, 1 + ν1ν2 * y)) / 2 - logbeta(ν1 / 2, ν2 / 2)
+    return x < 0 ? oftype(val, -Inf) : val
+end

src/distrs/gamma.jl

@@ -1,8 +1,8 @@
 # functions related to gamma distribution
 
-import .RFunctions:
-    gammapdf,
-    gammalogpdf,
+# R implementations
+# For pdf and logpdf we use the Julia implementation
+using .RFunctions:
     gammacdf,
     gammaccdf,
     gammalogcdf,
@@ -12,8 +12,13 @@ import .RFunctions:
     gammainvlogcdf,
     gammainvlogccdf
 
-# pdf for numbers with generic types
-gammapdf(k::Real, θ::Real, x::Number) = 1 / (gamma(k) * θ^k) * x^(k - 1) * exp(-x / θ)
+# Julia implementations
+gammapdf(k::Real, θ::Real, x::Real) = exp(gammalogpdf(k, θ, x))
 
-# logpdf for numbers with generic types
-gammalogpdf(k::Real, θ::Real, x::Number) = -loggamma(k) - k * log(θ) + (k - 1) * log(x) - x / θ
+gammalogpdf(k::Real, θ::Real, x::Real) = gammalogpdf(promote(k, θ, x)...)
+function gammalogpdf(k::T, θ::T, x::T) where {T<:Real}
+    # we ensure that `log(x)` does not error if `x < 0`
+    xθ = max(x, 0) / θ
+    val = -loggamma(k) + xlogy(k - 1, xθ) - log(θ) - xθ
+    return x < 0 ? oftype(val, -Inf) : val
+end

src/distrs/hyper.jl

@@ -1,6 +1,7 @@
 # functions related to hyper-geometric distribution
 
-import .RFunctions:
+# R implementations
+using .RFunctions:
     hyperpdf,
     hyperlogpdf,
     hypercdf,

src/distrs/nbeta.jl

@@ -1,6 +1,7 @@
 # functions related to noncentral beta distribution
 
-import .RFunctions:
+# R implementations
+using .RFunctions:
     nbetapdf,
     nbetalogpdf,
     nbetacdf,

src/distrs/nbinom.jl

@@ -1,6 +1,7 @@
 # functions related to negative binomial distribution
 
-import .RFunctions:
+# R implementations
+using .RFunctions:
     nbinompdf,
     nbinomlogpdf,
     nbinomcdf,

src/distrs/nchisq.jl

@@ -1,6 +1,7 @@
 # functions related to noncentral chi-square distribution
 
-import .RFunctions:
+# R implementations
+using .RFunctions:
     nchisqpdf,
     nchisqlogpdf,
     nchisqcdf,

src/distrs/nfdist.jl

@@ -1,6 +1,7 @@
 # functions related to noncentral F distribution
 
-import .RFunctions:
+# R implementations
+using .RFunctions:
     nfdistpdf,
     nfdistlogpdf,
     nfdistcdf,

src/distrs/ntdist.jl

@@ -1,6 +1,7 @@
 # functions related to noncentral T distribution
 
-import .RFunctions:
+# R implementations
+using .RFunctions:
     ntdistpdf,
     ntdistlogpdf,
     ntdistcdf,

src/distrs/pois.jl

@@ -1,8 +1,8 @@
 # functions related to Poisson distribution
 
-import .RFunctions:
-    poispdf,
-    poislogpdf,
+# R implementations
+# For pdf and logpdf we use the Julia implementation
+using .RFunctions:
     poiscdf,
     poisccdf,
     poislogcdf,
@@ -12,19 +12,11 @@ import .RFunctions:
     poisinvlogcdf,
     poisinvlogccdf
 
-# generic versions
+# Julia implementations
 poispdf(λ::Real, x::Real) = exp(poislogpdf(λ, x))
 
-poislogpdf(λ::T, x::T) where {T <: Real} = xlogy(x, λ) - λ - loggamma(x + 1)
-
-poislogpdf(λ::Number, x::Number) = poislogpdf(promote(float(λ), x)...)
-
-#=
-function poislogpdf(λ::Union{Float32,Float64}, x::Union{Float64,Float32,Integer})
-    if iszero(λ)
-        iszero(x) ? zero(λ) : oftype(λ, -Inf)
-    elseif iszero(x)
-        -λ
-    else
-        -lstirling_asym(x + 1)
-=#
+poislogpdf(λ::Real, x::Real) = poislogpdf(promote(λ, x)...)
+function poislogpdf(λ::T, x::T) where {T <: Real}
+    val = xlogy(x, λ) - λ - loggamma(x + 1)
+    return x >= 0 && isinteger(x) ? val : oftype(val, -Inf)
+end

src/distrs/srdist.jl

@@ -1,6 +1,7 @@
 # functions related to studentized range distribution
 
-import .RFunctions:
+# R implementations
+using .RFunctions:
     srdistcdf,
     srdistccdf,
     srdistlogcdf,

src/distrs/tdist.jl

@@ -1,8 +1,8 @@
 # functions related to student's T distribution
 
-import .RFunctions:
-    tdistpdf,
-    tdistlogpdf,
+# R implementations
+# For pdf and logpdf we use the Julia implementation
+using .RFunctions:
     tdistcdf,
     tdistccdf,
     tdistlogcdf,
@@ -12,8 +12,11 @@ import .RFunctions:
     tdistinvlogcdf,
     tdistinvlogccdf
 
-# pdf for numbers with generic types
-tdistpdf(ν::Real, x::Number) = gamma((ν + 1) / 2) / (sqrt(ν * pi) * gamma(ν / 2)) * (1 + x^2 / ν)^(-(ν + 1) / 2)
+# Julia implementations
+tdistpdf(ν::Real, x::Real) = exp(tdistlogpdf(ν, x))
 
-# logpdf for numbers with generic types
-tdistlogpdf(ν::Real, x::Number) = loggamma((ν + 1) / 2) - log(ν * pi) / 2 - loggamma(ν / 2) + (-(ν + 1) / 2) * log1p(x^2 / ν)
+tdistlogpdf(ν::Real, x::Real) = tdistlogpdf(promote(ν, x)...)
+function tdistlogpdf(ν::T, x::T) where {T<:Real}
+    νp12 = (ν + 1) / 2
+    return loggamma(νp12) - (logπ + log(ν)) / 2 - loggamma(ν / 2) - νp12 * log1p(x^2 / ν)
+end