Add `spreadmissings` #122

pdeffebach · 2020-10-31T17:08:24Z

Adds behavior described in #121

Implementation is easy enough to follow

function (f::SpreadMissings{F})(xs...) where {F}
    @assert all(x -> x isa AbstractVector, xs)

    x1 = first(xs)
    @assert all(x -> length(x) == length(x1), xs)

    if any(x -> x isa AbstractVector{>:Missing}, xs)
        nonmissinginds = collect(eachindex(skipmissings(xs...)))
        # TODO: narrow the type of the `view` to exclude `Missing`
        res = f.f((view(x, nonmissinginds) for x in xs)...)

        out = Vector{Union{Missing, eltype(res)}}(missing, length(x1))
        out[nonmissinginds] .= res

        return out
    else
        return f.f(xs...)
    end
end

pdeffebach · 2020-11-05T01:07:52Z

I just did some re-factoring. New implementation is

function (f::SpreadMissings{F})(xs...) where {F}
    if any(x -> x isa AbstractVector{>:Missing}, xs)
        vecs = Base.filter(x -> x isa AbstractVector, xs)
        s = skipmissings(vecs...)
        vecs_counter = 1
        newargs = ntuple(length(xs)) do i
            if xs[i] isa AbstractVector
                t = s[vecs_counter]
                vecs_counter += 1
            else
                t = xs[i]
            end
            t
        end

        res = f.f(newargs...)

        if res isa AbstractVector
            out = Vector{Union{Missing, eltype(res)}}(missing, length(first(vecs)))
            out[collect(eachindex(first(s)))] .= res
        else
            out = Vector{Union{Missing, typeof(res)}}(missing, length(first(vecs)))
            out[collect(eachindex(first(s)))] .= Ref(res)
        end

        return out
    else
        return f.f(xs...)
    end
end

Miraculously, this infers function infers.

pdeffebach · 2020-11-05T02:20:05Z

Okay after playing around with this here's what I think an API should be. Consider the call

f(v1::Vector, v2::Vector, s::Scalar)

Recall that skipmissings(x, y) returns a tuple of iterators sx, sy that iterate through x and y where both indices are not missing. We need

skipfun(f) such that skipfun(f)(v1, v2, s) is

sv1, sv2 = skipmissings(v1, v2)
f(sv1, sv2, x)

It automatically finds the vector values and calls skipmissings on those. Maybe we can dig into the broadcasting infrastructure to make this work more intelligently?

spreadmissings, defined in this PR. spreadmisings(f)(v1, v2, s) is equivalent to

sv1, sv2 = skipmissings(v1, v2)
res = f(sv1, sv2, x)
if res isa AbstractVector
    out = Vector{Union{Missing, eltype(res)}}(missing, length(v1))
    out[collect(eachindex(sv1))] .= res
else
    out = Vector{Union{Missing, typeof(res)}}(missing, length(v1))
    out[collect(eachindex(sv1))] .= Ref(res)
end
out

The problem with spreadmissings is that it is restricted to Vectors and it's hard to figure out all the types that really need to be "spread". Consider, for example

function maketable(v1, v2, s)
    # stuff which errors on missing values
    (n1 = v1 .+ v2 .* s, n2 = v1 .- v2 .* s)
end

If we use spreadmissings logic, we know that this should be a named tuple of vectors each of length v1. Unfortunately we can't just special case a named tuple of vectors to be the kind of thing that "spreads". I mean, maybe we can, but it's easy to see how that kind of logic can get more and more complicated.

pdeffebach · 2020-11-05T20:02:54Z

We also need

passmissingfalse which returns false instead of missing, for use in filtering and && etc.
spreadmissingfalse which fills in false instead of missing in the missing indices.

matthieugomez · 2020-11-07T18:38:22Z

Maybe it would be more elegant to restrict it to functions for which all arguments are AbstractVector, i.e. @assert all(x -> x isa AbstractVector, xs).
AFAIU, this does not hurt usability in DataFrames since users need to create anonymous function with columns anyway. Same thing for DataFramesMeta.

pdeffebach · 2020-11-07T18:41:14Z

Thats what I had initially. Then I thought about broadcasting and how it automatically figures out what should be broadcasted. So I updated this PR to emulate that behavior a little.

matthieugomez · 2020-11-07T18:57:07Z

Another thing is that spreadmissing always returns a Vector, but some functions may return AbstractVectors that are not Vectors (e.g. . cut returns a CategoricalVector)

So it may be better to use in spreadmissing a function like extend_missings which extends an AbstractVector to accept missings, i.e.

function extend_missings(v::AbstractVector{T}, esample::BitVector)
   out = Vector{Union{Missing, T}(missing, length(esample))
   out[esample] = v
   return out
end

This would allow external packages to define specialized methods of extend_missings for their particular type.

pdeffebach · 2020-11-07T19:02:01Z

That's a good point. Maybe I will try to formalize all of this behavior into a separate package first and see how it goes.

matthieugomez · 2020-11-07T19:04:30Z

It'd be great to have such a function! It's just hard to find the right abstraction, so it's good to experiment.

nalimilan · 2020-11-09T09:14:46Z

Requiring packages to extend extend_missings won't really work as they would all need to add a dependency on Missings, which most won't want to do. Why not just call allowmissing(res), which uses similar and should therefore return the right array type? for the case where a scalar is returned, similar(vecs[1], Union{Missing, typeof(res)}) shouldn't be too bad (at least it will return a CategroicalArray if res isa CategoricalValue).

src/Missings.jl

pdeffebach · 2020-11-30T01:42:18Z

which uses similar and should therefore return the right array type? for the case where a scalar is returned, similar(vecs[1], Union{Missing, typeof(res)}) shouldn't be too bad (at least it will return a CategroicalArray if res isa CategoricalValue).

I changed it, but I don't think the implementation is quite correct. In particular, I'm worried about the scalar case. I'm not sure what the importance of the first argument in similar(x, eltype, length) is. What's the purpose of vecs[1] in similar(vec[1], Union{typeof(res), Missing})?

pdeffebach · 2021-04-25T14:48:14Z

I think it would be totally awesome if @nalimilan or @quinnj took over this PR. It's over my head to deal with all the performance considerations and necessary benchmarking.

If possible maybe we can merge it as an undocumented feature and see if it works?

src/Missings.jl

nalimilan · 2021-05-17T13:17:22Z

src/Missings.jl

+    else
+        return f.f(xs...; kwargs...)
+    end


How about throwing an error in this case for now? It doesn't seem very useful.

No I disagree. I want people to be able to code defensively with this tool. throwing an error would defeat the purpose a bit.

OK. Something that occurred to me though: should we do something special if one of the non-vector arguments is missing (like returning missing)? Should we reserve this behavior for the future in case we want spreadmissings to be a more general version of passmissing?

I don't think so. We definitely can't return missing, we would have to return a vector of missings, which seems very restrictive.

Not sure what "restrictive" means here. That would be similar to e.g. broadcast(+, missing, [1, 2, 3]).

Whether that makes sense depends on what f does with its inputs, but I can't find examples of functions to which one would pass one or more vectors plus a missing argument and would not expect the resulting vector to be full of missings. So reserving the situation where one argument is missing could be a good idea in case we want to handle it later.

What do you think? At least throwing an error if any of the inputs is missing for now doesn't seem too problematic?

src/Missings.jl

bkamins · 2021-06-28T07:59:25Z

@nalimilan - please ping me when the first round of comments is resolved. Then I will review. Thank you!

Co-authored-by: Milan Bouchet-Valat <nalimilan@club.fr>

src/Missings.jl

pdeffebach · 2021-07-25T14:46:00Z

Okay after the merging of @rtransform etc. in DataFramesMeta, this will be my next focus.

just to confirm, do we want this new feature to live in Missings.jl for now? Or do we want me to move all this stuff to DataFramesMeta.

bkamins · 2021-07-25T18:47:53Z

Can you please summarize briefly the consensus how things should work? Thank you!

CameronBieganek · 2023-12-01T21:05:47Z

(Quoting myself.)

There might be a natural way to design the API so that users can collect if they need to.

Of course, skipmissings is already fairly natural in this regard. For example, if you want to use cor, you can do this:

cor(collect.(skipmissings(x, y))...)

But I don't think you've responded to the scenario with DataFrames? A key benefit of the current approach is that you don't lose length information, the way you would with skipmissings.

Well, to be honest, I'm more interested in reduction functions. I feel like the need for a uniform missing-skipping syntax for reduction functions is more pressing than the need to handle functions like center and zscore.

But I did address the "DataFrames scenario" with non-reduction functions. I proposed either writing them by hand, like this,

transform(df, :x => (x -> x .- mean(skipmissing(x))) => :x_c)

or adding keyword arguments to zscore, etc. I also said "But perhaps there's a more elegant way to do this. I will continue to think about it."

I think trying to combine the behavior for reduction functions and non-reduction functions into one function produces a complicated, hard to understand function.

jariji · 2023-12-01T21:18:39Z

Making cor accept SkipMissings would make

cor(collect.(skipmissings(x, y))...)

look a little nicer without the collect.

pdeffebach · 2023-12-01T21:21:44Z

Making cor accept SkipMissings would make
cor(collect.(skipmissings(x, y))...)

Base devs rejected that proposal. see here. Looking back, I agree with the logic a bit more. Vectors are a natural way to enforce indices matching, whereas iterators will never be as clear.

CameronBieganek · 2023-12-01T21:28:08Z

Yeah, it's debatable. But it seems like they might be open to a new method like cor(itr), where itr is an iterator of iterators. (Where the inner iterators are observations.)

CameronBieganek · 2023-12-01T21:54:41Z

Copying over from Discourse... It's a little goofy, but we could signal to skipm that an argument needs to be collected. Something like this:

Setup:

struct NeedsArray{T}
    x::T
end

const ⋆ = NeedsArray

What it would look like:

skipm(cor)(⋆x, ⋆y)

CameronBieganek · 2023-12-01T22:38:13Z

Wow, the cor(x::AbstractVector) = 1 method blows up any chance of having a cor(itr) method, where itr iterates observations. 😭

In view of that unfortunate situation, perhaps the Base devs could be convinced to allow cor(itr1, itr2).

nalimilan · 2023-12-01T22:49:20Z

@CameronBieganek I think you should develop your use cases and/or make a detailed proposal somewhere else. You have hijacked a pull request about a well-defined function which was in the final review phase. This is not a design issue intended at experimenting with various ideas. The result is a confusing discussion which hasn't allowed me to grasp what are your main requirements.

CameronBieganek · 2023-12-01T22:58:19Z

Apologies for hijacking a pull request. I have concerns about the design and usability of spreadmissings, which led me to suggest alternatives.

Co-authored-by: Milan Bouchet-Valat <nalimilan@club.fr>

…issings

pdeffebach · 2023-12-09T21:33:42Z

@nalimilan I have fixed all the issues you have highlighted. Thank you for your feedback!

Three things to keep in mind

spreadmissings currently hurts type stability.

julia> using Statistics

julia> using Statistics, Missings

julia> function foo(x)
           spreadmissings(mean)(x)
       end;

julia> @code_warntype foo([1, missing])
MethodInstance for foo(::Vector{Union{Missing, Int64}})
  from foo(x) @ Main REPL[27]:1
Arguments
  #self#::Core.Const(foo)
  x::Vector{Union{Missing, Int64}}
Body::Any
1 ─ %1 = Main.spreadmissings(Main.mean)::Core.Const(Missings.SpreadMissings{typeof(mean)}(Statistics.mean, :default))
│   %2 = (%1)(x)::Any
└──      return %2

I've determined this is not due to the fact that spread is a Symbol (as opposed to specialized structs) and not due to the fact that sometimes we return a vector without missing, in the case of no missing values in the inputs.

How much should I worry about this? Is there anything we can do? Maybe I could re-write the function so it dispatches on SpreadMIssings{F, spread}?

EDIT:

I' played around with this and it looks like creating specialized structs does fix the type stability issues. However I haven't been able to have both the Symbol keyword argument for the "spread" behavior and type stability. I have pushed an implementation that I thought might work but doesn't.

SpreadMissings(f, spread::Val{:default}) = SpreadMissings(f, SpreadDefault())
SpreadMissings(f, spread::Val{:nonmissing}) = SpreadMissings(f, SpreadNonMissing())
SpreadMissings(f, spread::Val{:none}) = SpreadMissings(f, SpreadNone())

function spreadmissings(f; spread::Symbol = :default)
    SpreadMissings(f, Val(spread))
#   throw(ArgumentError("`spread` must be one of `:default`, `:nonmissing`, or `:none`"))
end

Is there something we can do to make this work? I don't really want to make users write SpreadDefault or even define a variable spreaddefault. Those both seem kind of cumbersome.

EDIT 2: Maybe it's impossible to get type stability under any conditions. I'm not 100% sure.

I have added an error if missing is a positional or keyword argument. We can relax this in the future and propagate missing but I'm a little nervous about adding that behavior right now.
Should we have a spread = :all option? So that if there is a scalar output, it gets spread across the whole vector? That way it emulates skipmissing more. See my example above about @transform :m = mean(skipmissing(:x)) vs @transform @spreadmissings :m = mean(:x)

nalimilan · 2023-12-10T17:58:42Z

Have you tried adding @inlined to spreadmissings(f; spread::Symbol = :default) (and maybe @noinline to others)? At least that approach works for levels in DataAPI. You could also try using if spread === :default; SpreadMissings(f, SpreadDefault()) and so on inside that function.

spread=:all could be useful indeed. I just hope things don't get too complex to grasp.

jariji · 2023-12-10T18:49:25Z

I just hope things don't get too complex to grasp.

I'm well past that point. It would be easier for me to follow if each of these methods had its own function name rather than dispatching on keyword arguments.

pdeffebach · 2023-12-12T18:49:40Z

@nalimilan this is ready for a review!

The inference failures were due to a lack of function barriers. Adding spread to the type parameter of SpreadMissings and using dispatch to control behavior rather than if...else works well. Type hints in the smaller functions also appear helpful.

I've filed an issue upstream for a lack of type inference with mean. See here. The SubArray hack does not go as far as I would like, and still produces a lot of Union{Missing, Float64} inference. But that's okay since it's a small union.

I also added spread = :all

For scalar outputs, spreads the output along the full length of the input vector
For vector outputs, throws an error. This is because the inner function knows nothing about the full length of the input vectors to the outer function. Any scenario where the output vector matches the length of the input vectors is coincidence and the indices wouldn't correspond.

It's worth emphasizing again that if none of the inputs are vectors, then behavior is entirely unaffected. So no error is thrown if the inputs are not vectors and the output is a vector.

This behavior is indeed complicated, but it's all in the docstring.

pdeffebach · 2024-01-19T15:52:06Z

@nalimilan Bumping this. Remember that we ultimately want to try this out in DataFramesMeta.jl first. I will port the PR over there eventually but am editing it here.

nalimilan

Sorry. Here are more comments.

src/Missings.jl

nalimilan · 2024-01-22T20:33:56Z

src/Missings.jl

+function spread_missing(
+    res::AbstractVector{T},
+    vecs::Tuple,
+    nonmissinginds::AbstractVector{<:Integer},
+    nonmissingmask::AbstractVector{<:Bool})::AbstractVector{Union{Missing, T}} where {T}


Suggested change

function spread_missing(

res::AbstractVector{T},

vecs::Tuple,

nonmissinginds::AbstractVector{<:Integer},

nonmissingmask::AbstractVector{<:Bool})::AbstractVector{Union{Missing, T}} where {T}

function spread_missing(res::AbstractVector{T},

vecs::Tuple,

nonmissinginds::AbstractVector{<:Integer},

nonmissingmask::AbstractVector{<:Bool})::AbstractVector{Union{Missing, T}} where {T}

Same below (for consistency with current style of the package).

nalimilan · 2024-01-22T20:35:16Z

src/Missings.jl

+    nonmissingmask::AbstractVector{<:Bool})::AbstractVector{Union{Missing, T}} where {T}
+
+    if length(res) != length(nonmissinginds)
+        s = "When spreading a vector result with `spread=$(S)`, " *


S doesn't exist here. Apparently also needs testing.

nalimilan · 2024-01-22T20:38:31Z

src/Missings.jl

+        maybespread_missing(f, newargs, new_kwargs, vecs, nonmissinginds, nonmissingmask)
+    # There is at least one vector, but none of the vectors can contain missing
+    elseif any(x -> x isa AbstractVector, xs)
+        vecs = Base.filter(x -> x isa AbstractVector, xs)


Still applies.

nalimilan · 2024-01-22T20:43:59Z

src/Missings.jl

+julia> xmiss = [10, 20, 30, missing];
+
+julia> ymiss = [missing, 500, 400, 300];


Why not reuse the previous objects?

nalimilan · 2024-01-22T21:08:30Z

src/Missings.jl

+        if !(spread isa AbstractSpread)
+            throw(ArgumentError("spread must be either SpreadDefault(), SpreadNonMissing(), or SpreadNone()"))
+        end


This cannot happen.

Suggested change

if !(spread isa AbstractSpread)

throw(ArgumentError("spread must be either SpreadDefault(), SpreadNonMissing(), or SpreadNone()"))

end

nalimilan · 2024-01-22T21:11:28Z

src/Missings.jl

+    2. `fillmean_skip` returns a vector which does not allow for `missing`, while
+       `spreadmissings(fillmean)` does.
+
+    Use the keyword `spread = :all` to emulate the `skipmissing` behavior.


Show an example?

nalimilan · 2024-01-22T21:12:00Z

test/.ipynb_checkpoints/runtests-checkpoint.jl

@@ -0,0 +1,227 @@
+using Test, SparseArrays, Missings


What's this file?

nalimilan · 2024-01-22T21:12:20Z

test/spreadmissings.jl

+function right_vec(args...; kwargs...)
+    kwargs_vals = values(values(kwargs))
+    xs = tuple(args..., kwargs_vals...)
+    vecs = Base.filter(x -> x isa AbstractVector, xs)


Suggested change

vecs = Base.filter(x -> x isa AbstractVector, xs)

vecs = filter(x -> x isa AbstractVector, xs)

nalimilan · 2024-01-22T21:22:35Z

test/spreadmissings.jl

+    t = spreadmissings(categorical)(x)
+    @test t ≈ categorical([1, 2, 3, missing])
+    @test typeof(t) == typeof(categorical([1, 2, 3, missing]))
+end



Can you add tests that inference works?

Co-authored-by: Milan Bouchet-Valat <nalimilan@club.fr>

CameronBieganek · 2024-02-11T23:28:21Z

src/Missings.jl

+    P = typeof(a) # Type of parent array
+    I = Tuple{typeof(nonmissinginds)} # Type of the non-missing indices
+    L = Base.IndexStyle(a) === IndexLinear # If the type supports fast linear indexing
+    SubArray{T, N, P, I, L}(a, (nonmissinginds,), 0, 1)


The docstring for SubArray makes no mention of contructors, and in fact says "Construct SubArrays using the view function." So this direct usage of a SubArray constructor is usage of undocumented Base internals that could change in any minor or patch release.

Yeah, that's probably true.

I think it will be worthwhile to make our own array type that does this better... hopefully it's not too hard.

Can be relevant – my SentinelViews.jl package does kinda the opposite. It defines a view type that propagates the sentinel value from indices to the results, sentinelview([10, 20, 30], [1, nothing, 3]) == [10, nothing, 30].
It was reasonably straightforward to implement, as should be the "typesubtract view" needed here. With the obvious downside that ::SubArray function dispatches won't be triggered.

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Release v1.0 #115

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@where can't deal with NAs JuliaData/DataFramesMeta.jl#58

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Make dot handle missings JuliaLang/julia#40769

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Add @subset JuliaData/DataFramesMeta.jl#263

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fix mask

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Update src/Missings.jl

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Inference failure on mean with a subarray JuliaStats/Statistics.jl#160

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		julia> xmiss = [10, 20, 30, missing];

		julia> ymiss = [missing, 500, 400, 300];

	if !(spread isa AbstractSpread)
	throw(ArgumentError("spread must be either SpreadDefault(), SpreadNonMissing(), or SpreadNone()"))
	end

	vecs = Base.filter(x -> x isa AbstractVector, xs)
	vecs = filter(x -> x isa AbstractVector, xs)

Add spreadmissings #122

Are you sure you want to change the base?

Add spreadmissings #122

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Add `spreadmissings` #122

Add `spreadmissings` #122

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