Convert missing to a numerical value in Julia 1 - dataframe

I am trying to convert all missing values in a df to a numerical value, e.g. 0 (yes, knowing what I am doing..).
In Julia 0.6 I can write:
julia> df = DataFrame(
cat = ["green","blue","white"],
v1 = [1.0,missing,2.0],
v2 = [1,2,missing]
)
julia> [df[ismissing.(df[i]), i] = 0 for i in names(df)]
And get:
julia> df
3×3 DataFrames.DataFrame
│ Row │ cat │ v1 │ v2 │
├─────┼───────┼─────┼────┤
│ 1 │ green │ 1.0 │ 1 │
│ 2 │ blue │ 0.0 │ 2 │
│ 3 │ white │ 2.0 │ 0 │
If I try it in Julia 0.7 I get instead a very weird error:
MethodError: Cannot convert an object of type Float64 to an object
of type String
I can't get what I am trying to convert to a string ??? Any explanation (and workaround) ?

The reason for this problem is that broadcasting mechanism has changed between Julia 0.6 and Julia 1.0 (and it is used in insert_multiple_entries! function in DataFrames.jl). In the end fill! is called and it tries to do a conversion before checking if the collection is empty.
Actually if you want to do a fully general replacement in place (and I understand you want to) this is a bit complex and less efficient than what you have in Base (the reason is that you cannot rely on checking types of elements in vectors as e.g. you can assign Int to vector of Float64 and they have different types):
function myreplacemissing!(vec, val)
for i in eachindex(vec)
ismissing(vec[i]) && (vec[i] = val)
end
end
And now you are good to go:
foreach(col -> myreplacemissing!(col[2], 0), eachcol(df))

While I appreciate the answer of Bogumil Kaminski (also because now I understood the reasons behind the failure), its proposed solution fails if it happens to exists missing elements in non-numeric columns, e.g.:
df = DataFrame(
cat = ["green","blue",missing],
v1 = [1.0,missing,2.0],
v2 = [1,2,missing]
)
What I can instead do is to use (either or only one, depending on my needs):
[df[ismissing.(df[i]), i] = 0 for i in names(df) if typeintersect(Number, eltype(df[i])) != Union{}]
[df[ismissing.(df[i]), i] = "" for i in names(df) if typeintersect(String, eltype(df[i])) != Union{}]
The advantage is that I can select the type of value I need as "missing replacement" for different type of column (e.g. 0 for a number or "" for a string).
EDIT:
Maybe more readable, thanks again to Begumil's answer:
[df[ismissing.(df[i]), i] = 0 for i in names(df) if Base.nonmissingtype(eltype(df[i])) <: Number]
[df[ismissing.(df[i]), i] = "" for i in names(df) if Base.nonmissingtype(eltype(df[i])) <: String]

Related

ArgumentError: columns argument must be a vector of AbstractVector objects

I want to make a DataFrame in Julia with one column, but I get an error:
julia> using DataFrames
julia> r = rand(3);
julia> DataFrame(r, ["col1"])
ERROR: ArgumentError: columns argument must be a vector of AbstractVector objects
Why?
Update:
I figured out that I could say the following:
julia> DataFrame(reshape(r, :, 1), ["col1"])
3×1 DataFrame
Row │ col1
│ Float64
─────┼──────────
1 │ 0.800824
2 │ 0.989024
3 │ 0.722418
But it's not straightforward. Is there any better way? Why can't I easily create a DataFrame object from a Vector?
Why can't I easily create a DataFrame object from a Vector?
Because it would be ambiguous with the syntax where you pass positional arguments the way you tried. Many popular tables are vectors.
However, what you can write is just:
julia> r = rand(3);
julia> DataFrame(col1=r)
3×1 DataFrame
Row │ col1
│ Float64
─────┼────────────
1 │ 0.00676619
2 │ 0.554207
3 │ 0.394077
to get what you want.
An alternative more similar to your code would be:
julia> DataFrame([r], ["col1"])
3×1 DataFrame
Row │ col1
│ Float64
─────┼────────────
1 │ 0.00676619
2 │ 0.554207
3 │ 0.394077

Keep variables type after using data frame

I'm trying to use kproto() function from R package clustMixType to cluster mixed-type data in Julia, but I'm getting error No numeric variables in x! Try using kmodes() from package.... My data should have 3 variables: 2 continuous and 1 categorical. It seems after I used DataFrame() all the variables became categorical. Is there a way to avoid changing the variables type after using DataFrame() so that I have mixed-type data (continuous and categorical) to use kproto()?
using RCall
#rlibrary clustMixType
# group 1 variables
x1=rand(Normal(0,3),10)
x2=rand(Normal(1,2),10)
x3=["1","1","2","2","0","1","1","2","2","0"]
g1=hcat(x1,x2,x3)
# group 2 variables
y1=rand(Normal(0,4),10)
y2=rand(Normal(-1,6),10)
y3=["1","1","2","1","1","2","2","0","2","0"]
g2=hcat(y1,y2,y3)
#create the data
df0=vcat(g1,g2)
df1 = DataFrame(df0)
#use R function
R"kproto($df1, 2)"
I don't know anything about the R package and what kind of input it expects, but the issue is probably how you construct the data matrix from which you construct your DataFrame, not the DataFrame constructor itself.
When you concatenate a numerical and a string column, Julia falls back on the element type Any for the resulting matrix:
julia> g1=hcat(x1,x2,x3)
10×3 Matrix{Any}:
0.708309 -4.84767 "1"
0.566883 -0.214217 "1"
...
That means your df0 matrix is:
julia> #create the data
df0=vcat(g1,g2)
20×3 Matrix{Any}:
0.708309 -4.84767 "1"
0.566883 -0.214217 "1"
...
and the DataFrame constructor will just carry this lack of type information through rather than trying to infer column types.
julia> DataFrame(df0)
20×3 DataFrame
Row │ x1 x2 x3
│ Any Any Any
─────┼───────────────────────────
1 │ 0.708309 -4.84767 1
2 │ 0.566883 -0.214217 1
...
A simple way of getting around this is to just not concatenate your columns into a single matrix, but to construct the DataFrame from the columns:
julia> DataFrame([vcat(x1, y1), vcat(x2, y2), vcat(x3, y3)])
20×3 DataFrame
Row │ x1 x2 x3
│ Float64 Float64 String
─────┼───────────────────────────────
1 │ 0.708309 -4.84767 1
2 │ 0.566883 -0.214217 1
...
As you can see, we now have two Float64 numerical columns x1 and x2 in the resulting DataFrame.
As an addition to the nice answer by Nils (as the problem is indeed when a matrix is constructed not when DataFrame is created) there is this little trick:
julia> df = DataFrame([1 1.0 "1"; 2 2.0 "2"], [:int, :float, :string])
2×3 DataFrame
Row │ int float string
│ Any Any Any
─────┼────────────────────
1 │ 1 1.0 1
2 │ 2 2.0 2
julia> identity.(df)
2×3 DataFrame
Row │ int float string
│ Int64 Float64 String
─────┼────────────────────────
1 │ 1 1.0 1
2 │ 2 2.0 2

Issue with Left Outer Join in Julia DataFrame

This one has me stumped.
Im trying to join two dataframes in Julia but I get this wierd 'nothing' error. This works on a different machine so Im thinking it could be package problems. I Pkg.rm() everything and re-install but no go.
Julia v1.2
using PyCall;
using DataFrames;
using CSV;
using Statistics;
using StatsBase;
using Random;
using Plots;
using Dates;
using Missings;
using RollingFunctions;
# using Indicators;
using Pandas;
using GLM;
using Impute;
a = DataFrames.DataFrame(x = [1, 2, 3], y = ["a", "b", "c"])
b = DataFrames.DataFrame(x = [1, 2, 3, 4], z = ["d", "e", "f", "g"])
join(a, b, on=:x, kind =:left)
yields
ArgumentError: `nothing` should not be printed; use `show`, `repr`, or custom output instead.
Stacktrace:
[1] print(::Base.GenericIOBuffer{Array{UInt8,1}}, ::Nothing) at ./show.jl:587
[2] print_to_string(::String, ::Vararg{Any,N} where N) at ./strings/io.jl:129
[3] string at ./strings/io.jl:168 [inlined]
[4] #join#543(::Symbol, ::Symbol, ::Bool, ::Nothing, ::Tuple{Bool,Bool}, ::typeof(join), ::DataFrames.DataFrame, ::DataFrames.DataFrame) at /Users/username/.julia/packages/DataFrames/3ZmR2/src/deprecated.jl:298
[5] (::getfield(Base, Symbol("#kw##join")))(::NamedTuple{(:on, :kind),Tuple{Symbol,Symbol}}, ::typeof(join), ::DataFrames.DataFrame, ::DataFrames.DataFrame) at ./none:0
[6] top-level scope at In[15]:4
kind=:inner works fine but :left, :right, and :outer don't.
This is a problem caused by the way Julia 1.2 prints nothing (i.e. that it errors when trying to print it). If you would switch to Julia 1.4.1 the problem will disappear.
However, I can see you are on DataFrames.jl 0.21. In this version join function is deprecated. You should use innerjoin, leftjoin, rightjoin, outerjoin, etc. functions. Then all will work also on Julia 1.2, e.g.:
julia> leftjoin(a, b, on=:x)
3×3 DataFrame
│ Row │ x │ y │ z │
│ │ Int64 │ String │ String? │
├─────┼───────┼────────┼─────────┤
│ 1 │ 1 │ a │ d │
│ 2 │ 2 │ b │ e │
│ 3 │ 3 │ c │ f │

Convert data type string to float in DataFrame

I have a data in string format, when I use DataFrame, it will be in Substring format, but I want it in Float format. What should I do?
x = defect_positions[1:3]
>>>SubString{String}["4.71801", "17.2815", "0.187765"]
>>>SubString{String}["17.3681", "17.1425", "6.13644"]
>>>SubString{String}["0.439987", "0.00231646", "0.404172"]
DataFrame(permutedims(reduce(hcat, x))
x1 x2 x3
SubStrin… SubStrin… SubStrin…
1 4.71801 17.2815 0.187765
2 17.3681 17.1425 6.13644
3 0.439987 0.00231646 0.404172
How can I convert my DataFrame to float?
DataFrame uses the element types of the input collections You should convert your strings to a floating point number type before creating a DataFrame. You can parse a string as a floating number type of your choice with parse.
# we map each `SubString` array in x (`SubString` arrays)
# and parse each entries as `Float64` by broadcasting `parse`
parsed_x = map(i -> parse.(Float64, i), x)
DataFrame(permutedims(reduce(hcat, parsed_x)))
You may also choose to do the conversion after creating the DataFrame with strings.
df = DataFrame(permutedims(reduce(hcat, x))
for i in 1:size(df, 2)
df[i] = parse.(Float64, df[i])
end
df
Both methods give
│ Row │ x1 │ x2 │ x3 │
│ │ Float64 │ Float64 │ Float64 │
├─────┼─────────┼─────────┼──────────┤
│ 1 │ 4.71801 │ 17.2815 │ 0.187765 │
...

Select numerical columns of Julia DataFrame with missing values

I want to select all columns of a DataFrame in which the datatype is a subtype of Number. However, since there are columns with missing values, the numerical column datatypes can be something like Union{Missing, Int64}.
So far, I came up with:
using DataFrames
df = DataFrame([["a", "b"], [1, missing] ,[2, 5]])
df_numerical = df[typeintersect.(colwise(eltype, df), Number) .!= Union{}]
This yields the expected result.
Question
Is there a more simple, idiomatic way of doing this? Possibly simliar to:
df.select_dtypes(include=[np.number])
in pandas as taken from an answer to this question?
julia> df[(<:).(eltypes(df),Union{Number,Missing})]
2×2 DataFrame
│ Row │ x2 │ x3 │
├─────┼─────────┼────┤
│ 1 │ 1 │ 2 │
│ 2 │ missing │ 5 │
Please note that the . is the broadcasting operator and hence I had to use <: operator in a functional form.
An other way to do it could be:
df_numerical = df[[i for i in names(df) if Base.nonmissingtype(eltype(df[i])) <: Number]]
To retrieve all the columns that are subtype of Number, irrelevantly if they host missing data or not.