Summary Tables

You can make different summary tables of your data using the package SummaryTables.jl. SummaryTables.jl supports HTML and LaTeX output.

To write an output from a SummaryTables function to a file, you can show it with the correct MIME type:

tbl = table_one(...)
# save as HTML
open("tbl.html", "w") do io
    show(io, MIME"text/html"(), tbl)
end
# save as LaTeX code
open("tbl.tex", "w") do io
    show(io, MIME"text/latex"(), tbl)
end

table_one

SummaryTables.table_oneFunction
table_one(table, analyses; keywords...)

Construct a "Table 1" which summarises the patient baseline characteristics from the provided table dataset. This table is commonly used in biomedical research papers.

It can handle both continuous and categorical columns in table and summary statistics and hypothesis testing are able to be customised by the user. Tables can be stratified by one, or more, variables using the groupby keyword.

Keywords

  • groupby: Which columns to stratify the dataset with, as a Vector{Symbol}.
  • nonnormal: A vector of column names where hypothesis tests for the :nonnormal type are chosen.
  • minmax: A vector of column names where hypothesis tests for the :minmax type are chosen.
  • tests: a NamedTuple of hypothesis test types to use for categorical, nonnormal, minmax, and normal variables.
  • combine: an object from MultipleTesting to use when combining p-values.
  • show_overall: display the "Overall" column summary. Default is true.
  • show_n: Display the number of rows for each group key next to its label.
  • show_pvalues: display the P-Value column. Default is false.
  • show_testnames: display the Test column. Default is false.
  • show_confints: display the CI column. Default is false.

All other keywords are forwarded to the CellTable constructor, refer to its docstring for details.

Example

using SummaryTables
using Statistics

tbl = [
    :id => [1, 2, 3, 4, 5, 6, 7, 8],
    :sex => ["m", "f", "m", "f", "m", "f", "m", "f"],
    :age => [14, 36, 35, 63, 83, 23, 24, 26],
    :wgt => [52.3, 65.8, missing, 34.2, 80.2, 77.9, 55.0, 66.7],
    :dose => [50, 50, 50, 50, 100, 100, 100, 100],
    :group => [1, 1, 1, 1, 2, 2, 2, 2],
]

table_one(
    tbl,
    [
        :sex => "Sex",
        :age => "Age (years)",
        :wgt => "Weight (kg)",
    ],
    groupby = :group
)
group
Overall 1 2
Sex
f 4 (50%) 2 (50%) 2 (50%)
m 4 (50%) 2 (50%) 2 (50%)
Age (years)
Mean (SD) 38 (23.3) 37 (20.1) 39 (29.4)
Median [Min, Max] 30.5 [14, 83] 35.5 [14, 63] 25 [23, 83]
Weight (kg)
Mean (SD) 61.7 (16) 50.8 (15.9) 70 (11.6)
Median [Min, Max] 65.8 [34.2, 80.2] 52.3 [34.2, 65.8] 72.3 [55, 80.2]
Missing 1 (12.5%) 1 (25%) 0 (0%)

listingtable

SummaryTables.listingtableFunction
listingtable(table, variable;
    rows = [],
    cols = [],
    summarize_rows = [],
    summarize_cols = [],
    variable_header = true,
    celltable_kws...
)

Create a listing table CellTable from table which displays raw values from column variable.

Arguments

  • table: Data source which must be convertible to a DataFrames.DataFrame.
  • variable: Determines which variable's raw values are shown. Can either be a Symbol such as :ColumnA, or alternatively a Pair where the second element is the display name, such as :ColumnA => "Column A".

Keyword arguments

  • rows = []: Grouping structure along the rows. Should be a Vector where each element is a grouping variable, specified as a Symbol such as :Column1, or a Pair, where the first element is the symbol and the second a display name, such as :Column1 => "Column 1". Specifying multiple grouping variables creates nested groups, with the last variable changing the fastest.
  • cols = []: Grouping structure along the columns. Follows the same structure as rows.
  • summarize_rows = []: Specifies functions to summarize variable with along the rows. Should be a Vector, where each entry is one separate summary. Each summary can be given as a Function such as mean or maximum, in which case the display name is the function's name. Alternatively, a display name can be given using the pair syntax, such as mean => "Average". By default, one summary is computed over all groups. You can also pass Symbol => [...] where Symbol is a grouping column, to compute one summary for each level of that group.
  • summarize_cols = []: Specifies functions to summarize variable with along the columns. Follows the same structure as summarize_rows.
  • variable_header = true: Controls if the cell with the name of the summarized variable is shown.

All other keywords are forwarded to the CellTable constructor, refer to its docstring for details.

Example

using Statistics

tbl = [
    :Apples => [1, 2, 3, 4, 5, 6, 7, 8],
    :Batch => [1, 1, 1, 1, 2, 2, 2, 2],
    :Checked => [true, false, true, false, true, false, true, false],
    :Delivery => ['a', 'a', 'b', 'b', 'a', 'a', 'b', 'b'],
]

listingtable(
    tbl,
    :Apples => "Number of apples",
    rows = [:Batch, :Checked => "Checked for spots"],
    cols = [:Delivery],
    summarize_cols = [sum => "overall"],
    summarize_rows = :Batch => [mean => "average", sum]
)

Example

listingtable(
    tbl,
    :wgt => "Weight (kg)",
    rows = [:dose => "Dose (mg)", :sex => "Sex", :id => "ID"],
    summarize_rows = :sex => [mean ∘ skipmissing => "Mean", (x -> count(!ismissing, x)) => "Nonmissing"]
)
Dose (mg) Sex ID Weight (kg)
50 f 2 65.8
4 34.2
Mean 50
Nonmissing 2
50 m 1 52.3
3 missing
Mean 52.3
Nonmissing 1
100 f 6 77.9
8 66.7
Mean 72.3
Nonmissing 2
100 m 5 80.2
7 55
Mean 67.6
Nonmissing 2

summarytable

SummaryTables.summarytableFunction
summarytable(table, variable;
    rows = [],
    cols = [],
    summary = [],
    variable_header = true,
    celltable_kws...
)

Create a summary table CellTable from table, which summarizes values from column variable.

Arguments

  • table: Data source which must be convertible to a DataFrames.DataFrame.
  • variable: Determines which variable from table is summarized. Can either be a Symbol such as :ColumnA, or alternatively a Pair where the second element is the display name, such as :ColumnA => "Column A".

Keyword arguments

  • rows = []: Grouping structure along the rows. Should be a Vector where each element is a grouping variable, specified as a Symbol such as :Column1, or a Pair, where the first element is the symbol and the second a display name, such as :Column1 => "Column 1". Specifying multiple grouping variables creates nested groups, with the last variable changing the fastest.
  • cols = []: Grouping structure along the columns. Follows the same structure as rows.
  • summary = []: Specifies functions to summarize variable with. Should be a Vector, where each entry is one separate summary. Each summary can be given as a Function such as mean or maximum, in which case the display name is the function's name. Alternatively, a display name can be given using the pair syntax, such as mean => "Average". By default, one summary is computed over all groups. You can also pass Symbol => [...] where Symbol is a grouping column, to compute one summary for each level of that group.
  • variable_header = true: Controls if the cell with the name of the summarized variable is shown.

All other keywords are forwarded to the CellTable constructor, refer to its docstring for details.

Example

using Statistics

tbl = [
    :Apples => [1, 2, 3, 4, 5, 6, 7, 8],
    :Batch => [1, 1, 1, 1, 2, 2, 2, 2],
    :Delivery => ['a', 'a', 'b', 'b', 'a', 'a', 'b', 'b'],
]

summarytable(
    tbl,
    :Apples => "Number of apples",
    rows = [:Batch],
    cols = [:Delivery],
    summary = [length => "N", mean => "average", sum]
)

Example

summarytable(
    tbl,
    :wgt => "Weight (kg)",
    rows = [:sex => "Sex"],
    cols = [:dose => "Dose (mg)"],
    summary = [mean ∘ skipmissing => "Mean", (x -> count(!ismissing, x)) => "Nonmissing"]
)
Dose (mg)
50 100
Sex Weight (kg)
f Mean 50 72.3
Nonmissing 2 2
m Mean 52.3 67.6
Nonmissing 1 2