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Being inserted in automatic reporting is the ultimate goal of crosstables.
There are two cases to consider:
officer
The real power of crosstable
comes out when used with
David Gohel’s awesome package officer
,
which allows to automatically create MS Word documents.
For instance, let’s try to create a document like this:
You can also download this example here.
This code will produce the example above.
First, we create 3 crosstables using available datasets, along with a
ggplot. Then, we start a document (using
officer::read_docx()
), add some titles and paragraphs,
incorporate our tables and our plot, along with legends, and add some
page breaks. Note that the legends have a bookmark
argument
that can be referred to in the text for automatic numbering.
library(officer)
library(ggplot2)
ct1=crosstable(iris, by=Species, test=TRUE)
ct2=crosstable(mtcars2, c(mpg,cyl,disp), by=am, effect=TRUE,
total="both", showNA="always")
ct3=crosstable(esoph)
crosstable_options(
crosstable_fontsize_body=8,
crosstable_padding_v=0,
crosstable_units="cm"
)
my_plot = ggplot(data = iris ) +
geom_point(mapping = aes(Sepal.Length, Petal.Length))
doc = read_docx() %>% #default template
body_add_title("Dataset iris (nrow={nrow(iris)})", 1) %>%
body_add_title("Not compacted", 2) %>%
body_add_normal("Table \\@ref(table_autotest) is an example. However, automatic
testing is bad and I should feel bad.") %>%
body_add_crosstable(ct1) %>%
body_add_table_legend("Automatic testing is bad", bookmark="table_autotest") %>%
body_add_normal() %>%
body_add_normal("Let's add a figure as well. <br> You can see in Figure \\@ref(fig_iris)
that sepal length is somehow correlated with petal length.") %>%
body_add_figure_legend("Relation between Petal length and Sepal length",
bookmark="fig_iris") %>%
body_add_gg2(my_plot, w=14, h=10, scale=1.5) %>%
body_add_break() %>%
body_add_title("Compacted", 2) %>%
body_add_normal("When compacting, you might want to remove the test names.") %>%
body_add_crosstable(ct1, compact=TRUE, show_test_name=FALSE) %>%
body_add_break() %>%
body_add_title("Dataset mtcars2", 1) %>%
body_add_normal("This dataset has {nrow(ct3)} rows and {x} columns.",
x=ncol(ct3)) %>%
body_add_normal("Look, there are labels!") %>%
body_add_crosstable(ct2, compact=TRUE)
For demonstration purposes, I tried to cover as many features as possible, so it contains multiple syntaxes for the same result. Of course, you should use whatever syntax you are most comfortable with.
You can find other useful functions in the references.
To see the resulting Word document, use:
While you are still working on your code, you might want to omit the
name so that you open the docx file in a temporary file for a quick peek
(write_and_open(doc)
). This will prevent the errors that
happen when the file is already open.
You can also use print(doc, "vignette_officer.docx")
if
you don’t want the file to open right away.
Here is a brief description of the functions used in this example:
officer::read_docx()
: creates a bare MS Word
documentbody_add_title()
: adds a title paragraph of any
levelbody_add_normal()
: adds a normal style paragraph. You
can also incorporate variables using the syntax {nrow(ct3)}
and references using the syntax \\@ref(my_bookmark)
.body_add_crosstable()
: adds a crosstablebody_add_figure_legend()
and
body_add_table_legend()
: adds a figure/table legend. The
bookmark
is the key that can be added elsewhere in
body_add_normal()
.body_add_gg2()
: adds a ggplot. Unlike
officer::body_add_gg()
, you can change the unit using the
units
argument or the options
options(crosstable_units="cm")
.Browse https://davidgohel.github.io/officer/ for more insight
about how you can use {officer}
.
This is great, but large tables will unfortunately overflow your document.
This is a (known)
limitation that cannot be fixed using R
.
You would have to use MS Word autofit tools on each table one by one
(Table Tools > Layout > AutoFit > AutoFit Window
),
which can be really tedious.
But fear not! You can use a MS Word macro to do the job for you. Here is how:
In the R console, run generate_autofit_macro()
to
generate the file crosstable_autofit.bas
in your working
directory.
In MS Word, press Alt+F11 to open the VB Editor.
In the Editor, go to File
> Import
or press Ctrl+M
to open the import dialog, and import
crosstable_autofit.bas
. There should now be a
“CrosstableMacros” module in the “Normal” project.
Run the macro, either from the VB Editor or from
View
> Macros
> View Macros
> Run
.
This process will make the macro accessible from any Word file on
this computer. Note that, in the Editor, you can also drag the module to
your document project to make the macro accessible only from this file.
The file will have to be named with the docm
extension
though.
Crosstables uses Word styles to operate at full power .
Here, I used the default template of
officer::read_docx()
that comes with default styles. In
your own custom template, you can edit all styles (for instance you can
make “Normal” have a bold font of size 8) and add your own.
The best example here is body_add_list()
, which is
supposed to add a bullet list. Unfortunately, the default template does
not come with list styles so you will have to add one to your custom
template before using it:
doc = read_docx("my_template.docx) %>% #your custom template
body_add_list(c("this is item 1", "this is item 2"), style="bullet")
#alternatively, you can define the style globally and use the ordered parameter
options(crosstable_style_list_unordered="bullet")
options(crosstable_style_list_ordered="numbered")
doc = read_docx("my_template.docx) %>%
body_add_list(c("this is item 1", "this is item 2"), ordered=FALSE)
See ?crosstable_options
for a list of all styles you can
specify globally and use officer::styles_info(doc)
to see
which one are available in your template.
Note that you might sometimes encounter the error “Error: could not match any style named ‘xxx’” if you are not careful.
Depending on your version of {officer}
, Word will ask
you to update the fields
During the opening of the document, MS Word might ask you to
“update the fields”, to which you should answer “Yes”. If it does not
ask or if you answer “No”, the legends added with
body_add_table_legend()
or
body_add_figure_legend()
might have no actual numbers
displayed.
In this case, you have to manually update the references inside MS Word:
select all (+), then update (), sometimes twice. You might even need to
do this several times. See ?body_add_legend
for more
insight.
Be aware that you unfortunately cannot reference a bookmark more
than once using this method. Writing:
body_add_normal("Table \\@ref(iris_col1) is about flowers. I like this Table \\@ref(iris_col1).")
will prevent all the numbering from applying.
Rmarkdown
Knitting (knitr::knit()
or via RStudio)
this Rmd
code also creates a MS-Word file. Here, you can
use the power of bookdown
to generate the automatic
numbering of the tables.
---
title: "Iris"
output: bookdown::word_document2
---
```{r setup, include=FALSE}
library(crosstable)
library(flextable)
```
Table iris is given in Table \@ref(tab:irisTable).
```{r description, echo=FALSE, results='asis'}
cat("<caption> (\\#tab:irisTable) Table Iris </caption> \n\r ")
crosstable(iris, Sepal.Length, Sepal.Width, by=Species, test = TRUE, total="column") %>% as_flextable
```
You can example files here: vignette_markdown.Rmd and vignette_markdown.docx.
I have to admit that I don’t use Rmarkdown a lot with
crosstable
, so this feature might not be as maintained as
others.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.