Skip to content

Commit

Permalink
Fixing typos and some wording in the Combining jamovi and R-section o…
Browse files Browse the repository at this point in the history 
…f the user manual
  • Loading branch information
@sjentsch
sjentsch committed Jun 27, 2023
1 parent 8f47831 commit 8314c4b
Showing 1 changed file with 42 additions and 43 deletions.
85 changes: 42 additions & 43 deletions usermanual/um_6_jamovi_and_R.rst
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,17 +5,16 @@ Combining jamovi and R

A huge advantage of jamovi is that it is not only built on top of the R
statistical language, it also makes it also very easy to access R from jamovi,
and jamovi from R. The syntax mode, Rj, |jmvconnect| and |jmvReadWrite| help
and jamovi from R. The syntax mode, ``Rj``, |jmvconnect| and |jmvReadWrite| help
you to achieve that.

Syntax Mode
-----------

jamovi also provides an “R Syntax Mode”, in this mode, jamovi produces
equivalent R code for each analysis. To change to syntax mode, select the
application menu (⋮) at the top right of jamovi, and check the ``Syntax
mode`` checkbox there. It is possible to leave syntax mode by clicking this
a second time.
jamovi provides an “R Syntax Mode”, in this mode, jamovi produces equivalent
R code for each analysis. To change to syntax mode, select the application
menu (⋮) at the top right of jamovi, and check the ``Syntax mode`` checkbox
there. It is possible to leave syntax mode by clicking this a second time.

In syntax mode, analyses continue to operate as before, but now they produce
R syntax. Like all results objects in jamovi, you can right click on these
Expand All @@ -32,11 +31,11 @@ Syntax Mode

<div class="gif-player" data-anim-src="../_static/gifs/um_rSyntax.gif" data-static-src="../_static/gifs/um_rSyntax.png"></div>

At present, the provided R syntax does not include the data import step, and
this must be performed manually. The easiest way of reading and writing
jamovi data files in R is the |jmvReadWrite| R package. Alternatively, the
|jmvconnect| R-package permits you to access data sets that you have opened
in your jamovi session from R.
The provided R syntax does not include the data import step, but this can be
easily achieved by using the R packages |jmvconnect|_ and |jmvReadWrite|_
(explained in more detail below). |jmvReadWrite|_ enables you to read and
write jamovi data files (.omv) in R, |jmvconnect|_ permits you to access
data sets that you have opened in your jamovi session from R.

.. _rj_editor:

Expand Down Expand Up @@ -87,21 +86,20 @@ Syntax Mode
again.

By default, ``Rj`` makes use of the version of ``R`` bundled with jamovi.
This includes many packages (|jmv| and all it’s `dependencies
<https://cran.r-project.org/package=jmv>`_\ ), and will be sufficient for
many people, but if you need to make use of additional ``R`` packages then
you’ll need to make use of the ``System R`` version. If you select ⚙ (at
the top right of the code box), you’ll see an option to change the
``R version`` used. The ``System R`` version uses the version of ``R`` you
have installed on your system. This has the advantage that your ``R`` code
now has access to all of the packages you have installed for that version
of ``R``. The last thing you will need is to have the |jmvconnect| R
package installed in the R library on your system.

``jmvconnect`` R-package
This includes many packages (|jmv|_ and all it’s dependencies), and will be
sufficient for many people, but if you need to make use of additional R
packages then you’ll need to make use of the ``System R`` version. If you
select ⚙ (at the top right of the code box), you’ll see an option to change
the ``R version`` used. The ``System R`` version uses the version of ``R``
you have installed on your system. This has the advantage that your ``R``
code now has access to all of the packages you have installed for that
version of ``R``. The last thing you will need is to have the |jmvconnect|_
R package installed in the R library on your system.

``jmvconnect`` R package
------------------------

The |jmvconnect| R-package allows the ``R`` version on your system to access
The |jmvconnect|_ R package allows the ``R`` version on your system to access
the data sets that you opened in jamovi. You can install it in ``R`` with:

.. code-block:: R
Expand Down Expand Up @@ -137,8 +135,8 @@ Syntax Mode
are made to other columns.

There may be times where you’ll want to transition to an R session for
analysing a data set. This is where the |jmvconnect| R package comes in
handy. |jmvconnect| let’s you read the data sets from a running jamovi
analysing a data set. This is where the |jmvconnect|_ R package comes in
handy. |jmvconnect|_ lets you read the data sets from a running jamovi
instance into an R session. It has two functions: ``what()`` lists the
available data sets, and ``read()`` reads them. For example, you might use:

Expand All @@ -163,15 +161,15 @@ Syntax Mode
data <- read(2)
``jmvReadWrite`` R-package
``jmvReadWrite`` R package
--------------------------

The |jmvReadWrite| R-package reads and writes jamovi-data-files (.omv) in
The |jmvReadWrite|_ R package reads and writes jamovi-data-files (.omv) in
``R``. It can be installed with:

.. code-block:: R
install.packages('jmvconnect')
install.packages('jmvReadWrite')
A typical use case would be if you wanted to process a large number
Expand All @@ -190,18 +188,9 @@ Syntax Mode
Likewise does the ``read_omv``-function permit you to read jamovi-data-files
into ``R``. The most typical use case would
be reading a data file, doing manipulations that currently are not possible
in jamovi, and then writing back the resulting modified file (in the jamovi
file format). There is a couple of helper functions implemented in
|jmvReadWrite|. They enable operations such as re-arranging the columns /
variables of a data set (``arrange_cols_omv``), mass-converting a data files
into the jamovi file format (``convert_to_omv``), converting data files from
long to wide format (``long2wide_omv``) and from wide to long format
(``wide2long_omv``), adding variables from several data sets
(``merge_cols_omv``), adding cases from several data sets
(``merge_rows_omv``), or sort a data set after one or more variables
(``sort_omv``).
into ``R``. Another typical use case would be reading a data file, doing
manipulations that currently are not possible in jamovi, and then writing
back the resulting modified file (in the jamovi file format).

.. code-block:: R
Expand All @@ -214,18 +203,28 @@ Syntax Mode
write_omv(dtaSet, "FILENAME.omv")
There is a couple of helper functions implemented in |jmvReadWrite|_. They
enable operations such as re-arranging the columns / variables of a data set
(``arrange_cols_omv``), mass-converting a data files into the jamovi file
format (``convert_to_omv``; e.g. from a statistics software that you used
earlier), converting data files from long to wide format (``long2wide_omv``)
and from wide to long format (``wide2long_omv``), adding variables from
several data sets (``merge_cols_omv``), adding cases from several data sets
(``merge_rows_omv``), or sort a data set after one or more variables
(``sort_omv``).

Another possible use case for ``read_omv`` is the creation of R markdown
files using the results of your jamovi analyses. The ``getSyn``-parameter
determines whether the syntax of the analyses contained in the file is
extracted. For running the syntax, the |jmv| R-package needs to be
extracted. For running the syntax, the |jmv|_ R package needs to be
installed.

.. code-block:: R
library(jmvReadWrite)
library(jmv)
data <- jmvReadWrite::read_omv("FILENAME.omv", getSyn = TRUE)
data <- read_omv("FILENAME.omv", getSyn = TRUE)
# the analyses are stored in the attribute syntax
attr(data, "syntax")
Expand Down

0 comments on commit 8314c4b

Please sign in to comment.