Cleaning up and re-organizing the structure of the developer hub, the…

… how-to, and the analyses

analyses/jg_overview.rst

@@ -0,0 +1,134 @@
+.. sectionauthor:: `Jonas Rafi <https://www.su.se/english/profiles/jora9288-1.283149>`__ and `Sebastian Jentschke <https://www.uib.no/en/persons/Sebastian.Jentschke>`_
+
+======================
+Analyses: Introduction
+======================
+
+   The aim of the following section is to provide short, non-technical
+   tutorials on how to conduct common statistical procedures in jamovi, and was
+   originally created by Jonas Rafi under the name jamovi guide. However, this
+   is only intended as a brief overview. For a more in-depth treatment of these
+   analyses, we'd recommend you take a look at the many `community resources
+   <https://www.jamovi.org/community.html>`__ available.
+
+   **A Note On Measurement Types**: The following documentation describes each
+   of the analyses, and describes the variable measure types required. For
+   example, it might explain that a particular analysis requires a continuous
+   |continuous| dependent variable, and a nominal |nominal| grouping variable.
+   However it's possible that the columns in your data set, for a number of
+   different reasons, aren't set up with the correct measure types (as
+   indicated in the column header). You can adjust the measure type of columns
+   using the variable editor, however (for the most part) these measure types
+   are really just a guide and don't need to be set correctly. If you assign a
+   |continuous| continuous variable to an analysis expecting a |nominal|
+   nominal one, the analysis will simply treat the variable as nominal. All
+   this to say, if the documentation says that a particular measure type is
+   required, the data simply needs to be the correct 'shape', and you can save
+   yourself the labour of setting the measure types correctly if you don't want
+   to.
+
+
+======================
+Descriptive statistics
+======================
+
+   .. toctree::
+      :maxdepth: 1
+      :hidden:
+
+      jg_11_descriptive-analyses
+
+
+=======
+t-tests
+=======
+
+   The t-test is used to test whether the mean value in a normally distributed
+   data set deviates significantly from a null hypothesis (which assumes that
+   there is no difference).
+
+   There are three types of t-tests:
+
+   .. toctree::
+      :maxdepth: 1
+      :hidden:
+
+      jg_21_t-test-independent
+      jg_22_t-test-paired
+      jg_23_t-test-onesample
+
+
+   .. admonition:: Community resources
+
+      | A more comprehensive introduction into the concept is presented in this
+        `video <https://www.youtube.com/embed/mb7KCLYEis8?list=PLkk92zzyru5OAtc_ItUubaSSq6S_TGfRn>`__
+        by `Barton Poulson <https://datalab.cc/jamovi>`__.
+
+
+============================
+Analyses of Variance (ANOVA)
+============================
+
+   The Analysis of variance (ANOVA) is a statistical method that examines how
+   the impact of one or more factors affects an outcome (dependent) variable.
+   These factors are the predictor variables and are categorical. Typically,
+   such factors reflect an experimental manipulation (e.g. with or without
+   treatment), but a factor can also represent groups for whose influence one
+   would like to control (e.g. gender: men or women). The analysis of variance
+   is based on a concept similar to that of the t-test, but it goes beyond
+   that, in that factors can have several levels (t-tests only allow two), and
+   in that several factors can be examined simultaneously.
+
+   There are different types of analysis of variance, which differ in the
+   number of factors examined - one or more factors - or whether they compare
+   between people or within a person - repeated measurements:
+
+   .. toctree::
+      :maxdepth: 1
+      :hidden:
+
+      jg_31_unianova
+      jg_32_anova-factorial
+      jg_33_anova-rm
+      jg_34_anova-mixed
+
+
+   .. admonition:: Community resources
+
+      | An introduction into the concept of an ANOVA is presented in this
+        `video <https://www.youtube.com/embed/GcbMG6sizXs?list=PLkk92zzyru5OAtc_ItUubaSSq6S_TGfRn>`__
+        by `Barton Poulson <https://datalab.cc/jamovi>`__.
+
+
+==========================
+Correlation and regression
+==========================
+
+   Correlation and regression analyses are statistical methods for assessing
+   the relationships between a dependent / outcome variable and one or more
+   independent / predictor variables. While the *correlation* analysis examines
+   the *relationship* between one predictor and one outcome variable,
+   *regression* analysis mainly focuses on *prediction* (how well can one or
+   more variables predict another (outcome) variable). Often, a distinction is
+   made between linear and non-linear (e.g., logistic regression).
+
+   .. toctree::
+      :maxdepth: 1
+      :hidden:
+
+      jg_42_regression-linear
+      jg_43_regression-logistic
+
+
+   .. admonition:: Community resources
+
+      | An introduction into the concept of regression analyses is presented in
+        this `video <https://www.youtube.com/embed/gRhVjKNWiUs?list=PLkk92zzyru5OAtc_ItUubaSSq6S_TGfRn>`__
+        by `Barton Poulson <https://datalab.cc/jamovi>`__.
+
+.. ---------------------------------------------------------------------
+
+.. |nominal|                           image:: ../_images/variable-nominal.*
+   :width: 16px
+.. |continuous|                        image:: ../_images/variable-continuous.*
+   :width: 16px

developer/dh_overview.rst

@@ -1,111 +1,70 @@
 .. sectionauthor:: Jonathon Love
 
-=============
-developer hub
-=============
+============
+Introduction
+============
 
-   Welcome to the `developer hub <https://dev.jamovi.org>`__ for `jamovi <https://www.jamovi.org>`__.
+   Welcome to the developer hub for `jamovi <https://www.jamovi.org>`__.
 
-   Here you will find resources that cover the development of analyses for jamovi (and R). It’s still a work in progress, and we’ll be adding to it over time,
-   but the current tutorial series has everything you need to get up and running.
+   Here you will find resources that cover the development of analyses for jamovi
+   (and R). It’s still a work in progress, and we’ll be adding to it over time.
+
+   If you have questions about developing modules for jamovi, or feedback on
+   how we can improve the developer hub, we’re keen to hear from you. There are
+   forums available at `forum.jamovi.org <https://forum.jamovi.org>`__, a
+   communication platform at `jamovi.slack.com <jamovi.slack.com>`__ or you can
+   reach out via e-mail to `contact <at> jamovi.org <mailto:contact@jamovi.org>`.
+
+
+=========
+Tutorials
+=========
+
+   The following series of tutorials has everything you need to get up and
+   running.
 
    .. toctree::
       :maxdepth: 1
-      
+
       dh_tut_10_introduction
       dh_tut_20_advanced
       dh_tut_30_ui
 
 
-   In addition, there is a comprehensive overview over the API for module development:
+======================
+API for jamovi-modules
+======================
 
    .. toctree::
       :maxdepth: 1
+      :hidden:
 
       dh_api_overview
 
 
-   If you have questions about developing modules for jamovi, or feedback on how we can improve the developer hub, we’re keen to hear from you. There are
-   forums available at `forum.jamovi.org <https://forum.jamovi.org>`__, a communication platform at `jamovi.slack.com <jamovi.slack.com>`__ or you can reach
-   out via e-mail to `contact <at> jamovi.org`.
-
-   For those interested in the jamovi platform, it is hosted on `GitHub <https://github.com/jamovi/jamovi>`__. Don’t forget to ‘star’ us!
-
-   Underneath, you will find further information about the structure of the project, the jamovi-file-format and possible projects for the Google Summer of
-   Code:
-
-   .. toctree::
-      :titlesonly:
-
-      dh_info_overview
-
-
-.. raw:: html
-
-   <h2>News</h2>
-
-
-**08-07-2019**
-
-   We’ve :doc:`refined the advanced UI customization <dh_tut_33-advanced-customisation>` in jamovi 1.0.4 and newer. This is not backwards compatible, so we
-   discourage its use in existing modules for the time being (Until the 1.0.4+ is is in broader use). People developing or releasing modules for the first time
-   are encouraged to make use of it.
-
+   In addition, there is a comprehensive overview over :doc:`the API for module
+   development <dh_api_overview>`.
 
-**09-06-2017**
 
-   We’ve added a new document to our tutorial series describing how jamovi analyses can use :doc:`state <dh_tut_23-state>`. State is used with longer running
-   analyses, and allows the analysis to re-use results that were calculated previously. This can lead to much faster analyses, and a much nicer user
-   experience.
+======================
+Additional information
+======================
 
+   .. toctree::
+      :maxdepth: 1
+      :hidden:
 
-**20-04-2017: Changes to dev tools for jamovi 0.7.3**
-
-   We’ve just released a beta of jamovi 0.7.3, which brings some significant improvements, and minor changes to developing jamovi modules.
-
-*Changes to dependency resolution*
-
-   In the past, we’re had a number of difficulties with dependency resolution for jamovi modules. Sometimes jmvtools would install more dependencies than were
-   necessary, and other times not enough. This stemmed from contamination of the R library path, from R packages installed on the system. In this release we’ve
-   successfully isolated the system libraries from the jmvtools, and only the required dependencies will now be installed.
-
-*Improvements to* ``.u.yaml``-*files*
-
-   Previously, ``.u.yaml``-files (the UI definition) were automatically generated from ``.a.yaml``-files (the analysis definition). This was sometimes
-   problematic when additional changes were made to the ``.a.yaml``-files. It wasn’t always clear which changes should be propagated to the ``.u.yaml``-files,
-   and which should not.
-
-   In the 0.7.3, the ``.a.yaml`` and ``.u.yaml``-files work together. The ``.u.yaml``-file, by default, contains minimal information (mostly just describing
-   the layout), and the property values, for example labels, are taken directly from the ``.a.yaml``-file. For many people, they will only need to edit the
-   ``.a.yaml``-file, and jmvtools can take care of the ``.u.yaml``-file itself. More documentation for UI Design will be coming soon.
-
-   ``.u.yaml``-files using this new scheme will have the ``jus``, near the top of the file, specified as ``2.0``. ``.u.yaml``-files using the older ``jus`` of
-   ``1.0`` will be automatically upgraded. Upgraded files will be placed in ``tame`` ``compilerMode`` (explained next), you may want to change it to
-   ``aggressive``.
-
-``compilerMode``: *aggressive vs tame*
-
-   jmvtools also introduces a new option in ``.u.yaml``-files: ``compilerMode``. By default, ``.u.yaml``-files are created in ``aggressive`` mode. This means
-   that ``jmvtools`` will take a heavy handed approach when updating the ``.u.yaml``-files. If new options are added to the ``.a.yaml``-file, it will
-   aggressively add them into the ``.u.yaml``-file, overwriting any manual changes.
-
-   In contrast, the ``compilerMode`` of ``tame`` does not overwrite manual changes in the ``u.yaml``-file. The trade off is that it often can’t position UI
-   elements as optimally.
-
-   We recommend beginning with your ``.u.yaml``-files in ``compilerMode`` set to ``aggressive``, and when you begin to refine your UI by adding custom changes
-   to your ``.u.yaml``-files swap over to ``compilerMode`` set to ``tame`` so that your changes are preserved. Again, for a lot of people, ``aggressive`` mode
-   will be all that they will ever need.
-
-*Outstanding issues*
-
-   For the time being, changes to the ``.a.yaml`` and / or the ``.u.yaml``-files, will still require you to shut jamovi down and restart it before you’ll see
-   the changes to the UI. We hope to fix this issue in the next few weeks.
-
-   On windows, jmvtools is still not able to find the jamovi installation by default. You will still need to pass the ``home`` option, or set the
-   ``jamovi_home`` option.
+      dh_info_project-structure
+      dh_info_file-format
+      dh_info_gsoc-projects
 
 
-**02-04-2017: Added dev mode to jamovi 0.7.2.7**
+   For those interested in the jamovi platform, it is hosted on `GitHub
+   <https://github.com/jamovi/jamovi>`__. Don’t forget to ‘star’ us!
+
+   In addition, there is additional information, covering the :doc:`structure
+   of the project <dh_info_project-structure>`, the :doc:`jamovi file format
+   <dh_info_file-format>` and possible projects for the :doc:`Google Summer
+   of Code <dh_info_gsoc-projects>`.
 
-   jamovi 0.7.2.7 Adds dev mode, providing a stack trace when an analysis errors for whatever reason. The tutorial has been updated to describe this:
-   :doc:`Debugging an analysis <dh_tut_15-debugging-an-analysis>`.
+.. add Docker