From 598ce8064a9fff320e8aeeaa3bee523031e487ee Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20M=C3=BCller?= Date: Wed, 17 Feb 2021 10:57:39 +0100 Subject: [PATCH] docs: add warning that LMM does not work on frozen macOS app (#55) --- docs/sec_getting_started.rst | 6 ++++-- docs/sec_qg_lme4.rst | 7 +++++++ 2 files changed, 11 insertions(+), 2 deletions(-) diff --git a/docs/sec_getting_started.rst b/docs/sec_getting_started.rst index 6e11a6c..89c2466 100644 --- a/docs/sec_getting_started.rst +++ b/docs/sec_getting_started.rst @@ -2,6 +2,8 @@ Getting started =============== +.. _sec_installation: + Installation ============ Shape-Out 2 can be installed via multiple channels. @@ -19,9 +21,9 @@ Shape-Out 2 can be installed via multiple channels. .. code:: bash - pip install shapeout2 + python3 -m pip install shapeout2 - To start Shape-Out, simply run ``python -m shapeout2`` + To start Shape-Out, simply run ``python3 -m shapeout2`` or ``shapeout2`` in a command shell. diff --git a/docs/sec_qg_lme4.rst b/docs/sec_qg_lme4.rst index b98f150..2ee251e 100644 --- a/docs/sec_qg_lme4.rst +++ b/docs/sec_qg_lme4.rst @@ -8,6 +8,13 @@ significance (p-value) when comparing two measurement groups. The analysis uses linear mixed effects models (LMM) as described in :cite:`Herbig2018` and yields results identical to those obtained with Shape-Out 1. +.. warning:: + Unfortunately, LMM analysis currently does not work with the .app or + .pkg bundle on macOS. This problem is tracked in `issue #73 + `_. + If you are using macOS and you would like to use LMM analysis, you have to + install Shape-Out 2 as a Python package (see :ref:`sec_installation`). + The LMM analysis is performed using the lme4 R package and is based on the :ref:`implementation in dclab ` (please read for more information on the options available) which uses