<commit_before>.. _behavior:

Project 1: Behavioral Model
===========================

Statement of Problem:
---------------------

In order to differentiate mice, we need to create a detailed behavior
profile to describe:

1. how they drink, feed or move (locomotion) and
2. how they translate between active state or inactive state.

We have the following key background information from the paper:

    Mouses react differently during Active state and Inactive states and
    all behavioral record should be classified into 2 mutually exclusive
    categories, Active States (ASs) and Inactive States (ISs). To
    designate ISs, we examined all time intervals occurring between
    movement, feeding, and drinking events while the animal was outside
    the Home base. Those time intervals exceeding an IS Threshold (IST)
    duration value were classified as ISs; the set of ASs was then
    defined as the complement of these ISs. Equivalent mathematically,
    ASs can also be defined as those intervals resulting from connecting
    gaps between events outside the Home base of length at most IST; ISs
    are then defined as the complement of these ASs. (*Active State
    Organization of Spontaneous Behavior Patterns*, C. Hillar et al.)

Statement of statistical problems:
----------------------------------

The above flowchart shows the key metrics that are required by the study
to capture the behavioural profile:

http://cenzhuoyao.com/wp-content/uploads/2016/04/project1_behavior_profile.png

.. figure:: figure/distance.png
   :alt: alt tag

   Fix
<commit_msg>DOC: add paragraph about home cage monitoring (HCM)<commit_after>.. _behavior:

Project 1: Behavioral Model
===========================

Statement of Problem:
---------------------

In order to differentiate mice, we need to create a detailed behavior
profile to describe:

1. how they drink, feed or move (locomotion) and
2. how they translate between active state or inactive state.

We have the following key background information from the paper:

-  **Home Cage Monitoring System(HCM)** HCM cages were spatially
   discretized into a 12 x 24 array of cells and occupancy times for
   each MD were computed as the proportion of time spent within each of
   the 288 cells. To determine whether animals establish a Home base,
   HCM cages were spatially discretized into a 2 x 4 array of cells, and
   occupancy times for each mouse day were calculated as above. In the
   experiment, 56/158 animals displayed largest occupancy times in the
   cell containing the niche area, which was considered to be their Home
   base location.


-  **Active and Inactive State** Mice react differently during
   Active state and Inactive states and
   all behavioral record should be classified into 2 mutually exclusive
   categories, Active States (ASs) and Inactive States (ISs). To
   designate ISs, we examined all time intervals occurring between
   movement, feeding, and drinking events while the animal was outside
   the Home base. Those time intervals exceeding an IS Threshold (IST)
   duration value were classified as ISs; the set of ASs was then
   defined as the complement of these ISs. Equivalent mathematically,
   ASs can also be defined as those intervals resulting from connecting
   gaps between events outside the Home base of length at most IST; ISs
   are then defined as the complement of these ASs. (*Active State
   Organization of Spontaneous Behavior Patterns*, C. Hillar et al.)

Statement of statistical problems:
----------------------------------

The above flowchart shows the key metrics that are required by the study
to capture the behavioural profile:

http://cenzhuoyao.com/wp-content/uploads/2016/04/project1_behavior_profile.png

.. figure:: figure/distance.png
   :alt: alt tag

   Fix

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