hapsburg.PackagesSupport.simData
================================

.. py:module:: hapsburg.PackagesSupport.simData


Attributes
----------

.. autoapisummary::

   hapsburg.PackagesSupport.simData.sim


Classes
-------

.. autoapisummary::

   hapsburg.PackagesSupport.simData.Simulator
   hapsburg.PackagesSupport.simData.BinomSim
   hapsburg.PackagesSupport.simData.BinomSimCopyBoth
   hapsburg.PackagesSupport.simData.SimRef
   hapsburg.PackagesSupport.simData.BinomSimRefNoLD
   hapsburg.PackagesSupport.simData.MultiVariateNormalLD


Module Contents
---------------

.. py:class:: Simulator(refsim='BinomialNoLD')

   Bases: :py:obj:`object`


   Simulator Class for HMMs.
   This is the main Class, all specific Simulators can inherit from it
   and overwrite functions.
   Contains Parameters


   .. py:attribute:: l
      :value: 10000



   .. py:attribute:: lats
      :value: []



   .. py:attribute:: pure_stat
      :value: []



   .. py:attribute:: ob_stat
      :value: []



   .. py:attribute:: ref_states
      :value: []



   .. py:attribute:: ref_sim
      :value: 0



   .. py:attribute:: stats


   .. py:method:: set_ref_sim(sim)

      Set the Reference Simulator to sim



   .. py:method:: simulate_latent()
      :abstractmethod:


      Simulate all l latent States



   .. py:method:: error_model()

      Apply error model to all l latent States



   .. py:method:: simulate_full()

      Return all Statistics



   .. py:method:: simulate_ref()

      Generate the reference Data Set



   .. py:method:: apply_error()

      Applies the Error Model



   .. py:method:: copyHaplo()
      :abstractmethod:


      Copy from Haplotypes Refs via latent states



   .. py:method:: save_data(folder='../Simulated/Test0/')

      Save the simulated Data to a Directory



   .. py:method:: save_parameters(folder='../Simulated/Test0/')

      Save Parameters of Simulation



.. py:class:: BinomSim(refsim='BinomialNoLD')

   Bases: :py:obj:`Simulator`


   Bimomial Simulator.
   Assume equally spaced SNPs.
   Copying: 0: From HW state. 1,...,n from Reference Data Set [n]


   .. py:attribute:: spacing
      :value: []



   .. py:attribute:: roh_in
      :value: 0.002



   .. py:attribute:: roh_out
      :value: 0.01



   .. py:attribute:: roh_jump
      :value: 0.1



   .. py:method:: set_cons_spacing()

      Set the spacing of SNPs



   .. py:method:: set_params()
      :abstractmethod:


      Set the parameters



   .. py:method:: save_parameters(folder)

      Save Parameters to parameter.csv in folder



   .. py:method:: first_state()

      Generate the first latent state



   .. py:method:: sim_copying()

      Simulate the Vector with States to copy from



   .. py:method:: jump_no_roh()

      Generate length and next state not in ROH



   .. py:method:: jump_roh()

      Generate length and next state in ROH



   .. py:method:: simulate_latent()

      Simulate l latent States



   .. py:method:: copyHaplo()

      Copy from Haplotypes Refs via latent states



.. py:class:: BinomSimCopyBoth(refsim='BinomialNoLD')

   Bases: :py:obj:`Simulator`


   Bimomial Simulator.
   Assume equally spaced SNPs.
   Copy from two Individuals, even in non-ROH state


   .. py:attribute:: spacing
      :value: []



   .. py:attribute:: roh_in
      :value: 0.002



   .. py:attribute:: roh_out
      :value: 0.002



   .. py:attribute:: roh_jump
      :value: 0.1



   .. py:method:: set_cons_spacing()

      Set the spacing of SNPs



   .. py:method:: set_params()
      :abstractmethod:


      Set the parameters



   .. py:method:: jump_roh()

      Generate length and next state in ROH



   .. py:method:: sim_copying_inroh()

      Simulate Copying within ROH. Return Copy State [l]



   .. py:method:: sim_roh_inout()

      Return 0 1 vector [l] wether in or out ROH state



   .. py:method:: simulate_latent()

      Simulate and Return Vector with States to copy from



   .. py:method:: copyHaplo()

      Copy from Haplotypes Refs via latent states



.. py:class:: SimRef

   Bases: :py:obj:`object`


   Class for Simulating the Reference Strings


   .. py:attribute:: refs
      :value: []



   .. py:attribute:: haps
      :value: []



   .. py:method:: simulate_refs()
      :abstractmethod:


      Simulate and return Reference Strings



   .. py:method:: set_params(**kwargs)

      Set Attributes with keyworded Arguments



   .. py:method:: plot_ld_r2(haps=[], l=200, fs=18)

      Plot R2 across pw. Distances of SNPs



.. py:class:: BinomSimRefNoLD

   Bases: :py:obj:`SimRef`


   Simulate References under a Binomial Model.
   For the moment: Do not do any LD Structure


   .. py:attribute:: h
      :value: 2



   .. py:attribute:: k
      :value: 100



   .. py:attribute:: l
      :value: 1000



   .. py:attribute:: p
      :value: 0.5



   .. py:method:: simulate_refs()

      Simulate References under a Binomial Model



.. py:class:: MultiVariateNormalLD

   Bases: :py:obj:`SimRef`


   Simulate References under a Multivariate Normal Model.
   Simulate latent variable and push them through a logit function


   .. py:attribute:: l
      :value: 1000



   .. py:attribute:: k
      :value: 100



   .. py:attribute:: cov_dist
      :value: 200



   .. py:method:: logit(x)

      Define a Logit Function



   .. py:method:: simulate_refs()

      Simulate References under the multivariate Normal Model



.. py:data:: sim