update interface

reworkhow · Nov 6, 2021 · 2cb6da5 · 2cb6da5
1 parent 0dc08a1
commit 2cb6da5
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Showing 2 changed files with 13 additions and 5 deletions.
diff --git a/src/1.JWAS/src/JWAS.jl b/src/1.JWAS/src/JWAS.jl
@@ -183,8 +183,6 @@ function runMCMC(mme::MME,df;
  Pi = 0.0,
  estimatePi = false,
  estimateScale = false)
-
-
  #Neural Network
  is_nnbayes_partial = (mme.nonlinear_function != false && mme.is_fully_connected==false)
  if mme.nonlinear_function != false #modify data to add phenotypes for hidden nodes
@@ -259,6 +257,19 @@ function runMCMC(mme::MME,df;
  set_marker_hyperparameters_variances_and_pi(mme)
  end
  ############################################################################
+ #fast blocks #now only work for one geno
+ ############################################################################
+ if fast_blocks != false
+ if fast_blocks == true
+ block_size = Int(floor(sqrt(mme.M[1].nObs)))
+ elseif typeof(fast_blocks) <: Number
+ block_size = Int(floor(fast_blocks))
+ end
+ mme.MCMCinfo.fast_blocks = collect(range(1, step=block_size, stop=mme.M[1].nMarkers))
+ mme.MCMCinfo.chain_length = Int(floor(chain_length/(fast_blocks[2]-fast_blocks[1])))
+ end
+ println("BLOCK SIZE: $block_size")
+ ############################################################################
  # Adhoc functions
  ############################################################################
  #save MCMC samples for all parameters (?seperate function user call)

diff --git a/src/1.JWAS/src/MCMC/MCMC_BayesianAlphabet.jl b/src/1.JWAS/src/MCMC/MCMC_BayesianAlphabet.jl
@@ -21,9 +21,6 @@ function MCMC_BayesianAlphabet(mme,df)
  is_activation_fcn = mme.is_activation_fcn
  nonlinear_function = mme.nonlinear_function
  fast_blocks = mme.MCMCinfo.fast_blocks
- if fast_blocks != false
- chain_length = Int(floor(chain_length/(fast_blocks[2]-fast_blocks[1])))#not flexible
- end
  ############################################################################
  # Categorical Traits (starting values for maker effects defaulting to 0s)
  ############################################################################