Merge branch 'master' of github.com:halasadi/MAPS

README.md

@@ -86,7 +86,3 @@ Please see the `examples` folder for examples data-input, how to run MAPS, and h
 ## confused?
 
 The MAPS software is still being tested. I will appreciate any bugs/comments with the code/documentation. Please post an issue and I will get to it.
-
-## credits
-
-The MAPS software was developed by Hussein Al-Asadi with Desislava Petkova at the University of Chicago.  

src/Makefile

@@ -8,8 +8,6 @@ EIGEN_INC = /usr/local/include/eigen3
 BOOST_LIB = /usr/local/opt/boost@1.57/lib
 BOOST_INC = /usr/local/opt/boost@1.57/include
 
-
-
 EXE = runeems2
 OBJ = runeems2.o eems2.o util.o mcmc.o draw.o habitat.o graph.o
 

src/eems2.cpp

@@ -168,8 +168,7 @@ void EEMS2::initialize_state(const MCMC &mcmc) {
     nowmSeeds = MatrixXd::Zero(nowmtiles,2); randpoint_in_habitat(nowmSeeds);
 
 
-    //nowmrateS = params.min_omegam + draw.runif() * (params.max_omegam - params.min_omegam);
-    nowmrateS = 1;
+    nowmrateS = params.min_omegam + draw.runif() * (params.max_omegam - params.min_omegam);
     nowqrateS = params.min_omegaq + draw.runif() * (params.max_omegaq - params.min_omegaq);
 
     int niters = mcmc.num_iters_to_save();

src/params-test.ini

@@ -1,7 +1,7 @@
 datapath = ../data/overall/popressard_2_Inf/popressard_2_Inf
 mcmcpath = ../data/overall/popressard_2_Inf/popressard_2_Inf-test-sim
 nIndiv = 2800
-nDemes = 90
+nDemes = 70
 genomeSize = 2600
 dfProposalS2 = 0.1
 numMCMCIter = 2000000

src/util.cpp

@@ -64,8 +64,7 @@ Params::Params(const string &params_file, const long seed_from_command_line) {
 
     // prevent ei to be too large and might cause overflow error
     mEffctHalfInterval = 4;
-    // want rates 2sigma away from the mean
-    qEffctHalfInterval = 2;
+    qEffctHalfInterval = 4;
 
     min_omegaq = -10;
     min_omegam = -10;