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We use the msm package in R (Jackson, 2011) to fit the Markov models.
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DR data were analyzed in R (version 2.14.2) software environment, using the "msm" package (version 1.1.1).
We therefore fitted a hidden Markov model with misclassification to the data using the msm package for R [ 19] and examined the effect of individual level covariates on the transition intensities between states.
Surface areas were calculated using the msms package (version 1.3; Sanner et al., 1996).
The msm package also has some limitations.
The Markov models were implemented with the msm package for R (R Development Core Team 2009) 28 freely available from http://CRAN.R-project.org/package=msm.org/package=msm
Subsequently, the solution is calculated for different harmonics by using the MSM as one of the powerful perturbation techniques.
For visualization we use the OpenDX package.
Coalescent Simulations To assess the significance of identified PASS regions and to validate the statistical method used to show evidence for selection, we performed coalescent simulations using the software package msms (Ewing and Hermisson, 2010 ).
Use the packages for restrictions.
Use the packages for safety.
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