# Expand vector of free working parameters to vector of all working parameters including any fixed parameters (used in fitHMM.R and nLogLike.R) ```r expandPar( optPar, optInd, fixPar, wparIndex, betaCons, deltaCons, nbStates, nbCovsDelta, stationary, nbCovs, nbRecovs = 0, mixtures = 1, nbCovsPi = 0 ) ``` ## Arguments - `optPar`: vector of free working parameters - `optInd`: indices of constrained parameters - `fixPar`: Vector of working parameters which are assumed known prior to fitting the model (NA indicates parameters is to be estimated) - `wparIndex`: Vector of indices for the elements of `fixPar` that are not NA - `betaCons`: Matrix of the same dimension as `beta0` composed of integers identifying any equality constraints among the t.p.m. parameters. - `deltaCons`: Matrix of the same dimension as `delta0` composed of integers identifying any equality constraints among the initial distribution working scale parameters. - `nbStates`: Number of states of the HMM - `nbCovsDelta`: Number of initial distribution covariates - `stationary`: `FALSE` if there are time-varying covariates in `formula` or any covariates in `formulaDelta`. If `TRUE`, the initial distribution is considered equal to the stationary distribution. Default: `FALSE`. - `nbCovs`: Number of t.p.m. covariates - `nbRecovs`: Number of recharge covariates - `mixtures`: Number of mixtures for the state transition probabilities - `nbCovsPi`: Number of mixture probability covariates ## Returns A vector of all working parameters including any fixed parameters ## Examples ```r ## Not run: nbStates <- 2 stepDist <- "gamma" # step distribution angleDist <- "vm" # turning angle distribution # extract data from momentuHMM example data <- example$m$data ### 1. fit the model to the simulated data # define initial values for the parameters mu0 <- c(20,70) sigma0 <- c(10,30) kappa0 <- c(1,1) stepPar <- c(mu0,sigma0) # no zero-inflation, so no zero-mass included anglePar <- kappa0 # not estimating angle mean, so not included formula <- ~cov1+cos(cov2) # constrain cov1 effect to state 1 -> 2 and cov2 effect to state 2 -> 1 fixPar <- list(beta=c(NA,NA,0,NA,0,NA)) m <- fitHMM(data=data,nbStates=nbStates,dist=list(step=stepDist,angle=angleDist), Par0=list(step=stepPar,angle=anglePar),formula=formula,fixPar=fixPar) # convert free parameter vector (m$mod$wpar) to full set of working parameters (m$mod$estimate) est <- momentuHMM:::expandPar(m$mod$wpar,m$conditions$optInd,unlist(m$conditions$fixPar), m$conditions$wparIndex,m$conditions$betaCons,m$conditions$deltaCons, nbStates, ncol(m$covsDelta)-1,m$conditions$stationary,nrow(m$mle$beta)-1) all(est==m$mod$estimate) ## End(Not run) ```

expandPar function