checkPar0 | R Documentation |
fitHMM
(or MIfitHMM
) modelPrints parameters with labels based on DM
, formula
, and/or formulaDelta
. See fitHMM
for
further argument details.
checkPar0(data, ...) ## Default S3 method: checkPar0( data, nbStates, dist, Par0 = NULL, beta0 = NULL, delta0 = NULL, estAngleMean = NULL, circularAngleMean = NULL, formula = ~1, formulaDelta = NULL, stationary = FALSE, mixtures = 1, formulaPi = NULL, DM = NULL, userBounds = NULL, workBounds = NULL, betaCons = NULL, betaRef = NULL, deltaCons = NULL, stateNames = NULL, fixPar = NULL, prior = NULL, ... ) ## S3 method for class 'hierarchical' checkPar0( data, hierStates, hierDist, Par0 = NULL, hierBeta = NULL, hierDelta = NULL, estAngleMean = NULL, circularAngleMean = NULL, hierFormula = NULL, hierFormulaDelta = NULL, mixtures = 1, formulaPi = NULL, DM = NULL, userBounds = NULL, workBounds = NULL, betaCons = NULL, deltaCons = NULL, fixPar = NULL, prior = NULL, ... )
data |
|
... |
further arguments passed to or from other methods |
nbStates |
Number of states of the HMM. |
dist |
A named list indicating the probability distributions of the data streams. |
Par0 |
Optional named list containing vectors of state-dependent probability distribution parameters for
each data stream specified in |
beta0 |
Optional matrix of regression coefficients for the transition probabilities. If |
delta0 |
Optional values or regression coefficients for the initial distribution of the HMM. If |
estAngleMean |
An optional named list indicating whether or not to estimate the angle mean for data streams with angular distributions ('vm' and 'wrpcauchy'). |
circularAngleMean |
An optional named list indicating whether to use circular-linear or circular-circular regression on the mean of circular distributions ('vm' and 'wrpcauchy') for turning angles. |
formula |
Regression formula for the transition probability covariates. |
formulaDelta |
Regression formula for the initial distribution. |
stationary |
|
mixtures |
Number of mixtures for the state transition probabilities. |
formulaPi |
Regression formula for the mixture distribution probabilities.
Note that only the covariate values from the first row for each individual ID in |
DM |
An optional named list indicating the design matrices to be used for the probability distribution parameters of each data stream. |
userBounds |
An optional named list of 2-column matrices specifying bounds on the natural (i.e, real) scale of the probability distribution parameters for each data stream. |
workBounds |
An optional named list of 2-column matrices specifying bounds on the working scale of the probability distribution, transition probability, and initial distribution parameters. |
betaCons |
Matrix of the same dimension as |
betaRef |
Numeric vector of length |
deltaCons |
Matrix of the same dimension as |
stateNames |
Optional character vector of length nbStates indicating state names. |
fixPar |
An optional list of vectors indicating parameters which are assumed known prior to fitting the model. |
prior |
A function that returns the log-density of the working scale parameter prior distribution(s). |
hierStates |
A hierarchical model structure |
hierDist |
A hierarchical data structure |
hierBeta |
A hierarchical data structure |
hierDelta |
A hierarchical data structure |
hierFormula |
A hierarchical formula structure for the transition probability covariates for each level of the hierarchy ('formula'). See |
hierFormulaDelta |
A hierarchical formula structure for the initial distribution covariates for each level of the hierarchy ('formulaDelta'). See |
fitHMM
, MIfitHMM
m <- example$m checkPar0(data=m$data, nbStates=2, dist=m$conditions$dist, estAngleMean = m$conditions$estAngleMean, formula = m$conditions$formula) par <- getPar(m) checkPar0(data=m$data, nbStates=2, dist=m$conditions$dist, estAngleMean = m$conditions$estAngleMean, formula = m$conditions$formula, Par0=par$Par, beta0=par$beta, delta0=par$delta) dummyDat <- data.frame(step=0,angle=0,cov1=0,cov2=0) checkPar0(data=dummyDat, nbStates=2, dist=m$conditions$dist, estAngleMean = m$conditions$estAngleMean, formula = m$conditions$formula) ## Not run: simDat <- simData(nbStates=2, dist=m$conditions$dist, Par = par$Par, spatialCovs = list(forest=forest), centers = matrix(0,1,2), nbCovs = 2) checkPar0(data = simDat, nbStates=2, dist=m$conditions$dist, formula = ~forest, DM = list(step=list(mean=~cov1, sd=~cov2), angle=list(mean=~center1.angle,concentration=~1)), estAngleMean=list(angle=TRUE), circularAngleMean=list(angle=TRUE)) par <- list(step=rnorm(8),angle=rnorm(4)) beta0 <- matrix(rnorm(4),2,2) delta0 <- c(0.5,0.5) checkPar0(data = simDat, nbStates=2, dist=m$conditions$dist, Par0 = par, beta0 = beta0, delta0 = delta0, formula = ~forest, DM = list(step=list(mean=~cov1, sd=~cov2), angle=list(mean=~center1.angle,concentration=~1)), estAngleMean=list(angle=TRUE), circularAngleMean=list(angle=TRUE)) ## End(Not run)
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