NAMESPACE

import(methods)
import(stats4)

importFrom(stats, approxfun, density, dnorm, ecdf, pnorm,
           sd, uniroot, var, ar, dgamma, dpois, lm, rgamma, rnorm, runif,
           ks.test, punif, qnorm, shapiro.test, 
           Box.test, acf, pacf, tsdiag,
           constrOptim, optim)

importFrom(graphics, title, par, lines, hist)

importFrom(utils, head, str, tail, as.relistable, menu)
importFrom(MCMCpack, rdirichlet, ddirichlet)
importFrom(e1071, rdiscrete)
importFrom(permute, allPerms)
import(BB)


importFrom(combinat, permn)

## 2020-01-13: import selectively.
##   import(fGarch)
importFrom(fGarch, pstd, dstd, rstd, qstd)
importFrom(timeDate, skewness, kurtosis)

importFrom(gbutils, plotpdf, pseudoInverse, cdf2quantile)
importFrom(Rdpack, reprompt)

importFrom(mvtnorm, dmvnorm, rmvnorm)

S3method(tsdiag, "MixAR")
S3method(print, "tsdiagMixAR")

exportMethods(
    "-",
    "%of%",
    "*",
    "/",
    "[",
    "[[",
    "+",
    "initialize",
    "inner",
    "mix_cdf",
    "mix_ek",
    "mix_hatk",
    "mix_pdf",
    "mixFilter",
    "noise_dist",

    "mix_se",
    "fit_mixARreg",    ##new method
    "fit_mixVAR"
)
exportClasses(
    "MixAR",
    "MixARGaussian",
    "MixComp",
    "raggedCoef",
    "raggedCoefS",##new class
    "raggedCoefV",
    "MixVAR",
    "MixVARGaussian"
)

## exportPattern("^[[:alpha:]]+")

export(
"%of%",
adjustLengths,
b_show,
# cdf2q,
companion_matrix,
cond_loglik,
dist_norm,
distlist,
ed_nparam,
ed_parse,
ed_skeleton,
ed_src,
ed_stdnorm,
ed_stdt,
ed_stdt0,
ed_stdt1,
em_est_dist,
em_est_sigma,
em_rinit,
em_tau,
em_tau_safe,
est_templ,
etk2tau,
# extend_index,
fdist_stdnorm,
fdist_stdt,
fit_mixAR,
fn_stdt,
ft_stdt,
get_edist,
inner,
isStable,
lastn, # todo: deprecate
lik_params,
lik_params_bounds,
make_fcond_lik,
mix_cdf,
mix_central_moment,
mix_ek,
mix_ekurtosis,
mix_hatk,
mix_kurtosis,
mix_location,
mix_moment,
mix_ncomp, 
mix_pdf,
mix_qf,
mix_variance,
mixAny_sim,
mixAR,
mixAR_cond_probs,
mixAR_permute,
mixAR_sim,
mixAR_switch,
mixARemFixedPoint,
MixARGaussian,
mixARgen,
mixARgenemFixedPoint,
mixARnoise_sim,
mixFilter,
mixgenMstep,
mixMstep,
mixSubsolve,

# moWLar,      # exampleModels$WL_ibm@prob
# moWLprob,    # exampleModels$WL_ibm@scale
# moWLsigma,   # exampleModels$WL_ibm@arcoef@a
#
# moT_A,    these now are in exampleModels, see names(exampleModels)
# moT_B,
# moT_B2,
# moT_B3,
# moT_C1,
# moT_C2,
# moT_C3,
# moWL,
# moWL_A,
# moWL_B,
# moWL_I,
# moWL_II,
# moWLgen,
# moWLt3v,
# moWLtf,

multiStep_dist,
noise_dist,
noise_moment,
noise_params,
noise_rand,
param_score_stdt,
parameters,
permuteArpar,
# plotpdf,
predict_coef,
#pseudoInverse,  moved to gbutils
rag_modify,
ragged2char,
ragged2vec,
raggedCoef,
raghat1,
randomArCoefficients,
randomMarParametersKernel,
randomMarResiduals,
row_lengths,
set_noise_params,
"parameters<-", # to replace set_parameters
show_diff,
stdnormabsmoment,
stdnormmoment,
stdtabsmoment,
stdtmoment,
tabsmoment,
tau2arcoef,
tau2probhat,
tauCorrelate,
tauetk2sigmahat,
tomarparambyComp,
tomarparambyType,
tsDesignMatrixExtended,
exampleModels,
##ui, don't export internal functions  ## New functions from this line
bayes_mixAR,
err,
err_k,
bx_dx,
Choose_pk,
sampZpi,
sampMuShift,
sampSigmaTau,
marg_loglik,
mixSARfit,
mixARreg,
cond_loglikS,
label_switch,
mixVARfit,
mixVAR_sim,
fit_mixVAR,
mixAR_BIC,
mixAR_diag,
BIC_comp,
## from mixARsim
simuExperiment,
mixARExperiment,
permn_cols,
unswitch,
test_unswitch
)