R/focei.R

In nlmixr2est: Nonlinear Mixed Effects Models in Population PK/PD, Estimation Routines

.regFloat1 <- rex::rex(
  or(
    group(some_of("0":"9"), ".", any_of("0":"9")),
    group(any_of("0":"9"), ".", some_of("0":"9"))
  ),
  maybe(group(one_of("E", "e"), maybe(one_of("+", "-")), some_of("0":"9")))
)
.regFloat2 <- rex::rex(some_of("0":"9"), one_of("E", "e"), maybe(one_of("-", "+")), some_of("0":"9"))
.regDecimalint <- rex::rex(or("0", group("1":"9", any_of("0":"9"))))
.regNum <- rex::rex(maybe("-"), or(.regDecimalint, .regFloat1, .regFloat2))


use.utf <- function() {
  opt <- getOption("cli.unicode", NULL)
  if (!is.null(opt)) {
    isTRUE(opt)
  } else {
    l10n_info()$`UTF-8` && !is.latex()
  }
}

is.latex <- function() {
  if (!("knitr" %in% loadedNamespaces())) {
    return(FALSE)
  }
  get("is_latex_output", asNamespace("knitr"))()
}

.bobyqa <- function(par, fn, gr, lower = -Inf, upper = Inf, control = list(), ...) {
  .ctl <- control
  if (is.null(.ctl$npt)) .ctl$npt <- length(par) * 2 + 1
  .ctl$iprint <- 0L
  .ctl <- .ctl[names(.ctl) %in% c("npt", "rhobeg", "rhoend", "iprint", "maxfun")]
  .ret <- minqa::bobyqa(par, fn,
                        control = .ctl,
                        lower = lower,
                        upper = upper
                        )
  .ret$x <- .ret$par
  .ret$message <- .ret$msg
  .ret$convergence <- .ret$ierr
  .ret$value <- .ret$fval
  return(.ret)
}

.lbfgsb3c <- function(par, fn, gr, lower = -Inf, upper = Inf, control = list(), ...) {
  .w <- which(names(control) %in% c("trace", "factr", "pgtol", "abstol", "reltol", "lmm", "maxit", "iprint"))
  .control <- control[.w]
  .ret <- lbfgsb3c::lbfgsb3c(par = as.vector(par), fn = fn, gr = gr, lower = lower, upper = upper, control = .control)
  .ret$x <- .ret$par
  return(.ret)
}

.lbfgsbO <- function(par, fn, gr, lower = -Inf, upper = Inf, control = list(), ...) {
  .control <- control[names(control) %in% c("trace", "factr", "pgtol", "abstol", "reltol", "lmm", "maxit", "iprint")]
  .w <- which(sapply(.control, is.null))
  .control <- .control[-.w]
  .ret <- optim(
    par = par, fn = fn, gr = gr, method = "L-BFGS-B",
    lower = lower, upper = upper,
    control = .control, hessian = FALSE
  )
  .ret$x <- .ret$par
  return(.ret)
}

.nlminb <- function(par, fn, gr, lower = -Inf, upper = Inf, control = list(), ...) {
  .ctl <- control
  .ctl <- .ctl[names(.ctl) %in% c(
    "eval.max", "iter.max", "trace", "abs.tol", "rel.tol", "x.tol", "xf.tol", "step.min", "step.max", "sing.tol",
    "scale.inti", "diff.g"
  )]
  .ctl$trace <- 0
  .ret <- stats::nlminb(
    start = par, objective = fn, gradient = gr, hessian = NULL, control = .ctl,
    lower = lower, upper = upper
  )
  .ret$x <- .ret$par
  ## .ret$message   already there.
  ## .ret$convergence already there.
  return(.ret)
}

.nloptr <- function(par, fn, gr, lower = -Inf, upper = Inf, control = list(), ..., nloptrAlgoritm = "NLOPT_LD_MMA") {
  rxode2::rxReq("nloptr")
  .ctl <- list(
    algorithm = nloptrAlgoritm,
    xtol_rel = control$reltol,
    xtol_abs = rep_len(control$abstol, length(par)),
    ftol_abs = control$abstol,
    ftol_rel = control$reltol,
    print_level = 0,
    check_derivatives = FALSE,
    check_derivatives_print = FALSE,
    maxeval = control$maxOuterIterations
  )
  .ret <- nloptr::nloptr(
    x0 = par, eval_f = fn, eval_grad_f = gr,
    lb = lower, ub = upper,
    opts = .ctl
  )
  .ret$par <- .ret$solution
  .ret$x <- .ret$solution
  .ret$convergence <- .ret$status
  .ret$value <- .ret$objective
  return(.ret)
}

.bobyqaNLopt <- function(par, fn, gr, lower = -Inf, upper = Inf, control = list(), ...) {
  .ctl <- list(
    algorithm = "NLOPT_LN_BOBYQA",
    xtol_rel = control$reltol,
    xtol_abs = rep_len(control$abstol, length(par)),
    ftol_abs = control$abstol,
    ftol_rel = control$reltol,
    print_level = 0,
    check_derivatives = FALSE,
    check_derivatives_print = FALSE,
    maxeval = control$maxOuterIterations
  )
  .ret <- nloptr::nloptr(
    x0 = par, eval_f = fn,
    lb = lower, ub = upper,
    opts = .ctl
  )
  .ret$par <- .ret$solution
  .ret$x <- .ret$solution
  .ret$convergence <- .ret$status
  .ret$value <- .ret$objective
  return(.ret)
}

.slsqp <- function(par, fn, gr, lower = -Inf, upper = Inf, control = list(), ...) {
  return(.nloptr(par, fn, gr, lower, upper, control, ..., nloptrAlgoritm = "NLOPT_LD_SLSQP"))
}

.lbfgsbLG <- function(par, fn, gr, lower = -Inf, upper = Inf, control = list(), ...) {
  .ctlLocal <- list(
    algorithm = "NLOPT_LD_LBFGS",
    xtol_rel = control$reltol,
    xtol_abs = rep_len(control$abstol, length(par)),
    ftol_abs = control$abstol,
    ftol_rel = control$reltol,
    print_level = 0,
    check_derivatives = FALSE,
    check_derivatives_print = FALSE,
    maxeval = control$maxOuterIterations
  )
  .ctl <- opts <- list(
    "algorithm" = "NLOPT_LD_AUGLAG",
    xtol_rel = control$reltol,
    xtol_abs = rep_len(control$abstol, length(par)),
    ftol_abs = control$abstol,
    ftol_rel = control$reltol,
    maxeval = control$maxOuterIterations,
    "local_opts" = .ctlLocal,
    "print_level" = 0
  )
  .ret <- nloptr::nloptr(
    x0 = par, eval_f = fn, eval_grad_f = gr,
    lb = lower, ub = upper,
    opts = .ctl
  )
  .ret$par <- .ret$solution
  .ret$x <- .ret$solution
  .ret$convergence <- .ret$status
  .ret$value <- .ret$objective
  return(.ret)
}

#' Get the THETA/ETA lines from rxode2 UI
#'
#' @param rxui This is the rxode2 ui object
#' @return The theta/eta lines
#' @author Matthew L. Fidler
#' @noRd
.uiGetThetaEta <- function(rxui) {
  .iniDf <- rxui$iniDf
  .w <- which(!is.na(.iniDf$ntheta))
  .thetas <- lapply(.w, function(i) {
    eval(parse(text=paste0("quote(", .iniDf$name[i], " <- THETA[", .iniDf$ntheta[i],"])")))
  })
  .etas <- NULL
  .i2 <- .iniDf[-.w, ]
  if (length(.i2$name) > 0) {
    .i2 <- .i2[.i2$neta1 == .i2$neta2, ]
    .etas <- lapply(seq_along(.i2$name), function(i) {
      eval(parse(text=paste0("quote(", .i2$name[i], " <- ETA[", .i2$neta1[i], "])")))
    })
  }
  c(.thetas, .etas)
}

#' Get the THETA/ETA params from the rxode2 UI
#'
#' @param rxui This is the rxode2 ui object
#' @return The params eirxode2 UI
#' @author Matthew L. Fidler
#' @noRd
.uiGetThetaEtaParams <- function(rxui, str=FALSE) {
  .iniDf <- rxui$iniDf
  .w <- which(!is.na(.iniDf$ntheta))
  .thetas <- vapply(.w, function(i) {
    paste0("THETA[", .iniDf$ntheta[i],"]")
  }, character(1), USE.NAMES=FALSE)
  .etas <- NULL
  .i2 <- .iniDf[-.w, ]
  if (length(.i2$name) > 0) {
    .i2 <- .i2[.i2$neta1 == .i2$neta2, ]
    .etas <- vapply(seq_along(.i2$name), function(i) {
      paste0("ETA[", .i2$neta1[i],"]")
    }, character(1), USE.NAMES=FALSE)
  }
  .str <- paste(c(.thetas, .etas, rxui$covariates), collapse=", ")
  if (str) {
    paste0("params(", .str, ")")
  } else {
    eval(parse(text=paste0("quote(params(", .str, "))")))
  }
}

#' @export
rxUiGet.foceiParams <- function(x, ...) {
  .ui <- x[[1]]
  .uiGetThetaEtaParams(.ui, str=TRUE)
}

#' @export
rxUiGet.foceiCmtPreModel <- function(x, ...) {
  .ui <- x[[1]]
  .state <- rxode2::rxState(.ui$mv0)
  if (length(.state) == 0) return("")
  paste(paste0("cmt(", .state, ")"), collapse="\n")
}

# This handles the errors for focei
.createFoceiLineObject <- function(x, line) {
  .predDf <- rxUiGet.predDfFocei(list(x, TRUE))
  if (line > nrow(.predDf)) {
    return(NULL)
  }
  .predLine <- .predDf[line, ]
  .ret <- list(x, .predLine, line)
  class(.ret) <- c(paste(.predLine$distribution), "rxGetDistributionFoceiLines")
  .ret
}

#' This is a S3 method for getting the distribution lines for a base rxode2 focei problem
#'
#' @param line Parsed rxode2 model environment
#' @return Lines for the focei. This is based
#'   on the idea that the focei parameters are defined
#' @author Matthew Fidler
#' @keywords internal
#' @export
rxGetDistributionFoceiLines <- function(line) {
  UseMethod("rxGetDistributionFoceiLines")
}

.rxPredLlik <- NULL
#' Get pred only options
#'
#' @param env  rxode2 environment option
#'
#' @return  If the current method is requesting loglik instead of pred/r
#'  (required for cwres)
#'
#' @author Matthew L. Fidler
#'
#' @noRd
.getRxPredLlikOption <-function() {
  if (inherits(.rxPredLlik, "logical")) {
    return(.rxPredLlik)
  }
  return(FALSE)
}

#' @export
rxGetDistributionFoceiLines.norm <- function(line) {
  env <- line[[1]]
  pred1 <- line[[2]]
  .errNum <- line[[3]]
  if (rxode2hasLlik()) {
    rxode2::.handleSingleErrTypeNormOrTFoceiBase(env, pred1, .errNum,
                                                 rxPredLlik=.getRxPredLlikOption())
  } else {
    rxode2::.handleSingleErrTypeNormOrTFoceiBase(env, pred1)
  }
}

#' @export
rxGetDistributionFoceiLines.t <- function(line) {
  if (rxode2hasLlik()) {
    env <- line[[1]]
    pred1 <- line[[2]]
    .errNum <- line[[3]]
    rxode2::.handleSingleErrTypeNormOrTFoceiBase(env, pred1, .errNum,
                                                 rxPredLlik=.getRxPredLlikOption())
  } else {
    stop("t is not supported", call.=FALSE)
  }
}

#' @export
rxGetDistributionFoceiLines.cauchy <- function(line) {
  if (rxode2hasLlik()) {
    env <- line[[1]]
    pred1 <- line[[2]]
    .errNum <- line[[3]]
    rxode2::.handleSingleErrTypeNormOrTFoceiBase(env, pred1, .errNum,
                                                 rxPredLlik=.getRxPredLlikOption())
  } else {
    stop("t is not supported", call.=FALSE)
  }
}

#' @export
rxGetDistributionFoceiLines.default  <- function(line) {
  if (rxode2hasLlik()) {
    env <- line[[1]]
    pred1 <- line[[2]]
    .errNum <- line[[3]]
    rxode2::.handleSingleErrTypeNormOrTFoceiBase(env, pred1, .errNum,
                                                 rxPredLlik=.getRxPredLlikOption())
  } else {
    stop("unknown distribution", call.=FALSE)
  }
}

#' @export
rxGetDistributionFoceiLines.rxUi <- function(line) {
  .predDf <- rxUiGet.predDfFocei(list(line, TRUE))
  lapply(seq_along(.predDf$cond), function(c) {
    .mod <- .createFoceiLineObject(line, c)
    rxGetDistributionFoceiLines(.mod)
  })
}

#' @export
rxUiGet.foceiModel0 <- function(x, ...) {
  .f <- x[[1]]
  rxode2::rxCombineErrorLines(.f, errLines=rxGetDistributionFoceiLines(.f),
                              prefixLines=.uiGetThetaEta(.f),
                              paramsLine=NA, #.uiGetThetaEtaParams(.f),
                              modelVars=TRUE,
                              cmtLines=FALSE,
                              dvidLine=FALSE)
}
#attr(rxUiGet.foceiModel0, "desc") <- "FOCEi model base"

#' @export
rxUiGet.foceiModel0ll <- function(x, ...) {
  assignInMyNamespace(".rxPredLlik", TRUE)
  on.exit(assignInMyNamespace(".rxPredLlik", NULL))
  .f <- x[[1]]
  rxode2::rxCombineErrorLines(.f, errLines=rxGetDistributionFoceiLines(.f),
                              prefixLines=.uiGetThetaEta(.f),
                              paramsLine=NA, #.uiGetThetaEtaParams(.f),
                              modelVars=TRUE,
                              cmtLines=FALSE,
                              dvidLine=FALSE)
}


.foceiPrune <- function(x, fullModel=TRUE) {
  .x <- x[[1]]
  .x <- .x$foceiModel0[[-1]]
  .env <- new.env(parent = emptyenv())
  .env$.if <- NULL
  .env$.def1 <- NULL
  if (.getRxPredLlikOption()) {
    if (fullModel) {
      .malert(("pruning branches ({.code if}/{.code else}) of llik full model..."))
    } else {
      .malert("pruning branches ({.code if}/{.code else}) of llik model...")
    }
  } else {
    if (fullModel) {
      .malert(("pruning branches ({.code if}/{.code else}) of full model..."))
    } else {
      .malert("pruning branches ({.code if}/{.code else}) of model...")
    }
  }
  .ret <- rxode2::.rxPrune(.x, envir = .env)
  .mv <- rxode2::rxModelVars(.ret)
  ## Need to convert to a function
  if (rxode2::.rxIsLinCmt() == 1L) {
    .vars <- c(.mv$params, .mv$lhs, .mv$slhs)
    .mv <- rxode2::.rxLinCmtGen(length(.mv$state), .vars)
  }
  .msuccess("done")
  rxode2::rxNorm(.mv)
}

.loadSymengine <- function(newmod, promoteLinSens = TRUE, fullModel = FALSE) {
  if (.getRxPredLlikOption()) {
    if (fullModel) {
      .malert("loading full llik model into {.pkg symengine} environment...")
    } else {
      .malert("loading llik model into {.pkg symengine} environment...")
    }
  } else {
    if (fullModel) {
      .malert("loading full model into {.pkg symengine} environment...")
    } else {
      .malert("loading into {.pkg symengine} environment...")
    }
  }
  .ret <- rxode2::rxS(newmod, TRUE, promoteLinSens = promoteLinSens)
  if (inherits(.ret$rx_r_, "numeric")) {
    assign("rx_r_", symengine::S(as.character(.ret$rx_r_)), envir=.ret)
  }
  .ret
}

#' @export
rxUiGet.loadPruneSens <- function(x, ...) {
  .loadSymengine(.foceiPrune(x), promoteLinSens = TRUE)
}
#attr(rxUiGet.loadPruneSens, "desc") <- "load sensitivity with linCmt() promoted"

#' @export
rxUiGet.loadPrune <- function(x, ...) {
  .loadSymengine(.foceiPrune(x), promoteLinSens = FALSE)
}
#attr(rxUiGet.loadPrune, "desc") <- "load sensitivity without linCmt() promoted"

.sensEtaOrTheta <- function(s, theta=FALSE) {
  .etaVars <- NULL
  if (theta && exists("..maxTheta", s)) {
    .etaVars <- paste0("THETA_", seq(1, s$..maxTheta), "_")
  } else if (exists("..maxEta", s)) {
    .etaVars <- paste0("ETA_", seq(1, s$..maxEta), "_")
  }
  if (length(.etaVars) == 0L) {
    stop("cannot identify parameters for sensitivity analysis\n   with nlmixr2 an 'eta' initial estimate must use '~'", call. = FALSE)
  }
  .stateVars <- rxode2::rxState(s)
  rxode2::.rxJacobian(s, c(.stateVars, .etaVars))
  rxode2::.rxSens(s, .etaVars)
  s
}

#' @export
rxUiGet.foceiEtaS <- function(x, ..., theta=FALSE) {
  .s <- rxUiGet.loadPruneSens(x, ...)
  .sensEtaOrTheta(.s)
}
#attr(rxUiGet.foceiEtaS, "desc") <- "Get symengine environment with eta sensitivities"


#' @export
rxUiGet.foceiThetaS <- function(x, ..., theta=FALSE) {
  .s <- rxUiGet.loadPruneSens(x, ...)
  .sensEtaOrTheta(.s, theta=TRUE)
}
#attr(rxUiGet.foceiEtaS, "desc") <- "Get symengine environment with eta sensitivities"

#' @export
rxUiGet.foceiHdEta <- function(x, ...) {
  .s <- rxUiGet.foceiEtaS(x)
  .stateVars <- rxode2::rxState(.s)
  # FIXME: take out pred.minus.dv
  .predMinusDv <- rxode2::rxGetControl(x[[1]], "predMinusDv", TRUE)
  .grd <- rxode2::rxExpandFEta_(
    .stateVars, .s$..maxEta,
    ifelse(.predMinusDv, 1L, 2L)
  )
  if (rxode2::.useUtf()) {
    .malert("calculate \u2202(f)/\u2202(\u03B7)")
  } else {
    .malert("calculate d(f)/d(eta)")
  }
  rxode2::rxProgress(dim(.grd)[1])
  on.exit({
    rxode2::rxProgressAbort()
  })
  .any.zero <- FALSE
  .all.zero <- TRUE
  .ret <- apply(.grd, 1, function(x) {
    .l <- x["calc"]
    .l <- eval(parse(text = .l))
    .ret <- paste0(x["dfe"], "=", rxode2::rxFromSE(.l))
    .zErr <- suppressWarnings(try(as.numeric(get(x["dfe"], .s)), silent = TRUE))
    if (identical(.zErr, 0)) {
      .any.zero <<- TRUE
    } else if (.all.zero) {
      .all.zero <<- FALSE
    }
    rxode2::rxTick()
    return(.ret)
  })
  if (.all.zero) {
    stop("none of the predictions depend on 'ETA'", call. = FALSE)
  }
  if (.any.zero) {
    warning("some of the predictions do not depend on 'ETA'", call. = FALSE)
  }
  .s$..HdEta <- .ret
  .s$..pred.minus.dv <- .predMinusDv
  rxode2::rxProgressStop()
  .s
}
attr(rxUiGet.foceiHdEta, "desc") <- "Generate the d(err)/d(eta) values for FO related methods"


#' Finalize inner rxode2 based on symengine saved info
#'
#' @param .s Symengine/rxode2 object
#' @return Nothing
#' @author Matthew L Fidler
#' @noRd
.rxFinalizeInner <- function(.s, sum.prod = FALSE,
                             optExpression = TRUE) {
  .prd <- get("rx_pred_", envir = .s)
  .prd <- paste0("rx_pred_=", rxode2::rxFromSE(.prd))
  .r <- get("rx_r_", envir = .s)
  .r <- paste0("rx_r_=", rxode2::rxFromSE(.r))
  .yj <- paste(get("rx_yj_", envir = .s))
  .yj <- paste0("rx_yj_~", rxode2::rxFromSE(.yj))
  .lambda <- paste(get("rx_lambda_", envir = .s))
  .lambda <- paste0("rx_lambda_~", rxode2::rxFromSE(.lambda))
  .hi <- paste(get("rx_hi_", envir = .s))
  .hi <- paste0("rx_hi_~", rxode2::rxFromSE(.hi))
  .low <- paste(get("rx_low_", envir = .s))
  .low <- paste0("rx_low_~", rxode2::rxFromSE(.low))
  .ddt <- .s$..ddt
  if (is.null(.ddt)) .ddt <- character(0)
  .sens <- .s$..sens
  if (is.null(.sens)) .sens <- character(0)
  .s$..inner <- paste(c(
    .ddt,
    .sens,
    .yj,
    .lambda,
    .hi,
    .low,
    .prd,
    .s$..HdEta,
    .r,
    .s$..REta,
    .s$..stateInfo["statef"],
    .s$..stateInfo["dvid"],
    ""
  ), collapse = "\n")
  if (sum.prod) {
    .malert("stabilizing round off errors in inner problem...")
    .s$..inner <- rxode2::rxSumProdModel(.s$..inner)
    .msuccess("done")
  }
  if (optExpression) {
    .s$..inner <- rxode2::rxOptExpr(.s$..inner,
                                    ifelse(.getRxPredLlikOption(),
                                           "inner llik model",
                                           "inner model"))
  }
}

#' @export
rxUiGet.foceiEnv <- function(x, ...) {
  .s <- rxUiGet.foceiHdEta(x, ...)
  .stateVars <- rxode2::rxState(.s)
  .grd <- rxode2::rxExpandFEta_(.stateVars, .s$..maxEta, FALSE)
  if (rxode2::.useUtf()) {
    .malert("calculate \u2202(R\u00B2)/\u2202(\u03B7)")
  } else {
    .malert("calculate d(R^2)/d(eta)")
  }
  rxode2::rxProgress(dim(.grd)[1])
  on.exit({
    rxode2::rxProgressAbort()
  })
  .ret <- apply(.grd, 1, function(x) {
    .l <- x["calc"]
    .l <- eval(parse(text = .l))
    .ret <- paste0(x["dfe"], "=", rxode2::rxFromSE(.l))
    rxode2::rxTick()
    return(.ret)
  })

  .s$..REta <- .ret
  rxode2::rxProgressStop()
  .sumProd <- rxode2::rxGetControl(x[[1]], "sumProd", FALSE)
  .optExpression <- rxode2::rxGetControl(x[[1]], "optExpression", TRUE)
  .rxFinalizeInner(.s, .sumProd, .optExpression)
  .rxFinalizePred(.s, .sumProd, .optExpression)
  .s$..outer <- NULL
  .s
}
#attr(rxUiGet.foceiEnv, "desc") <- "Get the focei environment"

#' @export
rxUiGet.foceEnv <- function(x, ...) {
  .s <- rxUiGet.foceiHdEta(x, ...)
  .s$..REta <- NULL
  ## Take etas from rx_r
  eval(parse(text = rxode2::rxRepR0_(.s$..maxEta)))
  .sumProd <- rxode2::rxGetControl(x[[1]], "sumProd", FALSE)
  .optExpression <- rxode2::rxGetControl(x[[1]], "optExpression", TRUE)
  .rxFinalizeInner(.s, .sumProd, .optExpression)
  .rxFinalizePred(.s, .sumProd, .optExpression)
  .s$..outer <- NULL
  .s
}
#attr(rxUiGet.foceEnv, "desc") <- "Get the foce environment"


#' @export
rxUiGet.getEBEEnv <- function(x, ...) {
  .s <- rxUiGet.loadPrune(x, ...)
  .s$..inner <- NULL
  .s$..outer <- NULL
  .sumProd <- rxode2::rxGetControl(x[[1]], "sumProd", FALSE)
  .optExpression <- rxode2::rxGetControl(x[[1]], "optExpression", TRUE)
  .rxFinalizePred(.s, .sumProd, .optExpression)
  .s
}
#attr(rxUiGet.getEBEEnv, "desc") <- "Get the EBE environment"

.toRxParam <- ""
.toRxDvidCmt <- ""

.toRx <- function(x, msg) {
  if (is.null(x)) {
    return(NULL)
  }
  .malert(msg)
  .ret <- rxode2::rxode2(paste(.toRxParam, x, .toRxDvidCmt))
  .msuccess("done")
  return(.ret)
}

.nullInt <- function(x) {
  if (rxode2::rxIs(x, "integer") || rxode2::rxIs(x, "numeric")) {
    return(as.integer(x))
  } else {
    return(integer(0))
  }
}

#' @export
rxUiGet.predDfFocei <- function(x, ...) {
  .ui <- x[[1]]
  if (exists(".predDfFocei", envir=.ui)) {
    get(".predDfFocei", envir=.ui)
  } else {
    .predDf <- .ui$predDf
    if (all(.predDf$distribution == "norm")) {
      assign(".predDfFocei,", .predDf, envir=.ui)
      .predDf
    } else {
      .w <- which(.predDf$distribution == "norm")
      if (length(.w) > 0) {
        .predDf$distribution[.w] <- "dnorm"
      }
      assign(".predDfFocei", .predDf, envir=.ui)
      .predDf
    }
  }
}


.rxFinalizePred <- function(.s, sum.prod = FALSE,
                            optExpression = TRUE) {
  .prd <- get("rx_pred_", envir = .s)
  .prd <- paste0("rx_pred_=", rxode2::rxFromSE(.prd))
  .r <- get("rx_r_", envir = .s)
  .r <- paste0("rx_r_=", rxode2::rxFromSE(.r))
  .yj <- paste(get("rx_yj_", envir = .s))
  .yj <- paste0("rx_yj_~", rxode2::rxFromSE(.yj))
  .lambda <- paste(get("rx_lambda_", envir = .s))
  .lambda <- paste0("rx_lambda_~", rxode2::rxFromSE(.lambda))
  .hi <- paste(get("rx_hi_", envir = .s))
  .hi <- paste0("rx_hi_~", rxode2::rxFromSE(.hi))
  .low <- paste(get("rx_low_", envir = .s))
  .low <- paste0("rx_low_~", rxode2::rxFromSE(.low))
  .lhs0 <- .s$..lhs0
  if (is.null(.lhs0)) .lhs0 <- ""
  .lhs <- .s$..lhs
  if (is.null(.lhs)) .lhs <- ""
  .ddt <- .s$..ddt
  if (is.null(.ddt)) .ddt <- ""
  .s$..pred <- paste(c(
    .s$..stateInfo["state"],
    .lhs0,
    .ddt,
    .yj,
    .lambda,
    .hi,
    .low,
    .prd,
    .r,
    .lhs,
    .s$..stateInfo["statef"],
    .s$..stateInfo["dvid"],
    "tad=tad()",
    "dosenum=dosenum()",
    ""
  ), collapse = "\n")
  .s$..pred.nolhs <- paste(c(
    .s$..stateInfo["state"],
    .lhs0,
    .ddt,
    .yj,
    .lambda,
    .hi,
    .low,
    .prd,
    .r,
    .s$..stateInfo["statef"],
    .s$..stateInfo["dvid"],
    ""
  ), collapse = "\n")
  if (sum.prod) {
    .malert("stabilizing round off errors in predictions or EBE model...")
    .s$..pred <- rxode2::rxSumProdModel(.s$..pred)
    .msuccess("done")
  }
  if (optExpression) {
    .s$..pred <- rxode2::rxOptExpr(.s$..pred,
                                   ifelse(.getRxPredLlikOption(),"Llik EBE model","EBE model"))
  }
}

.innerInternal <- function(ui, s) {
  assignInMyNamespace(".toRxParam", paste0(.uiGetThetaEtaParams(ui, TRUE), "\n",
                                           ui$foceiCmtPreModel, "\n"))
  assignInMyNamespace(".toRxDvidCmt", .foceiToCmtLinesAndDvid(ui))
  if (exists("..maxTheta", s)) {
    .eventTheta <- rep(0L, s$..maxTheta)
  } else {
    .eventTheta <- integer()
  }
  if (exists("..maxEta", s)) {
    .eventEta <- rep(0L, s$..maxEta)
  } else {
    .eventEta <- integer()
  }
  for (.v in s$..eventVars) {
    .vars <- as.character(get(.v, envir = s))
    .vars <- rxode2::rxGetModel(paste0("rx_lhs=", rxode2::rxFromSE(.vars)))$params
    for (.v2 in .vars) {
      .reg <- rex::rex(start, "ETA[", capture(any_numbers), "]", end)
      if (regexpr(.reg, .v2) != -1) {
        .num <- as.numeric(sub(.reg, "\\1", .v2))
        .eventEta[.num] <- 1L
      }
      .reg <- rex::rex(start, "THETA[", capture(any_numbers), "]", end)
      if (regexpr(.reg, .v2) != -1) {
        .num <- as.numeric(sub(.reg, "\\1", .v2))
        .eventTheta[.num] <- 1L
      }
    }
  }
  pred.opt <- NULL
  inner <- .toRx(s$..inner, "compiling inner model...")
  .sumProd <- rxode2::rxGetControl(ui, "sumProd", FALSE)
  .optExpression <- rxode2::rxGetControl(ui, "optExpression", TRUE)
  .predMinusDv <- rxode2::rxGetControl(ui, "predMinusDv", TRUE)
  if (!is.null(inner)) {
    if (.sumProd) {
      .malert("stabilizing round off errors in FD model...")
      s$..pred.nolhs <- rxode2::rxSumProdModel(s$..pred.nolhs)
      .msuccess("done")
    }
    if (.optExpression) {
      s$..pred.nolhs <- rxode2::rxOptExpr(s$..pred.nolhs,
                                          ifelse(.getRxPredLlikOption(),"Llik FD model","FD model"))
    }
    s$..pred.nolhs <- paste(c(
      paste0("params(", paste(inner$params, collapse = ","), ")"),
      s$..pred.nolhs
    ), collapse = "\n")
    pred.opt <- s$..pred.nolhs
  }
  .ret <- list(
    inner = inner,
    predOnly = .toRx(s$..pred, ifelse(.getRxPredLlikOption(),
                                      "compiling Llik EBE model...",
                                      "compiling EBE model...")),
    extra.pars = s$..extraPars,
    outer = .toRx(s$..outer),
    predNoLhs = .toRx(pred.opt, ifelse(.getRxPredLlikOption(),
                                       "compiling events Llik FD model...",
                                       "compiling events FD model...")),
    theta = NULL,
    ## warn=.zeroSens,
    pred.minus.dv = .predMinusDv,
    log.thetas = .nullInt(s$..extraTheta[["exp"]]),
    log.etas = .nullInt(s$..extraEta[["exp"]]),
    extraProps = s$..extraTheta,
    eventTheta = .eventTheta,
    eventEta = .eventEta
    ## ,
    ## cache.file=cache.file
  )
  class(.ret) <- "foceiModelList"
  .ret
}

#' @export
rxUiGet.focei <- function(x, ...) {
  .ui <- x[[1]]
  # For t/cauchy/dnorm, predOnly model
  assignInMyNamespace(".rxPredLlik", FALSE)
  on.exit(assignInMyNamespace(".rxPredLlik", NULL))
  .s <- rxUiGet.foceiEnv(x, ...)
  .ret <-  .innerInternal(.ui, .s)
  .predDf <- .ui$predDfFocei
  if (any(.predDf$distribution %in% c("t", "cauchy", "dnorm"))) {
    assignInMyNamespace(".rxPredLlik", TRUE)
    .s <- rxUiGet.foceiEnv(x, ...)
    .s2 <- .innerInternal(.ui, .s)
    .w <- vapply(seq_along(.s2),
                 function(i) {
                   inherits(.s2[[i]], "rxode2")
                 }, logical(1), USE.NAMES=FALSE)
    .s2 <- .s2[.w]
    names(.s2) <- paste0(names(.s2), "Llik")
    .cls <- class(.ret)
    .ret <- c(.ret, .s2)
    class(.ret) <-.cls
  }
  .ret
}
#attr(rxUiGet.focei, "desc") <- "Get the FOCEi foceiModelList object"

#' @export
rxUiGet.foce <- function(x, ...) {
  .ui <- x[[1]]
  assignInMyNamespace(".rxPredLlik", FALSE)
  on.exit(assignInMyNamespace(".rxPredLlik", NULL))
  .s <- rxUiGet.foceEnv(x, ...)
  .ret <- .innerInternal(.ui, .s)
  .predDf <- .ui$predDfFocei
  if (any(.predDf$distribution %in% c("t", "cauchy", "dnorm"))) {
    assignInMyNamespace(".rxPredLlik", TRUE)
    .s <- rxUiGet.foceEnv(x, ...)
    .s2 <- .innerInternal(.ui, .s)
    .w <- vapply(seq_along(.s2),
                 function(i) {
                   inherits(.s2[[i]], "rxode2")
                 }, logical(1), USE.NAMES=FALSE)
    .s2 <- .s2[.w]
    names(.s2) <- paste0(names(.s2), "Llik")
    .cls <- class(.ret)
    .ret <- c(.ret, .s2)
    class(.ret) <-.cls
  }
  .ret
}
#attr(rxUiGet.foce, "desc") <- "Get the FOCE foceiModelList object"


#' @export
rxUiGet.ebe <- function(x, ...) {
  .ui <-x[[1]]
  assignInMyNamespace(".rxPredLlik", FALSE)
  on.exit(assignInMyNamespace(".rxPredLlik", NULL))
  .s <- rxUiGet.getEBEEnv(x, ...)
  .ret <- .innerInternal(.ui, .s)
  .predDf <- .ui$predDfFocei
  if (any(.predDf$distribution %in% c("t", "cauchy", "dnorm"))) {
    assignInMyNamespace(".rxPredLlik", TRUE)
    .s <- rxUiGet.getEBEEnv(x, ...)
    .s2 <- .innerInternal(.ui, .s)
    .w <- vapply(seq_along(.s2),
                 function(i) {
                   inherits(.s2[[i]], "rxode2")
                 }, logical(1), USE.NAMES=FALSE)
    .s2 <- .s2[.w]
    names(.s2) <- paste0(names(.s2), "Llik")
    .cls <- class(.ret)
    .ret <- c(.ret, .s2)
    class(.ret) <-.cls
  }
  .ret
}
#attr(rxUiGet.ebe, "desc") <- "Get the EBE foceiModelList object"

#' @export
rxUiGet.foceiModelDigest <- function(x, ...) {
  .ui <- x[[1]]
  .iniDf <- get("iniDf", .ui)
  .sumProd <- rxode2::rxGetControl(.ui, "sumProd", FALSE)
  .optExpression <- rxode2::rxGetControl(.ui, "optExpression", TRUE)
  .predMinusDv   <- rxode2::rxGetControl(.ui, "predMinusDv", TRUE)
  digest::digest(c(all(is.na(.iniDf$neta1)),
                   rxode2::rxGetControl(.ui, "interaction", 1L),
                   .sumProd, .optExpression, .predMinusDv,
                   rxode2::rxGetControl(.ui, "addProp", getOption("rxode2.addProp", "combined2")),
                   .ui$lstExpr))
}
#attr(rxUiGet.foceiModelDigest, "desc") <- "Get the md5 digest for the focei model"
#' @export
rxUiGet.foceiModelCache <- function(x, ...) {
  file.path(rxode2::rxTempDir(),
            paste0("focei-", rxUiGet.foceiModelDigest(x, ...), ".qs"))
}
#attr(rxUiGet.foceiModelCache, "desc") <- "Get the focei cache file for a model"

#' @export
rxUiGet.foceiModel <- function(x, ...) {
  .cacheFile <- rxUiGet.foceiModelCache(x, ...)
  if (file.exists(.cacheFile)) {
    .ret <- qs::qread(.cacheFile)
    lapply(seq_along(.ret), function(i) {
      if (inherits(.ret[[i]], "rxode2")) {
        rxode2::rxLoad(.ret[[i]])
      }
    })
    return(.ret)
  }
  .ui <- x[[1]]
  .iniDf <- get("iniDf", .ui)
  if (all(is.na(.iniDf$neta1))) {
    .ret <- rxUiGet.ebe(x, ...)
  } else {
    if (rxode2::rxGetControl(.ui, "interaction", 1L)) {
      .ret <- rxUiGet.focei(x, ...)
    } else {
      .ret <- rxUiGet.foce(x, ...)
    }
  }
  qs::qsave(.ret, .cacheFile)
  .ret
}
# attr(rxUiGet.foceiModel, "desc") <- "Get focei model object"

#' @export
rxUiGet.foceiFixed <- function(x, ...) {
  .x <- x[[1]]
  .df <- get("iniDf", .x)
  .dft <- .df[!is.na(.df$ntheta), ]
  .fix <- .dft$fix
  .dft <- .df[is.na(.df$ntheta), ]
  c(.fix, .dft$fix)
}
#attr(rxUiGet.foFixed, "desc") <- "focei theta fixed vector"

#' @export
rxUiGet.foceiEtaNames <- function(x, ...) {
  .x <- x[[1]]
  .df <- get("iniDf", .x)
  .dft <- .df[is.na(.df$ntheta), ]
  .dft[.dft$neta1 == .dft$neta2, "name"]
}
#attr(rxUiGet.foceiEtaNames, "desc") <- "focei eta names"


#' This assigns the tolerances based on a different tolerance for the sensitivity equations
#'
#' It will update and modify the control inside of the UI.
#'
#' It also updates the predNeq that is needed for numeric derivatives
#'
#' @param ui rxode2 UI object
#' @param env focei environment for solving
#' @return Called for side effects
#' @author Matthew L. Fidler
#' @noRd
.foceiOptEnvAssignTol <- function(ui, env) {
  .len <- length(env$model$predNoLhs$state)
  rxode2::rxAssignControlValue(ui, "predNeq", .len)
  if (!is.null(env$model$inner)) {
    .len0 <- length(env$model$inner$state)
    .len2 <- .len0 - .len
    if (.len2 > 0) {
      .rxControl <- rxode2::rxGetControl(ui, "rxControl", rxode2::rxControl())
      rxode2::rxAssignControlValue(ui, "rxControl", rxode2::rxControlUpdateSens(.rxControl, .len2, .len0))
    }
  }
}
#' Assign the number of log likelihood items that need to be allocated
#'
#' @param ui rxode2 ui
#' @param env optimization environment
#' @return Nothing called for side effects.  Will update env$rxControl
#'   to have the maximum number of llik items in the model set.
#' @author Matthew L. Fidler
#' @noRd
.foceiOptEnvAssignNllik <- function(ui, env) {
  if (rxode2hasLlik()) {
    .maxLl <- max(vapply(seq_along(env$model), function(i) {
      .model <- env$model[[i]]
      if (inherits(.model, "rxode2")) {
        return(rxode2::rxModelVars(.model)$flags["nLlik"])
      } else {
        return(0L)
      }
    }, integer(1), USE.NAMES=FALSE))
    if (.maxLl > 0) {
      .rxControl <- rxode2::rxGetControl(ui, "rxControl", rxode2::rxControl())
      .rxControl$nLlikAlloc <- .maxLl
      rxode2::rxAssignControlValue(ui, "rxControl", .rxControl)
    }
  }
}

#'  This sets up the initial omega/eta estimates and the boundaries for the whole system
#'
#' @param ui rxode2 UI object
#' @param env focei solving environment
#' @return NoHing, called for side effecs
#' @author Matthew L. Fidler
#' @noRd
.foceiOptEnvSetupBounds <- function(ui, env) {
  .iniDf <- ui$iniDf
  .w <- which(!is.na(.iniDf$ntheta))
  .lower <- .iniDf$lower[.w]
  .upper <- .iniDf$upper[.w]
  env$thetaIni <- ui$theta
  env$thetaIni <- setNames(env$thetaIni, paste0("THETA[", seq_along(env$thetaIni), "]"))
  rxode2::rxAssignControlValue(ui, "nfixed", sum(ui$iniDf$fix))
  .mixed <- !is.null(env$etaNames)
  if (.mixed && length(env$etaNames) == 0L) .mixed <- FALSE
  if (!.mixed) {
    rxode2::rxAssignControlValue(ui, "nomega", 0)
    rxode2::rxAssignControlValue(ui, "neta", 0)
    env$xType <- -1
    rxode2::rxAssignControlValue(ui, "ntheta", length(ui$iniDf$lower))
  } else {
    .om0 <- ui$omega
    .diagXform <- rxode2::rxGetControl(ui, "diagXform", "sqrt")
    env$rxInv <- rxode2::rxSymInvCholCreate(mat = .om0, diag.xform = .diagXform)
    env$xType <- env$rxInv$xType
    .om0a <- .om0
    .om0a <- .om0a / rxode2::rxGetControl(ui, "diagOmegaBoundLower", 100)
    .om0b <- .om0
    .om0b <- .om0b * rxode2::rxGetControl(ui, "diagOmegaBoundUpper", 5)
    .om0a <- rxode2::rxSymInvCholCreate(mat = .om0a, diag.xform = .diagXform)
    .om0b <- rxode2::rxSymInvCholCreate(mat = .om0b, diag.xform = .diagXform)
    .omdf <- data.frame(a = .om0a$theta, m = env$rxInv$theta, b = .om0b$theta, diag = .om0a$theta.diag)
    .omdf$lower <- with(.omdf, ifelse(a > b, b, a))
    .omdf$lower <- with(.omdf, ifelse(lower == m, -Inf, lower))
    .omdf$lower <- with(.omdf, ifelse(!diag, -Inf, lower))
    .omdf$upper <- with(.omdf, ifelse(a < b, b, a))
    .omdf$upper <- with(.omdf, ifelse(upper == m, Inf, upper))
    .omdf$upper <- with(.omdf, ifelse(!diag, Inf, upper))
    rxode2::rxAssignControlValue(ui, "nomega", length(.omdf$lower))
    rxode2::rxAssignControlValue(ui, "neta", sum(.omdf$diag))
    rxode2::rxAssignControlValue(ui, "ntheta", length(.lower))
    .lower <- c(.lower, .omdf$lower)
    .upper <- c(.upper, .omdf$upper)
  }
  env$lower <- .lower
  env$upper <- .upper
  env$etaMat <- rxode2::rxGetControl(ui, "etaMat", NULL)
  env
}

#' Setup the scaleC
#'
#' @param ui rxode2 UI
#' @param env Focei setup environment
#' @return NoHing called for side effects
#' @author Matthew L. Fidler
#' @noRd
.foceiOptEnvSetupScaleC <- function(ui, env) {
  .controlScaleC <- rxode2::rxGetControl(ui, "scaleC", NULL)
  .len <- length(env$lower)
  if (is.null(.controlScaleC)) {
    .scaleC <- rep(NA_real_, .len)
  } else {
    .scaleC <- as.double(.controlScaleC)
  }
  .lenC <- length(.scaleC)
  if (.len > .lenC) {
    .scaleC <- c(.scaleC, rep(NA_real_, .len - .lenC))
  } else if (.len < .lenC) {
    .scaleC <- .scaleC[seq(1, .lenC)]
    warning("'scaleC' control option has more options than estimated population parameters, please check",
            call.=FALSE)
  }

  .ini <- ui$iniDf
  .ini <- .ini[!is.na(.ini$err), c("est", "err", "ntheta")]
  for (.i in seq_along(.ini$err)) {
    if (is.na(.scaleC[.ini$ntheta[.i]])) {
      if (any(.ini$err[.i] == c("boxCox", "yeoJohnson", "pow2", "tbs", "tbsYj"))) {
        .scaleC[.ini$ntheta[.i]] <- 1
      } else if (any(.ini$err[.i] == c("prop", "add", "norm", "dnorm", "logn", "dlogn", "lnorm", "dlnorm"))) {
        .scaleC[.ini$ntheta[.i]] <- 0.5 * abs(.ini$est[.i])
      }
    }
  }
  .muRefCurEval <- ui$muRefCurEval
  .ini <- ui$iniDf
  for (.i in seq_along(.muRefCurEval$parameter)) {
    .curEval <- .muRefCurEval$curEval[.i]
    .par <- .muRefCurEval$parameter[.i]
    .w <- which(.ini$name == .par)
    if (length(.w) == 1) {
      if (!is.na(.ini$ntheta[.w])) {
        .j <- .ini$ntheta[.w]
        if (is.na(.scaleC[.j])) {
          # These have similar deriavtes on a log scale.
          if (.curEval == "exp") {
            # Hence D(S("log(exp(x))"}, "x")
            .scaleC[.j] <- 1 # log scaled
          } else if (.curEval == "factorial") {
            # Hence 1/D(S("log(factorial(x))"}, "x"):
            .scaleC[.j] <- abs(1 / digamma(.ini$est[.j] + 1))
          } else if (.curEval == "gamma") {
            #1/D(log(gamma(x)), x)
            .scaleC[.j] <- abs(1 / digamma(.ini$est[.j]))
          } else if (.curEval == "log") {
            #1/D(log(log(x)), x)
            .scaleC[.j] <- log(abs(.ini$est[.j])) * abs(.ini$est[.j])
          } else if (.curEval == "logit") {
            # 1/D(log(logit(x, a, b)))
            .a <- .muRefCurEval$low[.i]
            .b <- .muRefCurEval$hi[.i]
            .x <- .ini$est[.j]
            .scaleC[.j] <- -1.0*(-.a + .x)^2*(-1.0 + 1.0*(-.a + .b)/(-.a + .x))*log(abs(-1.0 + 1.0*(-.a + .b)/(-.a + .x)))/(-.a + .b)
          } else if (.curEval == "expit") {
            # 1/D(log(expit(x, a, b)))
            .a <- .muRefCurEval$low[.i]
            .b <- .muRefCurEval$hi[.i]
            .x <- .ini$est[.j]
            .scaleC[.j] <- 1.0*exp(.x)*(1.0 + exp(-.x))^2*(.a + 1.0*(-.a + .b)/(1.0 + exp(-.x)))/(-.a + .b)
          } else if (.curEval == "probitInv") {
            .a <- .muRefCurEval$low[.i]
            .b <- .muRefCurEval$hi[.i]
            .x <- .ini$est[.j]
            .scaleC[.j] <- 1.4142135623731*exp(0.5*.x^2)*sqrt(pi)*(.a + 0.5*(-.a + .b)*(1.0 + rxode2::erf(0.707106781186547*.x)))/(-.a + .b)
          } else if (.curEval == "probit") {
            .a <- .muRefCurEval$low[.i]
            .b <- .muRefCurEval$hi[.i]
            .x <- .ini$est[.j]
            erfinvF  <- function(y) {
              if(abs(y) > 1) return(NA_real_)
              sqrt(qchisq(abs(y),1)/2) * sign(y)
            }
            .scaleC[.j] <- sqrt(2)*(-.a+.b)*erfinvF(-1+2*(-.a+.x)/(-.a+.b))/sqrt(pi)/2*exp(((erfinvF(-1+2*(-.a+.x)/(-.a+.b))) ^ 2))
          }
        }
      }
    }
  }
  env$scaleC <- .scaleC
}

#' This sets up the transformation bounds and indexes and bounds for inner.cpp
#'
#' Note that the C code assumes the index starts at 1
#'
#' @param ui rxode2 ui environment
#' @param env focei environment used for solving
#' @return Nothing called for side effects
#' @author Matthew L. Fidler
#' @noRd
.foceiOptEnvSetupTransformIndexs <- function(ui, env) {
  .muRefCurEval <- ui$muRefCurEval
  .ini <- ui$iniDf
  .ini <- .ini[!is.na(.ini$ntheta), c("ntheta", "name")]
  names(.ini)[2] <- "parameter"
  .transform <- merge(.ini, .muRefCurEval)
  .transform <- .transform[order(.transform$ntheta), ]

  env$logThetasF <- .transform[which(.transform$curEval == "exp"), "ntheta"]

  env$logitThetasF <- .transform[which(.transform$curEval == "expit"), "ntheta"]
  env$logitThetasLowF <- .transform[which(.transform$curEval == "expit"), "low"]
  env$logitThetasHiF <- .transform[which(.transform$curEval == "expit"), "hi"]

  env$probitThetasF <- .transform[which(.transform$curEval == "probitInv"), "ntheta"]
  env$probitThetasLowF <- .transform[which(.transform$curEval == "probitInv"), "low"]
  env$probitThetasHiF <- .transform[which(.transform$curEval == "probitInv"), "hi"]
}

# focei.mu.ref
# eta# and the corresponding theta number

#' @export
rxUiGet.foceiMuRefVector <- function(x, ...) {
  .ui <- x[[1]]
  .iniDf <- .ui$iniDf
  .muRefDataFrame <- .ui$muRefDataFrame
  .w <- which(!is.na(.iniDf$ntheta))
  .i2 <- .iniDf[-.w, ]
  if (length(.i2$name) > 0) {
    .i2 <- .i2[.i2$neta1 == .i2$neta2, ]
    .i2 <- .i2[order(.i2$neta1), ]
    vapply(seq_along(.i2$neta1), function(i) {
      if (.i2$fix[i]) return(-1L)
      .name <- .i2$name[i]
      .w <- which(.muRefDataFrame$eta == .name)
      if (length(.w) != 1) return(-1L)
      .name <- .muRefDataFrame$theta[.w]
      .w <- which(.iniDf$name == .name)
      if (length(.w) != 1) return(-1L)
      if (.iniDf$fix[.w]) return(-1L)
      .iniDf$ntheta[.w] - 1L
    }, integer(1))
  } else {
    integer(0)
  }
}
#attr(rxUiGet.foceiMuRefVector, "desc") <- "focei mu ref vector"

#' @export
rxUiGet.foceiSkipCov <- function(x, ...) {
  .ui <- x[[1]]
  .maxTheta <- max(.ui$iniDf$ntheta, na.rm=TRUE)
  .theta <- .ui$iniDf[!is.na(.ui$iniDf$ntheta), ]
  .skipCov <- rep(FALSE, .maxTheta)
  .skipCov[which(!is.na(.theta$err))] <- TRUE
  .skipCov[.theta$fix] <- TRUE
  .skipCov
}
#attr(rxUiGet.foceiSkipCov, "desc") <- "what covariance elements to skip"

#'  Setup the skip covariate function
#'
#'
#' @param ui rxode2 parsed function
#' @param env environment
#' @return Nothing called for side effects.
#' @author Matthew L. Fidler
#' @noRd
.foceiSetupSkipCov <- function(ui, env) {
  env$skipCov <- rxode2::rxGetControl(ui, "skipCov", NULL)
  if (is.null(env$skipCov)) {
    env$skipCov <- ui$foceiSkipCov
  }
  .maxTheta <- max(ui$iniDf$ntheta, na.rm=TRUE)
  if (length(env$skipCov) > .maxTheta) {
    if (all(env$skipCov[-seq_len(.maxTheta)])) {
      assign("skipCov",env$skipCov[seq_len(.maxTheta)], env)
    }
  }
  if (length(env$skipCov) != .maxTheta) {
    stop("'skipCov' improperly specified", call.=FALSE)
  }
}

.foceiOptEnvLik <- function(ui, env) {
  #if (!exists("noLik", envir = env)){
  if (!exists("model", envir=env)) {
    env$model <- rxUiGet.foceiModel(list(ui))
  }
  #} else {
  #env$model <- rxUiGet.ebe(list(ui))
  #}
  .foceiOptEnvAssignTol(ui, env)
  .foceiOptEnvAssignNllik(ui, env)
  .foceiOptEnvSetupBounds(ui, env)
  .foceiOptEnvSetupScaleC(ui, env)
  .foceiOptEnvSetupTransformIndexs(ui, env)
  .foceiSetupSkipCov(ui, env)
  env$control <- get("control", envir=ui)
  env$control$nF <- 0
  env$control$printTop <- TRUE
  env
}

#' @export
rxUiGet.foceiOptEnv <- function(x, ...) {
  .x <- x[[1]]
  if (exists("foceiEnv", envir=.x)) {
    .env <- get("foceiEnv", envir=.x)
    rm("foceiEnv", envir=.x)
  } else {
    .env <- new.env(parent=emptyenv())
  }
  .env$etaNames <- rxUiGet.foceiEtaNames(x, ...)
  .env$thetaFixed <- rxUiGet.foceiFixed(x, ...)
  rxode2::rxAssignControlValue(.x, "foceiMuRef", .x$foceiMuRefVector)
  .env$adjLik <- rxode2::rxGetControl(.x, "adjLik", TRUE)
  .env$diagXformInv <- c("sqrt" = ".square", "log" = "exp", "identity" = "identity")[rxode2::rxGetControl(.x, "diagXform", "sqrt")]
  .env$thetaNames <- .x$iniDf[!is.na(.x$iniDf$ntheta), "name"]
  # FIXME is ODEmodel needed?
  .env$ODEmodel <- TRUE
  .foceiOptEnvLik(.x, .env)
  .env
}
attr(rxUiGet.foceiOptEnv, "desc") <- "Get focei optimization environment"
#' This function process the data for use in focei
#'
#' The $origData is the data that is fed into the focei before modification
#' The $dataSav is the data saved for focei
#'
#' @param data Input dataset
#' @param env focei environment where focei family is run
#' @param ui rxode2 ui
#' @return Nothing, called for side effects
#' @author Matthew L. Fidler
#' @keywords internal
#' @export
.foceiPreProcessData <- function(data, env, ui) {
  env$origData <- as.data.frame(data)
  data <- env$origData
  .covNames <- ui$covariates
  colnames(data) <- vapply(names(data), function(x) {
    if (any(x == .covNames)) {
      return(x)
    } else {
      return(toupper(x))
    }
  }, character(1))
  requiredCols <- c("ID", "DV", "TIME", .covNames)
  checkmate::assert_names(names(data), must.include = requiredCols)
  if (is.null(data$EVID)) data$EVID <- 0
  if (is.null(data$AMT)) data$AMT <- 0
  ## Make sure they are all double amounts.
  for (.v in c("DV", "TIME")) {
    data[[.v]] <- as.double(data[[.v]])
  }
  .lvls <- NULL
  for (.v in .covNames) {
    .d <- data[[.v]]
    if (inherits(.d, "character")) {
      .l <- factor(.d)
      data[[.v]] <- .l
      .lvls <- c(.lvls, setNames(list(levels(.l)), .v))
    } else if (inherits(.d, "factor")) {
      .lvls <- c(.lvls, setNames(list(levels(.d)), .v))
    }
  }
  data$nlmixrRowNums <- seq_len(nrow(data))
  .keep <- unique(c("nlmixrRowNums", env$table$keep))
  .et <- rxode2::etTrans(inData=data, obj=ui$mv0,
                         addCmt=TRUE, dropUnits=TRUE,
                         keep=unique(c("nlmixrRowNums", env$table$keep)),
                         allTimeVar=TRUE, keepDosingOnly=FALSE)
  .lst <- attr(class(.et), ".rxode2.lst")
  .keepL <- .lst$keepL[[1]]
  .idLvl <- .lst$idLvl
  .dat <- cbind(as.data.frame(.et), .keepL)
  env$dataSav <- .dat
  env$idLvl <- .idLvl
  env$covLvl <- .lvls
}

.thetaReset <- new.env(parent = emptyenv())
#' Internal focei fit function in R
#'
#' @param .ret Internal focei environment
#' @return Modified focei environment with fit information (from C++)
#' @author Matthew L. Fidler
#' @noRd
.foceiFitInternal <- function(.ret) {
  if (exists("objective", .ret)) {
    checkmate::assertNumeric(.ret$objective, len=1, .var.name="fitEnv$objective")
  }
  if (exists("etaObf", .ret)) {
    checkmate::assertDataFrame(.ret$etaObf, .var.name="fitEnv$etaObf")
    if (!(names(.ret$etaObf)[1] == "ID")) {
      stop("the first column of fitEnv$etaObj needs to be an integer and named ID",
           call.=FALSE)
    }
    checkmate::assertInteger(.ret$etaObf$ID, any.missing=FALSE, min=1, .var.name="fitEnv$etaObj$ID")
  }
  this.env <- new.env(parent=emptyenv())
  assign("err", "theta reset", this.env)
  .thetaReset$thetaNames <- .ret$thetaNames
  if (getOption("nlmixr2.retryFocei", TRUE)) {
    while (this.env$err == "theta reset") {
      assign("err", "", this.env)
      .ret0 <- tryCatch(
      {
        foceiFitCpp_(.ret)
      },
      error = function(e) {
        if (regexpr("theta reset", e$message) != -1) {
          assign("zeroOuter", FALSE, this.env)
          assign("zeroGrad", FALSE, this.env)
          if (regexpr("theta reset0", e$message) != -1) {
            assign("zeroGrad", TRUE, this.env)
          }  else if (regexpr("theta resetZ", e$message) != -1) {
            assign("zeroOuter", TRUE, this.env)
          }
          assign("err", "theta reset", this.env)
        } else {
          assign("err", e$message, this.env)
        }
      })
      if (this.env$err == "theta reset") {
        .nm <- names(.ret$thetaIni)
        .ret$thetaIni <- setNames(.thetaReset$thetaIni + 0.0, .nm)
        .ret$rxInv$theta <- .thetaReset$omegaTheta
        .ret$control$printTop <- FALSE
        .ret$etaMat <- .thetaReset$etaMat
        .ret$control$etaMat <- .thetaReset$etaMat
        .ret$control$maxInnerIterations <- .thetaReset$maxInnerIterations
        .ret$control$nF <- .thetaReset$nF
        #.ret$control$gillRetC <- .thetaReset$gillRetC
        #.ret$control$gillRet <- .thetaReset$gillRet
        #.ret$control$gillRet <- .thetaReset$gillRet
        #.ret$control$gillDf <- .thetaReset$gillDf
        #.ret$control$gillDf2 <- .thetaReset$gillDf2
        #.ret$control$gillErr <- .thetaReset$gillErr
        #.ret$control$rEps <- .thetaReset$rEps
        #.ret$control$aEps <- .thetaReset$aEps
        #.ret$control$rEpsC <- .thetaReset$rEpsC
        #.ret$control$aEpsC <- .thetaReset$aEpsC
        .ret$control$c1 <- .thetaReset$c1
        .ret$control$c2 <- .thetaReset$c2
        if (this.env$zeroOuter) {
          message("Posthoc reset")
          .ret$control$maxOuterIterations <- 0L
        } else if (this.env$zeroGrad) {
          message("Theta reset (zero/bad gradient values); Switch to bobyqa")
          rxode2::rxReq("minqa")
          .ret$control$outerOptFun <- .bobyqa
          .ret$control$outerOpt <- -1L
          .ret$control$outerOptTxt <- "bobyqa"
        } else {
          message("Theta reset (ETA drift)")
        }
      } else if (this.env$err != "") {
        stop(this.env$err)
      } else {
        return(.ret0)
      }
    }
  } else {
    foceiFitCpp_(.ret)
  }
}

.nlmixrCheckFoceiEnvironment <- function(ret) {
  checkmate::assertDataFrame(ret$dataSav, .var.name="focei$dataSav")
  checkmate::assertNumeric(ret$thetaIni, any.missing=FALSE,
                           null.ok=TRUE, .var.name="focei$thetaIni")
  checkmate::assertLogical(ret$skipCov, null.ok=TRUE,
                           any.missing=FALSE, .var.name="focei$skipCov")
  if (!inherits(ret$rxInv, "rxSymInvCholEnv")) {
    stop("focei$rxInv needs to be of class'rxSymInvCholEnv'",
         call.=FALSE)
  }
  checkmate::assertNumeric(ret$lower, null.ok=TRUE,
                           any.missing=FALSE, .var.name="focei$lower")
  checkmate::assertNumeric(ret$upper, null.ok=TRUE,
                           any.missing=FALSE, .var.name="focei$upper")
  checkmate::assertMatrix(ret$etaMat, mode="double", null.ok=TRUE,
                          any.missing=FALSE, .var.name="focei$etaMat")
  if (!inherits(ret$control, "foceiControl")) {
    stop("focei$control must be a focei control object",
         call.=FALSE)
  }
}

#'  Restart the estimation if it wasn't successful by moving the parameters (randomly)
#'
#' @param .ret0 Fit
#' @param .ret Input focei environment
#' @param control Control represents the foceiControl to restart the fit
#' @return final focei fit, may still not work
#' @author Matthew L. Fidler
#' @noRd
.nlmixrFoceiRestartIfNeeded <- function(.ret0, .ret, control) {
  .n <- 1
  .est0 <- .ret$thetaIni
  lower <- .ret$lower
  upper <- .ret$upper
  while (inherits(.ret0, "try-error") && control$maxOuterIterations != 0 && .n <= control$nRetries) {
    .draw <- TRUE
    if (attr(.ret0, "condition")$message == "Evaluation error: On initial gradient evaluation, one or more parameters have a zero gradient\nChange model, try different initial estimates or use outerOpt=\"bobyqa\").") {
      message("Changing to \"bobyqa\"")
      rxode2::rxReq("minqa")
      .ret$control$outerOpt <- -1L
      .ret$control$outerOptFun <- .bobyqa
      .ret$control$outerOptTxt <- "bobyqa"
      .draw <- FALSE
    }
    ## Maybe change scale?
    message(sprintf("Restart %s", .n))
    .ret$control$nF <- 0
    .estNew <- .est0 + 0.2 * .n * abs(.est0) * stats::runif(length(.est0)) - 0.1 * .n
    .estNew <- vapply(
      seq_along(.est0),
      function(.i) {
        if (!.draw || .ret$thetaFixed[.i]) {
          return(.est0[.i])
        } else if (.estNew[.i] < lower[.i]) {
          return(lower[.i] + (.Machine$double.eps)^(1 / 7))
        } else if (.estNew[.i] > upper[.i]) {
          return(upper[.i] - (.Machine$double.eps)^(1 / 7))
        } else {
          return(.estNew[.i])
        }
      }, numeric(1), USE.NAMES=FALSE)
    .ret$thetaIni <- setNames(.estNew, names(.est0))
    .nlmixrCheckFoceiEnvironment(.ret)
    if (getOption("nlmixr2.retryFocei", TRUE)) {
      .ret0 <- try(.foceiFitInternal(.ret))
    } else {
      .ret0 <- .foceiFitInternal(.ret)
    }

    .n <- .n + 1
  }
  .ret0
}
#'  Assign the control to the ui
#'
#' @param env Estimation/output environment
#' @param ... Other arguments
#' @return nothing, called for side effects
#' @author Matthew L. Fidler
#' @noRd
.foceiFamilyControl <- function(env, ...) {
  .ui <- env$ui
  .control <- env$control
  if (is.null(.control)) {
    .control <- foceiControl()
  }
  if (!inherits(.control, "foceiControl")) {
    .control <- do.call(nlmixr2est::foceiControl, .control)
  }
  .control$needOptimHess <- any(.ui$predDfFocei$distribution != "norm")
  if (.control$needOptimHess) {
    .control$interaction <- 0L
  }
  assign("control", .control, envir=.ui)
}

#' Get the cmt() and dvid() lines
#'
#' @param ui rxode UI
#' @return cmt() and dvid() string
#' @author Matthew L. Fidler
#' @noRd
.foceiToCmtLinesAndDvid <- function(ui) {
  .cmtLines <- ui$cmtLines
  paste(c("", vapply(seq_along(.cmtLines),
                     function(i){deparse1(.cmtLines[[i]])},
                     character(1), USE.NAMES=FALSE),
          deparse1(ui$dvidLine)),
        collapse="\n")
}

#' Setup the par history information
#'
#' @param .ret Return data
#' @return Nothing called for side effects
#' @author Matthew L. Fidler
#' @noRd
.foceiSetupParHistData <- function(.ret) {
  if (exists("parHistData", envir=.ret)) {
    .tmp <- .ret$parHistData
    .tmp <- .tmp[.tmp$type == "Unscaled", names(.tmp) != "type"]
    .iter <- .tmp$iter
    .tmp <- .tmp[, names(.tmp) != "iter"]
    ## .ret$parHistStacked <- data.frame(stack(.tmp), iter = .iter)
    ## names(.ret$parHistStacked) <- c("val", "par", "iter")
    .ret$parHist <- data.frame(iter = .iter, .tmp)
  }
}


.foceiFamilyReturn <- function(env, ui, ..., method=NULL, est="none") {
  .control <- ui$control
  .env <- ui$foceiOptEnv
  .env$table <- env$table
  .data <- env$data
  .foceiPreProcessData(.data, .env, ui)
  if (!is.null(.env$cov)) {
    checkmate::assertMatrix(.env$cov, any.missing=FALSE, min.rows=1, .var.name="env$cov",
                            row.names="strict", col.names="strict")
  }
  if (getOption("nlmixr2.retryFocei", TRUE)) {
    .ret0 <- try(.foceiFitInternal(.env))
  } else {
    .ret0 <- .foceiFitInternal(.env)
  }
  .ret0 <- .nlmixrFoceiRestartIfNeeded(.ret0, .env, .control)
  if (inherits(.ret0, "try-error")) {
    stop("Could not fit data\n  ", attr(.ret0, "condition")$message, call.=FALSE)
  }
  .ret <- .ret0
  if (!is.null(method))
    .ret$method <- method
  .ret$ui <- ui
  .foceiSetupParHistData(.ret)
  if (!all(is.na(ui$iniDf$neta1))) {
    .etas <- .ret$ranef
    .thetas <- .ret$fixef
    .pars <- .Call(`_nlmixr2est_nlmixr2Parameters`, .thetas, .etas)
    .ret$shrink <- .Call(`_nlmixr2est_calcShrinkOnly`, .ret$omega, .pars$eta.lst, length(.etas$ID))
  }
  assign("est", est, envir=.ret)
  .updateParFixed(.ret)
  if (!exists("table", .ret)) {
    .ret$table <- tableControl()
  }
  .nlmixr2FitUpdateParams(.ret)
  .ret$IDlabel <- rxode2::.getLastIdLvl()
  if (exists("skipTable", envir=.ret)) {
    if (is.na(.ret$skipTable)) {
    } else if (.ret$skipTable) {
      .control$calcTables <- FALSE
    }
  }
  assign("skipCov", .env$skipCov, envir=.ret)
  nmObjHandleModelObject(.ret$model, .ret)
  nmObjHandleControlObject(get("control", envir=.ret), .ret)
  assignInMyNamespace(".currentTimingEnvironment", .ret) # add environment for updating timing info
  if (.control$calcTables) {
    .ret <- addTable(.ret, updateObject="no", keep=.ret$table$keep, drop=.ret$table$drop,
                     table=.ret$table)
  }
  nlmixrWithTiming("compress", {
    if (exists("saem", .env)) {
      .saem <- get("saem", envir=.env)
      .saemCfg <- attr(.saem, "saem.cfg")
      # Delete unneeded variables
      .saemCfg2 <- list()
      for (.v in c("i1", "nphi1", "nphi0", "N", "ntotal", "ix_endpnt", "y", "nmc", "niter", "opt", "inits", "Mcovariables")) {
        .saemCfg2[[.v]] <- .saemCfg[[.v]]
      }
      attr(.saem, "saem.cfg") <- .saemCfg2
      rm(list="saem", envir=.env)
      .env$saem0 <- .saem
    }
    if (.control$compress) {
      for (.item in c("origData", "phiM", "parHist", "saem0")) {
        if (exists(.item, .env)) {
          .obj <- get(.item, envir=.env)
          .size <- utils::object.size(.obj)
          .objC <- qs::qserialize(.obj)
          .size2 <- utils::object.size(.objC)
          if (.size2 < .size) {
            .size0 <- (.size - .size2)
            .malert("compress {  .item } in nlmixr2 object, save { .size0 }" )
            assign(.item, .objC, envir=.env)
          }
        }
      }
    }
    for (.item in c("adj", "adjLik", "diagXformInv", "etaMat", "etaNames",
                    "fullTheta", "scaleC", "gillRet", "gillRetC",
                    "logitThetasF", "logitThetasHiF", "logitThetasLowF", "logThetasF",
                    "lower", "noLik", "objf", "OBJF", "probitThetasF", "probitThetasHiF", "probitThetasLowF",
                    "rxInv", "scaleC", "se", "skipCov", "thetaFixed", "thetaIni", "thetaNames", "upper",
                    "xType", "IDlabel", "ODEmodel",
                    # times
                    "optimTime", "setupTime", "covTime",
                    "parHistData", "dataSav", "idLvl", "theta",
                    "missingTable", "missingControl", "missingEst")) {
      if (exists(.item, .env)) {
        rm(list=.item, envir=.env)
      }
    }
    assign("ui", rxode2::rxUiCompress(.env$ui), envir=.env)
  })
  if (any(names(.ret) == "CWRES") && regexpr("^fo", est) == -1) {
    # focei is available; add objective function
    .setOfvFo(.ret, "focei")
  }
  .ret
}

#'@rdname nlmixr2Est
#'@export
nlmixr2Est.focei <- function(env, ...) {
  .ui <- env$ui
  rxode2::assertRxUiRandomOnIdOnly(.ui, " for the estimation routine 'focei'", .var.name=.ui$modelName)
  if (!rxode2hasLlik()) {
    rxode2::assertRxUiTransformNormal(.ui, " for the estimation routine 'focei'", .var.name=.ui$modelName)
  }

  .foceiFamilyControl(env, ...)
  on.exit({
    if (exists("control", envir=.ui)) {
      rm("control", envir=.ui)
    }
  })
  .foceiFamilyReturn(env, .ui, ..., est="focei")
}


#'@rdname nlmixr2Est
#'@export
nlmixr2Est.foce <- function(env, ...) {
  .ui <- env$ui
  rxode2::assertRxUiRandomOnIdOnly(.ui, " for the estimation routine 'foce'", .var.name=.ui$modelName)
  if (!rxode2hasLlik()) {
    rxode2::assertRxUiTransformNormal(.ui, " for the estimation routine 'focei'", .var.name=.ui$modelName)
  }

  .foceiFamilyControl(env, ...)
  rxode2::rxAssignControlValue(.ui, "interaction", 0L)
  on.exit({
    if (exists("control", envir=.ui)) {
      rm("control", envir=.ui)
    }
  })
  env$est <- "foce"
  .foceiFamilyReturn(env, .ui, ..., est="focei")
}

#'@rdname nlmixr2Est
#'@export
nlmixr2Est.posthoc <- function(env, ...) {
  .ui <- env$ui
  rxode2::assertRxUiRandomOnIdOnly(.ui, " for the estimation routine 'posthoc'", .var.name=.ui$modelName)
  .foceiFamilyControl(env, ...)
  rxode2::rxAssignControlValue(.ui, "interaction", 0L)
  rxode2::rxAssignControlValue(.ui, "covMethod", 0L)
  rxode2::rxAssignControlValue(.ui, "maxOuterIterations", 0L)
  on.exit({
    if (exists("control", envir=.ui)) {
      rm("control", envir=.ui)
    }
  })
  env$est <- "posthoc"
  .foceiFamilyReturn(env, .ui, ..., est="posthoc")
}

#' Add objective function line to the return object
#'
#' @param ret Return object
#' @param objDf Objective function data frame to add
#' @return Nothing, called for side effects
#' @author Matthew L. Fidler
#' @noRd
.addObjDfToReturn <- function(ret, objDf) {
  if (inherits(ret, "nlmixr2FitData")) {
    ret <- attr(class(ret), ".foceiEnv")
  }
  .objDf1 <- get("objDf", ret)
  if (any(names(.objDf1) == "Condition#(Cov)")) {
    if (!any(names(objDf) == "Condition#(Cov)")) {
      objDf[["Condition#(Cov)"]] <- NA_real_
    }
  } else if (any(names(objDf) == "Condition#(Cov)")) {
    if (!any(names(.objDf1) == "Condition#(Cov)")) {
      .objDf1[["Condition#(Cov)"]] <- NA_real_
    }
  }
  if (any(names(.objDf1) == "Condition#(Cor)")) {
    if (!any(names(objDf) == "Condition#(Cor)")) {
      objDf[["Condition#(Cor)"]] <- NA_real_
    }
  } else if (any(names(objDf) == "Condition#(Cor)")) {
    if (!any(names(.objDf1) == "Condition#(Cor)")) {
      .objDf1[["Condition#(Cor)"]] <- NA_real_
    }
  }
  assign("objDf", rbind(.objDf1, objDf), envir=ret)
}

#'@rdname nlmixr2Est
#'@export
nlmixr2Est.foi <- function(env, ...) {
  .ui <- env$ui
  rxode2::assertRxUiTransformNormal(.ui, " for the estimation routine 'foi'", .var.name=.ui$modelName)
  rxode2::assertRxUiRandomOnIdOnly(.ui, " for the estimation routine 'foi'", .var.name=.ui$modelName)
  rxode2::assertRxUiRandomOnIdOnly(.ui, " for the estimation routine 'foi'", .var.name=.ui$modelName)
  rxode2::assertRxUiMixedOnly(.ui, " for the estimation routine 'foi'", .var.name=.ui$modelName)

  .foceiFamilyControl(env, ...)
  .control <- .ui$control
  rxode2::rxAssignControlValue(.ui, "interaction", 0L)
  rxode2::rxAssignControlValue(.ui, "covMethod", 0L)
  rxode2::rxAssignControlValue(.ui, "fo", TRUE)
  rxode2::rxAssignControlValue(.ui, "boundTol", 0)
  on.exit({
    if (exists("control", envir=.ui)) {
      rm("control", envir=.ui)
    }
  })
  env$skipTable <- TRUE
  .ret <- .foceiFamilyReturn(env, .ui, ...)
  .objDf <- .ret$objDf
  .ui <- .ret$ui
  assign("control", .control, envir=.ui)
  .foceiFamilyControl(env, ...)
  rxode2::rxAssignControlValue(.ui, "interaction", 1L)
  rxode2::rxAssignControlValue(.ui, "maxOuterIterations", 0L)
  env$skipTable <- FALSE
  .ret <- .foceiFamilyReturn(env, .ui, ..., method="FO", est="foi")
  .addObjDfToReturn(.ret, .objDf)
  .ret
}


#'@rdname nlmixr2Est
#'@export
nlmixr2Est.fo <- function(env, ...) {
  .ui <- env$ui
  rxode2::assertRxUiTransformNormal(.ui, " for the estimation routine 'fo'", .var.name=.ui$modelName)
  rxode2::assertRxUiRandomOnIdOnly(.ui, " for the estimation routine 'fo'", .var.name=.ui$modelName)
  rxode2::assertRxUiMixedOnly(.ui, " for the estimation routine 'fo'", .var.name=.ui$modelName)

  .foceiFamilyControl(env, ...)
  .control <- .ui$control
  rxode2::rxAssignControlValue(.ui, "interaction", 0L)
  rxode2::rxAssignControlValue(.ui, "covMethod", 0L)
  rxode2::rxAssignControlValue(.ui, "fo", TRUE)
  rxode2::rxAssignControlValue(.ui, "boundTol", 0)
  on.exit({
    if (exists("control", envir=.ui)) {
      rm("control", envir=.ui)
    }
  })
  env$skipTable <- TRUE
  .ret <- .foceiFamilyReturn(env, .ui, ...)
  .objDf <- .ret$objDf
  .ui <- .ret$ui
  assign("control", .control, envir=.ui)
  .foceiFamilyControl(env, ...)
  rxode2::rxAssignControlValue(.ui, "interaction", 0L)
  rxode2::rxAssignControlValue(.ui, "maxOuterIterations", 0L)
  .ret <- .foceiFamilyReturn(env, .ui, ..., method="FO", est="fo")
  .addObjDfToReturn(.ret, .objDf)
  .ret
}

#'@rdname nlmixr2Est
#'@export
nlmixr2Est.output <- function(env, ...) {
  .ui <- env$ui
  rxode2::assertRxUiRandomOnIdOnly(.ui, " for the estimation routine 'output'", .var.name=.ui$modelName)
  if (!rxode2hasLlik()) {
    rxode2::assertRxUiTransformNormal(.ui, " for the estimation routine 'output'", .var.name=.ui$modelName)
  }

  .foceiFamilyControl(env, ...)
  rxode2::rxAssignControlValue(.ui, "interaction", 0L)
  rxode2::rxAssignControlValue(.ui, "maxOuterIterations", 0L)
  rxode2::rxAssignControlValue(.ui, "maxInnerIterations", 0L)
  on.exit({
    if (exists("control", envir=.ui)) {
      rm("control", envir=.ui)
    }
  })
  if (!exists("est", envir=env)) env$est <- "posthoc"
  .foceiFamilyReturn(env, .ui, ..., est=env$est)
}

#' Create nlmixr output from the UI
#'
#'
#' @param ui This is the UI that will be used for the translation
#' @param data This has the data
#' @param control focei control for data creation
#' @param table Table options
#' @param env Environment setup which needs the following:
#' - `$table` for table options
#' - `$origData` -- Original Data
#' - `$dataSav` -- Processed data from .foceiPreProcessData
#' - `$idLvl` -- Level information for ID factor added
#' - `$covLvl` -- Level information for items to convert to factor
#' - `$ui` for ui object
#' - `$fullTheta` Full theta information
#' - `$etaObf` data frame with ID, etas and OBJI
#' - `$cov` For covariance
#' - `$covMethod` for the method of calculating the covariance
#' - `$adjObf` Should the objective function value be adjusted
#' - `$objective` objective function value
#' - `$extra` Extra print information
#' - `$method` Estimation method (for printing)
#' - `$omega` Omega matrix
#' - `$theta` Is a theta data frame
#' - `$model` a list of model information for table generation.  Needs a `predOnly` model
#' - `$message` Message for display
#' - `$est` estimation method
#' - `$ofvType` (optional) tells the type of ofv is currently being use
#'
#' There are some more details that need to be described here
#'
#' @param est Estimation method
#' @return nlmixr fit object
#' @author Matthew L. Fidler
#' @export
nlmixr2CreateOutputFromUi <- function(ui, data=NULL, control=NULL, table=NULL, env=NULL, est="none") {
  assignInMyNamespace(".finalUiCompressed", FALSE)
  on.exit(assignInMyNamespace(".finalUiCompressed", TRUE))
  if (inherits(ui, "function")) {
    ui <- rxode2::rxode2(ui)
  }
  if (!inherits(ui, "rxUi")) {
    stop("the first argument needs to be from rxode2 ui", call.=FALSE)
  }
  ui <- rxode2::rxUiDecompress(ui)
  if (inherits(env, "environment")) {
    assign("foceiEnv", env, envir=ui)
  }
  if (!inherits(data, "data.frame")) {
    stop("the 'data' argument must be a data.frame", call.=FALSE)
  }
  .env <- new.env(parent=emptyenv())
  assign("ui", ui, envir=.env)
  .env$data <- data
  .env$control <- control
  .env$table <- table
  .env$est <- est
  class(.env) <- c("output", "nlmixr2Est")
  nlmixr2Est(.env)
}