Rename saemix file, option to suppress saemix messages

1 files changed, 0 insertions, 416 deletions

diff --git a/R/saemix.R b/R/saemix.R
deleted file mode 100644
index 50497423..00000000
--- a/R/saemix.R
+++ /dev/null
@@ -1,416 +0,0 @@
-#' Fit nonlinear mixed models with SAEM
-#'
-#' This function uses [saemix::saemix()] as a backend for fitting nonlinear mixed
-#' effects models created from [mmkin] row objects using the Stochastic Approximation
-#' Expectation Maximisation algorithm (SAEM).
-#'
-#' An mmkin row object is essentially a list of mkinfit objects that have been
-#' obtained by fitting the same model to a list of datasets using [mkinfit].
-#'
-#' Starting values for the fixed effects (population mean parameters, argument
-#' psi0 of [saemix::saemixModel()] are the mean values of the parameters found
-#' using [mmkin].
-#'
-#' @param object An [mmkin] row object containing several fits of the same
-#'   [mkinmod] model to different datasets
-#' @param verbose Should we print information about created objects?
-#' @param cores The number of cores to be used for multicore processing using
-#'   [parallel::mclapply()]. Using more than 1 core is experimental and may
-#'   lead to uncontrolled forking, apparently depending on the BLAS version
-#'   used.
-#' @param suppressPlot Should we suppress any plotting that is done
-#'   by the saemix function?
-#' @param control Passed to [saemix::saemix]
-#' @param \dots Further parameters passed to [saemix::saemixData]
-#'   and [saemix::saemixModel].
-#' @return An S3 object of class 'saem.mmkin', containing the fitted
-#'   [saemix::SaemixObject] as a list component named 'so'. The
-#'   object also inherits from 'mixed.mmkin'.
-#' @seealso [summary.saem.mmkin] [plot.mixed.mmkin]
-#' @examples
-#' \dontrun{
-#' ds <- lapply(experimental_data_for_UBA_2019[6:10],
-#'  function(x) subset(x$data[c("name", "time", "value")]))
-#' names(ds) <- paste("Dataset", 6:10)
-#' f_mmkin_parent_p0_fixed <- mmkin("FOMC", ds, cores = 1,
-#'   state.ini = c(parent = 100), fixed_initials = "parent", quiet = TRUE)
-#' f_saem_p0_fixed <- saem(f_mmkin_parent_p0_fixed)
-#'
-#' f_mmkin_parent <- mmkin(c("SFO", "FOMC", "DFOP"), ds, quiet = TRUE)
-#' f_saem_sfo <- saem(f_mmkin_parent["SFO", ])
-#' f_saem_fomc <- saem(f_mmkin_parent["FOMC", ])
-#' f_saem_dfop <- saem(f_mmkin_parent["DFOP", ])
-#'
-#' # The returned saem.mmkin object contains an SaemixObject, therefore we can use
-#' # functions from saemix
-#' library(saemix)
-#' compare.saemix(list(f_saem_sfo$so, f_saem_fomc$so, f_saem_dfop$so))
-#' plot(f_saem_fomc$so, plot.type = "convergence")
-#' plot(f_saem_fomc$so, plot.type = "individual.fit")
-#' plot(f_saem_fomc$so, plot.type = "npde")
-#' plot(f_saem_fomc$so, plot.type = "vpc")
-#'
-#' f_mmkin_parent_tc <- update(f_mmkin_parent, error_model = "tc")
-#' f_saem_fomc_tc <- saem(f_mmkin_parent_tc["FOMC", ])
-#' compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so))
-#'
-#' sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"),
-#'   A1 = mkinsub("SFO"))
-#' fomc_sfo <- mkinmod(parent = mkinsub("FOMC", "A1"),
-#'   A1 = mkinsub("SFO"))
-#' dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),
-#'   A1 = mkinsub("SFO"))
-#' # The following fit uses analytical solutions for SFO-SFO and DFOP-SFO,
-#' # and compiled ODEs for FOMC, both are fast
-#' f_mmkin <- mmkin(list(
-#'     "SFO-SFO" = sfo_sfo, "FOMC-SFO" = fomc_sfo, "DFOP-SFO" = dfop_sfo),
-#'   ds, quiet = TRUE)
-#' # These take about five seconds each on this system, as we use
-#' # analytical solutions written for saemix. When using the analytical
-#' # solutions written for mkin this took around four minutes
-#' f_saem_sfo_sfo <- saem(f_mmkin["SFO-SFO", ])
-#' f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ])
-#' # We can use print, plot and summary methods to check the results
-#' print(f_saem_dfop_sfo)
-#' plot(f_saem_dfop_sfo)
-#' summary(f_saem_dfop_sfo, data = FALSE)
-#'
-#' # Using a single core, the following takes about 6 minutes as we do not have an
-#' # analytical solution. Using 10 cores it is slower instead of faster
-#' #f_saem_fomc <- saem(f_mmkin["FOMC-SFO", ], cores = 1)
-#' }
-#' @export
-saem <- function(object, control, ...) UseMethod("saem")
-
-#' @rdname saem
-#' @export
-saem.mmkin <- function(object,
-  control = list(displayProgress = FALSE, print = FALSE,
-    save = FALSE, save.graphs = FALSE),
-  cores = 1,
-  verbose = FALSE, suppressPlot = TRUE, ...)
-{
-  m_saemix <- saemix_model(object, cores = cores, verbose = verbose)
-  d_saemix <- saemix_data(object, verbose = verbose)
-  if (suppressPlot) {
-    # We suppress the log-likelihood curve that saemix currently
-    # produces at the end of the fit by plotting to a file
-    # that we discard afterwards
-    tmp <- tempfile()
-    grDevices::png(tmp)
-  }
-  fit_time <- system.time({
-    f_saemix <- saemix::saemix(m_saemix, d_saemix, control)
-    f_pred <- try(saemix::saemix.predict(f_saemix), silent = TRUE)
-    if (!inherits(f_pred, "try-error")) {
-      f_saemix <- f_pred
-    } else {
-      warning("Creating predictions from the saemix model failed")
-    }
-  })
-  if (suppressPlot) {
-    grDevices::dev.off()
-    unlink(tmp)
-  }
-  transparms_optim <- f_saemix@results@fixed.effects
-  names(transparms_optim) <- f_saemix@results@name.fixed
-  bparms_optim <- backtransform_odeparms(transparms_optim,
-    object[[1]]$mkinmod,
-    object[[1]]$transform_rates,
-    object[[1]]$transform_fractions)
-
-  result <- list(
-    mkinmod = object[[1]]$mkinmod,
-    mmkin = object,
-    solution_type = object[[1]]$solution_type,
-    transform_rates = object[[1]]$transform_rates,
-    transform_fractions = object[[1]]$transform_fractions,
-    so = f_saemix,
-    time = fit_time,
-    mean_dp_start = attr(m_saemix, "mean_dp_start"),
-    bparms.optim = bparms_optim,
-    bparms.fixed = object[[1]]$bparms.fixed,
-    data = nlme_data(object),
-    err_mod = object[[1]]$err_mod,
-    date.fit = date(),
-    saemixversion = as.character(utils::packageVersion("saemix")),
-    mkinversion = as.character(utils::packageVersion("mkin")),
-    Rversion = paste(R.version$major, R.version$minor, sep=".")
-  )
-
-  class(result) <- c("saem.mmkin", "mixed.mmkin")
-  return(result)
-}
-
-#' @export
-#' @rdname saem
-#' @param x An saem.mmkin object to print
-#' @param digits Number of digits to use for printing
-print.saem.mmkin <- function(x, digits = max(3, getOption("digits") - 3), ...) {
-  cat( "Kinetic nonlinear mixed-effects model fit by SAEM" )
-  cat("\nStructural model:\n")
-  diffs <- x$mmkin[[1]]$mkinmod$diffs
-  nice_diffs <- gsub("^(d.*) =", "\\1/dt =", diffs)
-  writeLines(strwrap(nice_diffs, exdent = 11))
-  cat("\nData:\n")
-  cat(nrow(x$data), "observations of",
-    length(unique(x$data$name)), "variable(s) grouped in",
-    length(unique(x$data$ds)), "datasets\n")
-
-  cat("\nLikelihood computed by importance sampling\n")
-  print(data.frame(
-      AIC = AIC(x$so, type = "is"),
-      BIC = BIC(x$so, type = "is"),
-      logLik = logLik(x$so, type = "is"),
-      row.names = " "), digits = digits)
-
-  cat("\nFitted parameters:\n")
-  conf.int <- x$so@results@conf.int[c("estimate", "lower", "upper")]
-  rownames(conf.int) <- x$so@results@conf.int[["name"]]
-  print(conf.int, digits = digits)
-
-  invisible(x)
-}
-
-#' @rdname saem
-#' @return An [saemix::SaemixModel] object.
-#' @export
-saemix_model <- function(object, cores = 1, verbose = FALSE, ...) {
-  if (nrow(object) > 1) stop("Only row objects allowed")
-
-  mkin_model <- object[[1]]$mkinmod
-  solution_type <- object[[1]]$solution_type
-
-  degparms_optim <-  mean_degparms(object)
-  degparms_fixed <- object[[1]]$bparms.fixed
-
-  # Transformations are done in the degradation function
-  transform.par = rep(0, length(degparms_optim))
-
-  odeini_optim_parm_names <- grep('_0$', names(degparms_optim), value = TRUE)
-  odeini_fixed_parm_names <- grep('_0$', names(degparms_fixed), value = TRUE)
-
-  odeparms_fixed_names <- setdiff(names(degparms_fixed), odeini_fixed_parm_names)
-  odeparms_fixed <- degparms_fixed[odeparms_fixed_names]
-
-  odeini_fixed <- degparms_fixed[odeini_fixed_parm_names]
-  names(odeini_fixed) <- gsub('_0$', '', odeini_fixed_parm_names)
-
-  model_function <- FALSE
-
-  # Model functions with analytical solutions
-  # Fixed parameters, use_of_ff = "min" and turning off sinks currently not supported here
-  # In general, we need to consider exactly how the parameters in mkinfit were specified,
-  # as the parameters are currently mapped by position in these solutions
-  sinks <- sapply(mkin_model$spec, function(x) x$sink)
-  if (length(odeparms_fixed) == 0 & mkin_model$use_of_ff == "max" & all(sinks)) {
-    # Parent only
-    if (length(mkin_model$spec) == 1) {
-      parent_type <- mkin_model$spec[[1]]$type
-      if (length(odeini_fixed) == 1) {
-        if (parent_type == "SFO") {
-          stop("saemix needs at least two parameters to work on.")
-        }
-        if (parent_type == "FOMC") {
-          model_function <- function(psi, id, xidep) {
-            odeini_fixed / (xidep[, "time"]/exp(psi[id, 2]) + 1)^exp(psi[id, 1])
-          }
-        }
-        if (parent_type == "DFOP") {
-          model_function <- function(psi, id, xidep) {
-            g <- plogis(psi[id, 3])
-            t <- xidep[, "time"]
-            odeini_fixed * (g * exp(- exp(psi[id, 1]) * t) +
-              (1 - g) * exp(- exp(psi[id, 2]) * t))
-          }
-        }
-        if (parent_type == "HS") {
-          model_function <- function(psi, id, xidep) {
-            tb <- exp(psi[id, 3])
-            t <- xidep[, "time"]
-            k1 = exp(psi[id, 1])
-            odeini_fixed * ifelse(t <= tb,
-              exp(- k1 * t),
-              exp(- k1 * t) * exp(- exp(psi[id, 2]) * (t - tb)))
-          }
-        }
-      } else {
-        if (parent_type == "SFO") {
-          model_function <- function(psi, id, xidep) {
-            psi[id, 1] * exp( - exp(psi[id, 2]) * xidep[, "time"])
-          }
-        }
-        if (parent_type == "FOMC") {
-          model_function <- function(psi, id, xidep) {
-            psi[id, 1] / (xidep[, "time"]/exp(psi[id, 3]) + 1)^exp(psi[id, 2])
-          }
-        }
-        if (parent_type == "DFOP") {
-          model_function <- function(psi, id, xidep) {
-            g <- plogis(psi[id, 4])
-            t <- xidep[, "time"]
-            psi[id, 1] * (g * exp(- exp(psi[id, 2]) * t) +
-              (1 - g) * exp(- exp(psi[id, 3]) * t))
-          }
-        }
-        if (parent_type == "HS") {
-          model_function <- function(psi, id, xidep) {
-            tb <- exp(psi[id, 4])
-            t <- xidep[, "time"]
-            k1 = exp(psi[id, 2])
-            psi[id, 1] * ifelse(t <= tb,
-              exp(- k1 * t),
-              exp(- k1 * t) * exp(- exp(psi[id, 3]) * (t - tb)))
-          }
-        }
-      }
-    }
-
-    # Parent with one metabolite
-    # Parameter names used in the model functions are as in
-    # https://nbviewer.jupyter.org/urls/jrwb.de/nb/Symbolic%20ODE%20solutions%20for%20mkin.ipynb
-    if (length(mkin_model$spec) == 2) {
-      types <- unname(sapply(mkin_model$spec, function(x) x$type))
-      # Initial value for the metabolite (n20) must be fixed
-      if (names(odeini_fixed) == names(mkin_model$spec)[2]) {
-        n20 <- odeini_fixed
-        parent_name <- names(mkin_model$spec)[1]
-        if (identical(types, c("SFO", "SFO"))) {
-          model_function <- function(psi, id, xidep) {
-            t <- xidep[, "time"]
-            n10 <- psi[id, 1]
-            k1 <- exp(psi[id, 2])
-            k2 <- exp(psi[id, 3])
-            f12 <- plogis(psi[id, 4])
-            ifelse(xidep[, "name"] == parent_name,
-              n10 * exp(- k1 * t),
-              (((k2 - k1) * n20 - f12 * k1 * n10) * exp(- k2 * t)) / (k2 - k1) +
-                (f12 * k1 * n10 * exp(- k1 * t)) / (k2 - k1)
-            )
-          }
-        }
-        if (identical(types, c("DFOP", "SFO"))) {
-          model_function <- function(psi, id, xidep) {
-            t <- xidep[, "time"]
-            n10 <- psi[id, 1]
-            k2 <- exp(psi[id, 2])
-            f12 <- plogis(psi[id, 3])
-            l1 <- exp(psi[id, 4])
-            l2 <- exp(psi[id, 5])
-            g <- plogis(psi[id, 6])
-            ifelse(xidep[, "name"] == parent_name,
-              n10 * (g * exp(- l1 * t) + (1 - g) * exp(- l2 * t)),
-              ((f12 * g - f12) * l2 * n10 * exp(- l2 * t)) / (l2 - k2) -
-                (f12 * g * l1 * n10 * exp(- l1 * t)) / (l1 - k2) +
-                ((((l1 - k2) * l2 - k2 * l1 + k2^2) * n20 +
-                    ((f12 * l1 + (f12 * g - f12) * k2) * l2 -
-                      f12 * g * k2 * l1) * n10) * exp( - k2 * t)) /
-                ((l1 - k2) * l2 - k2 * l1 + k2^2)
-            )
-          }
-        }
-      }
-    }
-  }
-
-  if (is.function(model_function)) {
-    solution_type = "analytical saemix"
-  } else {
-    model_function <- function(psi, id, xidep) {
-
-      uid <- unique(id)
-
-      res_list <- parallel::mclapply(uid, function(i) {
-          transparms_optim <- psi[i, ]
-          names(transparms_optim) <- names(degparms_optim)
-
-          odeini_optim <- transparms_optim[odeini_optim_parm_names]
-          names(odeini_optim) <- gsub('_0$', '', odeini_optim_parm_names)
-
-          odeini <- c(odeini_optim, odeini_fixed)[names(mkin_model$diffs)]
-
-          ode_transparms_optim_names <- setdiff(names(transparms_optim), odeini_optim_parm_names)
-          odeparms_optim <- backtransform_odeparms(transparms_optim[ode_transparms_optim_names], mkin_model,
-            transform_rates = object[[1]]$transform_rates,
-            transform_fractions = object[[1]]$transform_fractions)
-          odeparms <- c(odeparms_optim, odeparms_fixed)
-
-          xidep_i <- subset(xidep, id == i)
-
-          if (solution_type == "analytical") {
-            out_values <- mkin_model$deg_func(xidep_i, odeini, odeparms)
-          } else {
-
-            i_time <- xidep_i$time
-            i_name <- xidep_i$name
-
-            out_wide <- mkinpredict(mkin_model,
-              odeparms = odeparms, odeini = odeini,
-              solution_type = solution_type,
-              outtimes = sort(unique(i_time)),
-              na_stop = FALSE
-            )
-
-            out_index <- cbind(as.character(i_time), as.character(i_name))
-            out_values <- out_wide[out_index]
-          }
-          return(out_values)
-        }, mc.cores = cores)
-        res <- unlist(res_list)
-        return(res)
-    }
-  }
-
-  error.model <- switch(object[[1]]$err_mod,
-    const = "constant",
-    tc = "combined",
-    obs = "constant")
-
-  if (object[[1]]$err_mod == "obs") {
-    warning("The error model 'obs' (variance by variable) can currently not be transferred to an saemix model")
-  }
-
-  error.init <- switch(object[[1]]$err_mod,
-    const = c(a = mean(sapply(object, function(x) x$errparms)), b = 1),
-    tc = c(a = mean(sapply(object, function(x) x$errparms[1])),
-      b = mean(sapply(object, function(x) x$errparms[2]))),
-    obs = c(a = mean(sapply(object, function(x) x$errparms)), b = 1))
-
-  psi0_matrix <- matrix(degparms_optim, nrow = 1)
-  colnames(psi0_matrix) <- names(degparms_optim)
-
-  res <- saemix::saemixModel(model_function,
-    psi0 = psi0_matrix,
-    "Mixed model generated from mmkin object",
-    transform.par = transform.par,
-    error.model = error.model,
-    verbose = verbose
-  )
-  attr(res, "mean_dp_start") <- degparms_optim
-  return(res)
-}
-
-#' @rdname saem
-#' @return An [saemix::SaemixData] object.
-#' @export
-saemix_data <- function(object, verbose = FALSE, ...) {
-  if (nrow(object) > 1) stop("Only row objects allowed")
-  ds_names <- colnames(object)
-
-  ds_list <- lapply(object, function(x) x$data[c("time", "variable", "observed")])
-  names(ds_list) <- ds_names
-  ds_saemix_all <- purrr::map_dfr(ds_list, function(x) x, .id = "ds")
-  ds_saemix <- data.frame(ds = ds_saemix_all$ds,
-    name = as.character(ds_saemix_all$variable),
-    time = ds_saemix_all$time,
-    value = ds_saemix_all$observed,
-    stringsAsFactors = FALSE)
-
-  res <- saemix::saemixData(ds_saemix,
-    name.group = "ds",
-    name.predictors = c("time", "name"),
-    name.response = "value",
-    verbose = verbose,
-    ...)
-  return(res)
-}