fmeMcmcControl: Control for fmeMcmc estimation method in nlmixr2
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fmeMcmcControl

R Documentation

Control for fmeMcmc estimation method in nlmixr2

Description

Control for fmeMcmc estimation method in nlmixr2

Usage

fmeMcmcControl(
  jump = NULL,
  prior = NULL,
  niter = 1000L,
  outputlength = niter,
  burninlength = 0,
  updatecov = niter,
  covscale = NULL,
  ntrydr = 1,
  drscale = NULL,
  verbose = FALSE,
  returnFmeMcmc = FALSE,
  stickyRecalcN = 4,
  maxOdeRecalc = 5,
  odeRecalcFactor = 10^(0.5),
  useColor = crayon::has_color(),
  printNcol = floor((getOption("width") - 23)/12),
  print = 1L,
  normType = c("rescale2", "mean", "rescale", "std", "len", "constant"),
  scaleType = c("none", "nlmixr2", "norm", "mult", "multAdd"),
  scaleCmax = 1e+05,
  scaleCmin = 1e-05,
  scaleC = NULL,
  scaleTo = 1,
  rxControl = NULL,
  optExpression = TRUE,
  sumProd = FALSE,
  literalFix = TRUE,
  literalFixRes = TRUE,
  addProp = c("combined2", "combined1"),
  calcTables = TRUE,
  compress = TRUE,
  covMethod = c("mcmc", "r", ""),
  adjObf = TRUE,
  ci = 0.95,
  sigdig = 4,
  sigdigTable = NULL,
  ...
)

Arguments

`jump`	jump length, either a number, a vector with length equal to the total number of parameters, a covariance matrix, or a function that takes as input the current values of the parameters and produces as output the perturbed parameters. See details.
`prior`	-2*log(parameter prior probability), either a function that is called as `prior(p)` or `NULL`; in the latter case a non-informative prior is used (i.e. all parameters are equally likely, depending on `lower` and `upper` within min and max bounds).
`niter`	number of iterations for the MCMC.
`outputlength`	number of iterations kept in the output; should be smaller or equal to `niter`.
`burninlength`	number of initial iterations to be removed from output.
`updatecov`	number of iterations after which the parameter covariance matrix is (re)evaluated based on the parameters kept thus far, and used to update the MCMC jumps.
`covscale`	scale factor for the parameter covariance matrix, used to perform the MCMC jumps.
`ntrydr`	maximal number of tries for the delayed rejection procedure. It is generally not a good idea to set this to a too large value.
`drscale`	for each try during delayed rejection, the cholesky decomposition of the proposal matrix is scaled with this amount; if `NULL`, it is assumed to be `c(0.2,0.25, 0.333, 0.333, ...)`
`verbose`	if `TRUE` or `1`: prints extra output, if numeric value `i > 1`, prints status information every `i` iterations.
`returnFmeMcmc`	return the fmeMcmc output instead of the nlmixr2 fit
`stickyRecalcN`	The number of bad ODE solves before reducing the atol/rtol for the rest of the problem.
`maxOdeRecalc`	Maximum number of times to reduce the ODE tolerances and try to resolve the system if there was a bad ODE solve.
`odeRecalcFactor`	The ODE recalculation factor when ODE solving goes bad, this is the factor the rtol/atol is reduced
`useColor`	Boolean indicating if focei can use ASCII color codes
`printNcol`	Number of columns to printout before wrapping parameter estimates/gradient
`print`	Integer representing when the outer step is printed. When this is 0 or do not print the iterations. 1 is print every function evaluation (default), 5 is print every 5 evaluations.
`normType`	This is the type of parameter normalization/scaling used to get the scaled initial values for nlmixr2. These are used with `scaleType` of. With the exception of `rescale2`, these come from Feature Scaling. The `rescale2` The rescaling is the same type described in the OptdesX software manual. In general, all all scaling formula can be described by: `v_{scaled}` = ( `v_{unscaled}-C_{1}` )/ `C_{2}` Where The other data normalization approaches follow the following formula `v_{scaled}` = ( `v_{unscaled}-C_{1}` )/ `C_{2}` `rescale2` This scales all parameters from (-1 to 1). The relative differences between the parameters are preserved with this approach and the constants are: `C_{1}` = (max(all unscaled values)+min(all unscaled values))/2 `C_{2}` = (max(all unscaled values) - min(all unscaled values))/2 `rescale` or min-max normalization. This rescales all parameters from (0 to 1). As in the `rescale2` the relative differences are preserved. In this approach: `C_{1}` = min(all unscaled values) `C_{2}` = max(all unscaled values) - min(all unscaled values) `mean` or mean normalization. This rescales to center the parameters around the mean but the parameters are from 0 to 1. In this approach: `C_{1}` = mean(all unscaled values) `C_{2}` = max(all unscaled values) - min(all unscaled values) `std` or standardization. This standardizes by the mean and standard deviation. In this approach: `C_{1}` = mean(all unscaled values) `C_{2}` = sd(all unscaled values) `len` or unit length scaling. This scales the parameters to the unit length. For this approach we use the Euclidean length, that is: `C_{1}` = 0 `C_{2}` = `\sqrt(v_1^2 + v_2^2 + \cdots + v_n^2)` `constant` which does not perform data normalization. That is `C_{1}` = 0 `C_{2}` = 1
`scaleType`	The scaling scheme for nlmixr2. The supported types are: `nlmixr2` In this approach the scaling is performed by the following equation: `v_{scaled}` = ( `v_{current} - v_{init}` )scaleC[i] + scaleTo The `scaleTo` parameter is specified by the `normType`, and the scales are specified by `scaleC`. `norm` This approach uses the simple scaling provided by the `normType` argument. `mult` This approach does not use the data normalization provided by `normType`, but rather uses multiplicative scaling to a constant provided by the `scaleTo` argument. In this case: `v_{scaled}` = `v_{current}` / `v_{init}` scaleTo `multAdd` This approach changes the scaling based on the parameter being specified. If a parameter is defined in an exponential block (ie exp(theta)), then it is scaled on a linearly, that is: `v_{scaled}` = ( `v_{current}-v_{init}` ) + scaleTo Otherwise the parameter is scaled multiplicatively. `v_{scaled}` = `v_{current}` / `v_{init}` *scaleTo
`scaleCmax`	Maximum value of the scaleC to prevent overflow.
`scaleCmin`	Minimum value of the scaleC to prevent underflow.
`scaleC`	The scaling constant used with `scaleType=nlmixr2`. When not specified, it is based on the type of parameter that is estimated. The idea is to keep the derivatives similar on a log scale to have similar gradient sizes. Hence parameters like log(exp(theta)) would have a scaling factor of 1 and log(theta) would have a scaling factor of ini_value (to scale by 1/value; ie d/dt(log(ini_value)) = 1/ini_value or scaleC=ini_value) For parameters in an exponential (ie exp(theta)) or parameters specifying powers, boxCox or yeoJohnson transformations , this is 1. For additive, proportional, lognormal error structures, these are given by 0.5abs(initial_estimate) Factorials are scaled by abs(1/digamma(initial_estimate+1)) parameters in a log scale (ie log(theta)) are transformed by log(abs(initial_estimate))abs(initial_estimate) These parameter scaling coefficients are chose to try to keep similar slopes among parameters. That is they all follow the slopes approximately on a log-scale. While these are chosen in a logical manner, they may not always apply. You can specify each parameters scaling factor by this parameter if you wish.
`scaleTo`	Scale the initial parameter estimate to this value. By default this is 1. When zero or below, no scaling is performed.
`rxControl`	'rxode2' ODE solving options during fitting, created with 'rxControl()'
`optExpression`	Optimize the rxode2 expression to speed up calculation. By default this is turned on.
`sumProd`	Is a boolean indicating if the model should change multiplication to high precision multiplication and sums to high precision sums using the PreciseSums package. By default this is `FALSE`.
`literalFix`	boolean, substitute fixed population values as literals and re-adjust ui and parameter estimates after optimization; Default is 'TRUE'.
`literalFixRes`	boolean, substitute fixed population values as literals and re-adjust ui and parameter estimates after optimization; Default is 'TRUE'.
`addProp`	specifies the type of additive plus proportional errors, the one where standard deviations add (combined1) or the type where the variances add (combined2). The combined1 error type can be described by the following equation: `y = f + (a + b\times f^c) \times \varepsilon` The combined2 error model can be described by the following equation: `y = f + \sqrt{a^2 + b^2\times f^{2\times c}} \times \varepsilon` Where: - y represents the observed value - f represents the predicted value - a is the additive standard deviation - b is the proportional/power standard deviation - c is the power exponent (in the proportional case c=1)
`calcTables`	This boolean is to determine if the foceiFit will calculate tables. By default this is `TRUE`
`compress`	Should the object have compressed items
`covMethod`	Method for calculating covariance. In this discussion, R is the Hessian matrix of the objective function. The S matrix is the sum of individual gradient cross-product (evaluated at the individual empirical Bayes estimates). "`r,s`" Uses the sandwich matrix to calculate the covariance, that is: `solve(R) %% S %% solve(R)` "`r`" Uses the Hessian matrix to calculate the covariance as `2 %% solve(R)` "`s`" Uses the cross-product matrix to calculate the covariance as `4 %% solve(S)` "" Does not calculate the covariance step.
`adjObf`	is a boolean to indicate if the objective function should be adjusted to be closer to NONMEM's default objective function. By default this is `TRUE`
`ci`	Confidence level for some tables. By default this is 0.95 or 95% confidence.
`sigdig`	Optimization significant digits. This controls: The tolerance of the inner and outer optimization is `10^-sigdig` The tolerance of the ODE solvers is `0.510^(-sigdig-2)`; For the sensitivity equations and steady-state solutions the default is `0.510^(-sigdig-1.5)` (sensitivity changes only applicable for liblsoda) The tolerance of the boundary check is `5 * 10 ^ (-sigdig + 1)`
`sigdigTable`	Significant digits in the final output table. If not specified, then it matches the significant digits in the 'sigdig' optimization algorithm. If 'sigdig' is NULL, use 3.
`...`	Ignored parameters

Value

fmeMcmc control structure

Author(s)

Matthew L. Fidler

Examples



# A logit regression example with emax model

dsn <- data.frame(i=1:1000)
dsn$time <- exp(rnorm(1000))
dsn$DV=rbinom(1000,1,exp(-1+dsn$time)/(1+exp(-1+dsn$time)))

mod <- function() {
 ini({
   E0 <- 0.5
   Em <- 0.5
   E50 <- 2
   g <- fix(2)
 })
 model({
   v <- E0+Em*time^g/(E50^g+time^g)
   ll(bin) ~ DV * v - log(1 + exp(v))
 })
}

fit2 <- nlmixr(mod, dsn, est="fmeMcmc")

print(fit2)

# you can also get the FME modMCMC output with

# fit2$fmeMcmc

# And use it in the summaries from FME, i.e.

summary(fit2$fmeMcmc)

pairs(fit2$fmeMcmc)

# and you can also use the coda package with `as.mcmc()`
coda::raftery.diag(coda::as.mcmc(fit2))

babelmixr2 documentation built on Aug. 31, 2025, 5:07 p.m.