nlmixr2 7.0's covariance step, all grown up
By Matthew Fidler in nlmixr2
August 17, 2026
In the 7.0 post, I talked mostly about
parallel solving in focei. This time I want to talk about a feature
that has been requested frequently: a full covariance step, and other
refinements to the covariance steps.
Two things changed there, and they are related:
Nearly any covariance method can now be requested from nearly any estimation method, and you can switch a finished fit to a different one without refitting.
The default covariance step now actually covers every estimated parameter, not just the structural ones.
Neither of these will show up in a benchmark. Both of them will show
up the next time you stare at a $parFixed table wondering why a
residual-error parameter has a standard error, or wondering whether
your saem fit’s confidence intervals would look different under a
different covariance method.
The easiest way to look at this is the most modeled drug – theophylline:
library(nlmixr2)## ── Attaching packages ───────────────────────────────────────────────────────────────────────────────────── nlmixr2 6.0.0 ──## ★ lotri 1.0.5 ◯ nlmixr2auto 1.0.0
## ★ nlmixr2data 2.0.10 ◯ nlmixr2autoinit 1.0.0
## ★ nlmixr2save 0.2.0 ◯ nlmixr2lib 0.3.2
## ★ nlmixr2est 7.0.3 ◯ nlmixr2rpt 0.2.2
## ★ nlmixr2extra 5.2.0 ◯ nlmixr2targets 0.1.0
## ★ nlmixr2plot 5.1.0 ◯ nonmem2rx 0.1.10
## ★ rxode2 5.1.7 ◯ pmxNODE 0.1.0
## ◯ admixr2 0.2.0 ◯ PopED 0.7.0
## ◯ babelmixr2 0.1.11.9000 ◯ posologyr 1.2.8
## ◯ FME 1.3.6.4 ◯ shinyMixR 0.5.3
## ◯ ggPMX 1.3.2 ◯ xpose.nlmixr2 0.4.2
## ◯ monolix2rx 0.0.7## ── Conflicts ───────────────────────────────────────────────────────────────────────────────────────── nlmixr2conflicts() ──
## ✖ rxode2::boxCox() masks nlmixr2est::boxCox()
## ✖ coda::traceplot() masks babelmixr2::traceplot(), nlmixr2plot::traceplot()
## ✖ rxode2::yeoJohnson() masks nlmixr2est::yeoJohnson()pheno <- function() {
ini({
tcl <- log(0.008) # typical value of clearance
tv <- log(0.6) # typical value of volume
## var(eta.cl)
eta.cl + eta.v ~ c(1,
0.01, 1) ## cov(eta.cl, eta.v), var(eta.v)
# interindividual variability on clearance and volume
add.sd <- 0.1 # residual variability
})
model({
cl <- exp(tcl + eta.cl) # individual value of clearance
v <- exp(tv + eta.v) # individual value of volume
ke <- cl / v # elimination rate constant
d/dt(A1) = - ke * A1 # model differential equation
cp = A1 / v # concentration in plasma
cp ~ add(add.sd) # define error model
})
}The covariance step now includes every parameter
Look at add.sd in that model. It is the additive residual error
standard deviation – a parameter you fit just like tka, tcl or
tv. Before 7.0, if you ran
fit := nlmixr2(pheno, pheno_sd, est="focei")## ℹ parameter labels from comments are typically ignored in non-interactive mode## ℹ Need to run with the source intact to parse comments## ℹ parameter labels from comments are typically ignored in non-interactive mode## ℹ Need to run with the source intact to parse comments## ℹ loading fit from fit.R## ℹ parameter labels from comments are typically ignored in non-interactive mode## ℹ Need to run with the source intact to parse comments## ℹ removing unzipped fit filesadd.sd would come back in fit$parFixed with an estimate and
nothing else – no SE, no %RSE, no confidence interval.
Now all parameter describing how much noise is in your assay did not.
print(fit)## ── nlmixr² FOCEi (outer: bobyqa) ──
##
## OBJF AIC BIC Log-likelihood Condition#(Cov) Condition#(Cor)
## FOCEi 1255.203 1552.074 1570.334 -770.0368 1130201 67945.75
##
## ── Time (sec $time): ──
##
## setup optimize covariance preprocess postprocess table compress
## elapsed 2.606588 1.281938 1.153731 0.028 0.03 0.046 0.001
## other
## elapsed 0.1897427
##
## ── Population Parameters ($parFixed or $parFixedDf): ──
##
## Est. SE %RSE Back-transformed(95%CI) BSV(CV%) Shrink(SD)%
## tcl -0.474 0.335 70.7 0.622 (0.323, 1.20) 21500 81.5
## tv 3.51 0.227 6.47 33.3 (21.3, 51.9) 1210 81.4
## add.sd 0.951 0.00855 0.900 0.951 (0.934, 0.967)
##
## Covariance Type ($covMethod): r,s
## Some strong fixed parameter correlations exist ($cor) :
## cor:tv,tcl cor:add.sd,tcl
## 0.943 0.806
## cor:om.eta.cl,tcl cor:cov.eta.v.eta.cl,tcl
## -0.723 -0.163
## cor:om.eta.v,tcl cor:add.sd,tv
## 0.708 0.857
## cor:om.eta.cl,tv cor:cov.eta.v.eta.cl,tv
## -0.900 -0.389
## cor:om.eta.v,tv cor:om.eta.cl,add.sd
## 0.888 -0.850
## cor:cov.eta.v.eta.cl,add.sd cor:om.eta.v,add.sd
## -0.356 0.836
## cor:cov.eta.v.eta.cl,om.eta.cl cor:om.eta.v,om.eta.cl
## 0.679 -0.999
## cor:om.eta.v,cov.eta.v.eta.cl
## -0.715
##
##
## Correlations in between subject variability (BSV) matrix:
## cor:eta.v,eta.cl
## 0.989
##
##
## Full BSV covariance ($omega) or correlation ($omegaR; diagonals=SDs)
## Distribution stats (mean/skewness/kurtosis/p-value) available in $shrink
## Information about run found ($runInfo):
## • gradient problems with covariance; see $scaleInfo
## • using S matrix to calculate covariance, can check sandwich or R matrix with $covRS and $covR
## • last objective function was not at minimum, possible problems in optimization
## • ETAs were reset to zero during optimization; (Can control by foceiControl(resetEtaP=.))
## Censoring ($censInformation): No censoring
## Minimization message ($message):
## Normal exit from bobyqa
##
## ── Fit Data (object is a modified tibble): ──
## # A tibble: 155 × 20
## ID TIME DV PRED RES WRES IPRED IRES IWRES CPRED CRES CWRES
## <fct> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 1 2 17.3 0.723 16.6 8.73 17.6 -0.261 -0.274 -38.1 55.4 1.41
## 2 1 112. 31 0.515 30.5 16.1 30.8 0.150 0.158 -79.7 111. 1.44
## 3 2 2 9.7 0.434 9.27 6.76 11.6 -1.94 -2.04 -26.4 36.1 1.38
## # ℹ 152 more rows
## # ℹ 8 more variables: eta.cl <dbl>, eta.v <dbl>, A1 <dbl>, cl <dbl>, v <dbl>,
## # ke <dbl>, tad <dbl>, dosenum <int>The old behavior was an intentional choice for a few reasons:
We as a
nlmixr2team think when simulating with uncertainty,omegaandsigmaterms should be simulated using the inverse Wishart distribution instead of standard errors.To get the
omegaand residuals standard errors required quite a bit more effort than the approach we originally took.
In 7.0 a full covariance step gives a real standard error.
Fit the model above and you’ll see something like add.sd at an SE of
about 0.008 (roughly 0.9% RSE) – a number that, before this release,
simply was not there.
There are only a few things that are still not calculated:
fix()ed parameters- inter-occasion variability (IOV) parameter, or
- it is a mixture-probability parameter on the mlogit scale (yes, we have mixtures now too, more about this later).
If you look at the full covariance ($cov) you can also see the omega
values:
fit$cov## tcl tv add.sd om.eta.cl
## tcl 0.1007818584 0.0844061440 0.0202130847 -0.079945054
## tv 0.0844061440 0.0795411612 0.0191069019 -0.088355112
## add.sd 0.0202130847 0.0191069019 0.0062453761 -0.023386122
## om.eta.cl -0.0799450543 -0.0883551116 -0.0233861219 0.121181972
## cov.eta.v.eta.cl -0.0002333045 -0.0004938735 -0.0001265396 0.001064201
## om.eta.v 0.0338458103 0.0377106888 0.0099461957 -0.052337068
## cov.eta.v.eta.cl om.eta.v
## tcl -2.333045e-04 0.0338458103
## tv -4.938735e-04 0.0377106888
## add.sd -1.265396e-04 0.0099461957
## om.eta.cl 1.064201e-03 -0.0523370678
## cov.eta.v.eta.cl 2.024341e-05 -0.0004845114
## om.eta.v -4.845114e-04 0.0226690310As a note about naming for the omega matrix
Every other estimated theta – structural, covariate, and now every
residual-error parameter – is included, and covFull=TRUE (the
default) reports the full theta + residual + Omega covariance, with
the Omega rows named by the random effect (om.eta.cl,
cov.eta.cl.eta.v) so you can find what you’re looking for without
guessing at row order.
Any covariance, on any method
The second change is that covMethod stopped being tied to a specific
estimation method. Historically, the SAEM Louis stochastic-approximation
FIM only came out of saem, and the importance-sampling Monte Carlo
observed information only came out of imp/impmap. If you wanted
that covariance on a focei fit, you were out of luck.
Now sa and imp are covariance methods first and estimation methods
second. Either one can be requested as the covMethod of any
mixed-effects fit, computed post-fit at the converged estimates:
# the SAEM Louis stochastic-approximation FIM, on a focei fit,
# without refitting anything
setCov(fit, "sa")## [====|====|====|====|====|====|====|====|====|====] 0:00:00
##
## Key: X: Back-transformed parameters; SA: Stochastic-approximation (burn-in) phase; EM: EM phase
##
## | #| tcl | tv | V(eta.cl) | V(eta.v) |
## |.....|cov.eta.v.eta.cl | add.sd |...........|...........|
## |-----+-----------+-----------+-----------+-----------|
## | 1| -0.8429 | 3.083 | 10.79 | 4.857 |
## |.....| 0.000 | 24.68 |...........|...........|
## |SA: X| 0.4304 | 21.83 | 10.79 | 4.857 |
## |.....| 0.000 | 24.68 |...........|...........|
## | 2| -1.269 | 3.029 | 13.47 | 4.614 |
## |.....| 0.000 | 23.40 |...........|...........|
## |SA: X| 0.2811 | 20.67 | 13.47 | 4.614 |
## |.....| 0.000 | 23.40 |...........|...........|
## | 3| -1.907 | 2.687 | 14.62 | 4.464 |
## |.....| 0.000 | 22.66 |...........|...........|
## |SA: X| 0.1485 | 14.68 | 14.62 | 4.464 |
## |.....| 0.000 | 22.66 |...........|...........|
## | 4| -2.591 | 2.510 | 13.89 | 4.241 |
## |.....| 0.000 | 21.83 |...........|...........|
## |SA: X| 0.07493 | 12.31 | 13.89 | 4.241 |
## |.....| 0.000 | 21.83 |...........|...........|
## | 5| -3.245 | 1.974 | 13.19 | 4.029 |
## |.....| 0.000 | 21.16 |...........|...........|
## |SA: X| 0.03896 | 7.197 | 13.19 | 4.029 |
## |.....| 0.000 | 21.16 |...........|...........|
## | 6| -3.797 | 1.643 | 12.53 | 3.828 |
## |.....| 0.000 | 19.38 |...........|...........|
## |SA: X| 0.02244 | 5.171 | 12.53 | 3.828 |
## |.....| 0.000 | 19.38 |...........|...........|
## | 7| -4.416 | 1.266 | 11.90 | 3.636 |
## |.....| 0.000 | 17.92 |...........|...........|
## |SA: X| 0.01209 | 3.546 | 11.90 | 3.636 |
## |.....| 0.000 | 17.92 |...........|...........|
## | 8| -5.320 | 1.128 | 11.31 | 3.454 |
## |.....| 0.000 | 15.51 |...........|...........|
## |SA: X| 0.004893 | 3.088 | 11.31 | 3.454 |
## |.....| 0.000 | 15.51 |...........|...........|
## | 9| -5.730 | 1.030 | 10.74 | 3.282 |
## |.....| 0.000 | 13.83 |...........|...........|
## |SA: X| 0.003246 | 2.802 | 10.74 | 3.282 |
## |.....| 0.000 | 13.83 |...........|...........|
## | 10| -6.043 | 0.9290 | 10.21 | 3.118 |
## |.....| 0.000 | 12.04 |...........|...........|
## |SA: X| 0.002375 | 2.532 | 10.21 | 3.118 |
## |.....| 0.000 | 12.04 |...........|...........|
##
## | #| tcl | tv | V(eta.cl) | V(eta.v) |
## |.....|cov.eta.v.eta.cl | add.sd |...........|...........|
## |-----+-----------+-----------+-----------+-----------|
## | 11| -6.724 | 0.7889 | 9.697 | 2.962 |
## |.....| 0.000 | 10.51 |...........|...........|
## |SA: X| 0.001202 | 2.201 | 9.697 | 2.962 |
## |.....| 0.000 | 10.51 |...........|...........|
## | 12| -6.993 | 0.8007 | 9.212 | 2.814 |
## |.....| 0.000 | 9.420 |...........|...........|
## |SA: X| 0.0009182 | 2.227 | 9.212 | 2.814 |
## |.....| 0.000 | 9.420 |...........|...........|
## | 13| -7.199 | 0.6530 | 8.751 | 2.673 |
## |.....| 0.000 | 8.218 |...........|...........|
## |SA: X| 0.0007477 | 1.921 | 8.751 | 2.673 |
## |.....| 0.000 | 8.218 |...........|...........|
## | 14| -7.172 | 0.5915 | 8.314 | 2.539 |
## |.....| 0.000 | 7.023 |...........|...........|
## |SA: X| 0.0007679 | 1.807 | 8.314 | 2.539 |
## |.....| 0.000 | 7.023 |...........|...........|
## | 15| -7.224 | 0.6265 | 7.898 | 2.412 |
## |.....| 0.000 | 6.775 |...........|...........|
## |SA: X| 0.0007292 | 1.871 | 7.898 | 2.412 |
## |.....| 0.000 | 6.775 |...........|...........|
## | 16| -6.960 | 0.5780 | 7.503 | 2.292 |
## |.....| 0.000 | 6.326 |...........|...........|
## |SA: X| 0.0009490 | 1.782 | 7.503 | 2.292 |
## |.....| 0.000 | 6.326 |...........|...........|
## | 17| -6.874 | 0.6068 | 7.128 | 2.177 |
## |.....| 0.000 | 6.128 |...........|...........|
## |SA: X| 0.001034 | 1.835 | 7.128 | 2.177 |
## |.....| 0.000 | 6.128 |...........|...........|
## | 18| -6.797 | 0.5649 | 6.772 | 2.068 |
## |.....| 0.000 | 5.801 |...........|...........|
## |SA: X| 0.001117 | 1.759 | 6.772 | 2.068 |
## |.....| 0.000 | 5.801 |...........|...........|
## | 19| -6.946 | 0.4999 | 6.433 | 1.965 |
## |.....| 0.000 | 5.200 |...........|...........|
## |SA: X| 0.0009630 | 1.649 | 6.433 | 1.965 |
## |.....| 0.000 | 5.200 |...........|...........|
## | 20| -6.764 | 0.4885 | 6.111 | 1.867 |
## |.....| 0.000 | 5.097 |...........|...........|
## |SA: X| 0.001154 | 1.630 | 6.111 | 1.867 |
## |.....| 0.000 | 5.097 |...........|...........|
##
## | #| tcl | tv | V(eta.cl) | V(eta.v) |
## |.....|cov.eta.v.eta.cl | add.sd |...........|...........|
## |-----+-----------+-----------+-----------+-----------|
## | 21| -6.474 | 0.4693 | 5.806 | 1.773 |
## |.....| 0.000 | 4.811 |...........|...........|
## |SA: X| 0.001543 | 1.599 | 5.806 | 1.773 |
## |.....| 0.000 | 4.811 |...........|...........|
## | 22| -6.439 | 0.4646 | 5.515 | 1.685 |
## |.....| 0.000 | 4.672 |...........|...........|
## |SA: X| 0.001597 | 1.591 | 5.515 | 1.685 |
## |.....| 0.000 | 4.672 |...........|...........|
## | 23| -6.397 | 0.4865 | 5.240 | 1.600 |
## |.....| 0.000 | 4.557 |...........|...........|
## |SA: X| 0.001667 | 1.627 | 5.240 | 1.600 |
## |.....| 0.000 | 4.557 |...........|...........|
## | 24| -6.376 | 0.4784 | 4.978 | 1.520 |
## |.....| 0.000 | 4.395 |...........|...........|
## |SA: X| 0.001702 | 1.614 | 4.978 | 1.520 |
## |.....| 0.000 | 4.395 |...........|...........|
## | 25| -6.307 | 0.4780 | 4.729 | 1.444 |
## |.....| 0.000 | 4.285 |...........|...........|
## |SA: X| 0.001824 | 1.613 | 4.729 | 1.444 |
## |.....| 0.000 | 4.285 |...........|...........|
## | 26| -6.239 | 0.4748 | 4.492 | 1.372 |
## |.....| 0.000 | 4.132 |...........|...........|
## |SA: X| 0.001952 | 1.608 | 4.492 | 1.372 |
## |.....| 0.000 | 4.132 |...........|...........|
## | 27| -6.219 | 0.4652 | 4.268 | 1.304 |
## |.....| 0.000 | 4.207 |...........|...........|
## |SA: X| 0.001992 | 1.592 | 4.268 | 1.304 |
## |.....| 0.000 | 4.207 |...........|...........|
## | 28| -6.193 | 0.4195 | 4.054 | 1.238 |
## |.....| 0.000 | 3.879 |...........|...........|
## |SA: X| 0.002043 | 1.521 | 4.054 | 1.238 |
## |.....| 0.000 | 3.879 |...........|...........|
## | 29| -6.136 | 0.4393 | 3.852 | 1.176 |
## |.....| 0.000 | 3.891 |...........|...........|
## |SA: X| 0.002164 | 1.552 | 3.852 | 1.176 |
## |.....| 0.000 | 3.891 |...........|...........|
## | 30| -6.099 | 0.4454 | 3.659 | 1.118 |
## |.....| 0.000 | 3.758 |...........|...........|
## |SA: X| 0.002246 | 1.561 | 3.659 | 1.118 |
## |.....| 0.000 | 3.758 |...........|...........|
##
## | #| tcl | tv | V(eta.cl) | V(eta.v) |
## |.....|cov.eta.v.eta.cl | add.sd |...........|...........|
## |-----+-----------+-----------+-----------+-----------|
## | 31| -5.965 | 0.4526 | 3.476 | 1.062 |
## |.....| 0.000 | 3.627 |...........|...........|
## |SA: X| 0.002567 | 1.572 | 3.476 | 1.062 |
## |.....| 0.000 | 3.627 |...........|...........|
## | 32| -5.761 | 0.4248 | 3.302 | 1.009 |
## |.....| 0.000 | 3.544 |...........|...........|
## |SA: X| 0.003148 | 1.529 | 3.302 | 1.009 |
## |.....| 0.000 | 3.544 |...........|...........|
## | 33| -5.809 | 0.4150 | 3.137 | 0.9582 |
## |.....| 0.000 | 3.419 |...........|...........|
## |SA: X| 0.003002 | 1.514 | 3.137 | 0.9582 |
## |.....| 0.000 | 3.419 |...........|...........|
## | 34| -5.824 | 0.4302 | 2.980 | 0.9103 |
## |.....| 0.000 | 3.380 |...........|...........|
## |SA: X| 0.002955 | 1.537 | 2.980 | 0.9103 |
## |.....| 0.000 | 3.380 |...........|...........|
## | 35| -5.710 | 0.4015 | 2.831 | 0.8648 |
## |.....| 0.000 | 3.100 |...........|...........|
## |SA: X| 0.003314 | 1.494 | 2.831 | 0.8648 |
## |.....| 0.000 | 3.100 |...........|...........|
## | 36| -5.632 | 0.4014 | 2.690 | 0.8215 |
## |.....| 0.000 | 2.970 |...........|...........|
## |SA: X| 0.003581 | 1.494 | 2.690 | 0.8215 |
## |.....| 0.000 | 2.970 |...........|...........|
## | 37| -5.523 | 0.4160 | 2.555 | 0.7805 |
## |.....| 0.000 | 3.032 |...........|...........|
## |SA: X| 0.003995 | 1.516 | 2.555 | 0.7805 |
## |.....| 0.000 | 3.032 |...........|...........|
## | 38| -5.598 | 0.4272 | 2.428 | 0.7414 |
## |.....| 0.000 | 3.115 |...........|...........|
## |SA: X| 0.003706 | 1.533 | 2.428 | 0.7414 |
## |.....| 0.000 | 3.115 |...........|...........|
## | 39| -5.608 | 0.3971 | 2.306 | 0.7044 |
## |.....| 0.000 | 3.081 |...........|...........|
## |SA: X| 0.003670 | 1.488 | 2.306 | 0.7044 |
## |.....| 0.000 | 3.081 |...........|...........|
## | 40| -5.594 | 0.3903 | 2.191 | 0.6692 |
## |.....| 0.000 | 2.990 |...........|...........|
## |SA: X| 0.003719 | 1.477 | 2.191 | 0.6692 |
## |.....| 0.000 | 2.990 |...........|...........|
##
## | #| tcl | tv | V(eta.cl) | V(eta.v) |
## |.....|cov.eta.v.eta.cl | add.sd |...........|...........|
## |-----+-----------+-----------+-----------+-----------|
## | 41| -5.587 | 0.3986 | 2.081 | 0.6357 |
## |.....| 0.000 | 3.083 |...........|...........|
## |SA: X| 0.003745 | 1.490 | 2.081 | 0.6357 |
## |.....| 0.000 | 3.083 |...........|...........|
## | 42| -5.478 | 0.4035 | 1.977 | 0.6039 |
## |.....| 0.000 | 2.986 |...........|...........|
## |SA: X| 0.004177 | 1.497 | 1.977 | 0.6039 |
## |.....| 0.000 | 2.986 |...........|...........|
## | 43| -5.526 | 0.4045 | 1.878 | 0.5737 |
## |.....| 0.000 | 3.076 |...........|...........|
## |SA: X| 0.003983 | 1.499 | 1.878 | 0.5737 |
## |.....| 0.000 | 3.076 |...........|...........|
## | 44| -5.433 | 0.3848 | 1.784 | 0.5450 |
## |.....| 0.000 | 3.079 |...........|...........|
## |SA: X| 0.004368 | 1.469 | 1.784 | 0.5450 |
## |.....| 0.000 | 3.079 |...........|...........|
## | 45| -5.478 | 0.3924 | 1.695 | 0.5178 |
## |.....| 0.000 | 3.158 |...........|...........|
## |SA: X| 0.004179 | 1.480 | 1.695 | 0.5178 |
## |.....| 0.000 | 3.158 |...........|...........|
## | 46| -5.418 | 0.3927 | 1.610 | 0.4919 |
## |.....| 0.000 | 3.013 |...........|...........|
## |SA: X| 0.004435 | 1.481 | 1.610 | 0.4919 |
## |.....| 0.000 | 3.013 |...........|...........|
## | 47| -5.387 | 0.3710 | 1.530 | 0.4673 |
## |.....| 0.000 | 2.922 |...........|...........|
## |SA: X| 0.004576 | 1.449 | 1.530 | 0.4673 |
## |.....| 0.000 | 2.922 |...........|...........|
## | 48| -5.356 | 0.3775 | 1.453 | 0.4439 |
## |.....| 0.000 | 2.919 |...........|...........|
## |SA: X| 0.004720 | 1.459 | 1.453 | 0.4439 |
## |.....| 0.000 | 2.919 |...........|...........|
## | 49| -5.284 | 0.3530 | 1.381 | 0.4217 |
## |.....| 0.000 | 3.005 |...........|...........|
## |SA: X| 0.005071 | 1.423 | 1.381 | 0.4217 |
## |.....| 0.000 | 3.005 |...........|...........|
## | 50| -5.394 | 0.3829 | 1.312 | 0.4006 |
## |.....| 0.000 | 2.969 |...........|...........|
## |SA: X| 0.004542 | 1.467 | 1.312 | 0.4006 |
## |.....| 0.000 | 2.969 |...........|...........|
##
## | #| tcl | tv | V(eta.cl) | V(eta.v) |
## |.....|cov.eta.v.eta.cl | add.sd |...........|...........|
## |-----+-----------+-----------+-----------+-----------|
## | 51| -5.444 | 0.3878 | 1.246 | 0.3806 |
## |.....| 0.000 | 3.002 |...........|...........|
## |SA: X| 0.004322 | 1.474 | 1.246 | 0.3806 |
## |.....| 0.000 | 3.002 |...........|...........|
## | 52| -5.450 | 0.3920 | 1.184 | 0.3616 |
## |.....| 0.000 | 2.956 |...........|...........|
## |SA: X| 0.004297 | 1.480 | 1.184 | 0.3616 |
## |.....| 0.000 | 2.956 |...........|...........|
## | 53| -5.410 | 0.3861 | 1.125 | 0.3435 |
## |.....| 0.000 | 2.929 |...........|...........|
## |SA: X| 0.004473 | 1.471 | 1.125 | 0.3435 |
## |.....| 0.000 | 2.929 |...........|...........|
## | 54| -5.403 | 0.3861 | 1.068 | 0.3263 |
## |.....| 0.000 | 2.853 |...........|...........|
## |SA: X| 0.004504 | 1.471 | 1.068 | 0.3263 |
## |.....| 0.000 | 2.853 |...........|...........|
## | 55| -5.390 | 0.3907 | 1.015 | 0.3100 |
## |.....| 0.000 | 2.945 |...........|...........|
## |SA: X| 0.004561 | 1.478 | 1.015 | 0.3100 |
## |.....| 0.000 | 2.945 |...........|...........|
## | 56| -5.375 | 0.3741 | 0.9642 | 0.2945 |
## |.....| 0.000 | 2.912 |...........|...........|
## |SA: X| 0.004629 | 1.454 | 0.9642 | 0.2945 |
## |.....| 0.000 | 2.912 |...........|...........|
## | 57| -5.356 | 0.3799 | 0.9160 | 0.2798 |
## |.....| 0.000 | 2.978 |...........|...........|
## |SA: X| 0.004722 | 1.462 | 0.9160 | 0.2798 |
## |.....| 0.000 | 2.978 |...........|...........|
## | 58| -5.361 | 0.3852 | 0.8702 | 0.2658 |
## |.....| 0.000 | 2.996 |...........|...........|
## |SA: X| 0.004698 | 1.470 | 0.8702 | 0.2658 |
## |.....| 0.000 | 2.996 |...........|...........|
## | 59| -5.321 | 0.3730 | 0.8267 | 0.2525 |
## |.....| 0.000 | 2.854 |...........|...........|
## |SA: X| 0.004889 | 1.452 | 0.8267 | 0.2525 |
## |.....| 0.000 | 2.854 |...........|...........|
## | 60| -5.300 | 0.3911 | 0.7854 | 0.2399 |
## |.....| 0.000 | 2.872 |...........|...........|
## |SA: X| 0.004992 | 1.479 | 0.7854 | 0.2399 |
## |.....| 0.000 | 2.872 |...........|...........|
##
## | #| tcl | tv | V(eta.cl) | V(eta.v) |
## |.....|cov.eta.v.eta.cl | add.sd |...........|...........|
## |-----+-----------+-----------+-----------+-----------|
## | 61| -5.296 | 0.3837 | 0.7461 | 0.2279 |
## |.....| 0.000 | 2.862 |...........|...........|
## |SA: X| 0.005012 | 1.468 | 0.7461 | 0.2279 |
## |.....| 0.000 | 2.862 |...........|...........|
## | 62| -5.309 | 0.3783 | 0.7088 | 0.2165 |
## |.....| 0.000 | 2.879 |...........|...........|
## |SA: X| 0.004945 | 1.460 | 0.7088 | 0.2165 |
## |.....| 0.000 | 2.879 |...........|...........|
## | 63| -5.290 | 0.3806 | 0.6734 | 0.2114 |
## |.....| 0.000 | 2.856 |...........|...........|
## |SA: X| 0.005043 | 1.463 | 0.6734 | 0.2114 |
## |.....| 0.000 | 2.856 |...........|...........|
## | 64| -5.300 | 0.3960 | 0.6397 | 0.2008 |
## |.....| 0.000 | 2.909 |...........|...........|
## |SA: X| 0.004991 | 1.486 | 0.6397 | 0.2008 |
## |.....| 0.000 | 2.909 |...........|...........|
## | 65| -5.266 | 0.3876 | 0.6077 | 0.1984 |
## |.....| 0.000 | 2.948 |...........|...........|
## |SA: X| 0.005166 | 1.473 | 0.6077 | 0.1984 |
## |.....| 0.000 | 2.948 |...........|...........|
## | 66| -5.260 | 0.3676 | 0.5773 | 0.2021 |
## |.....| 0.000 | 3.001 |...........|...........|
## |SA: X| 0.005195 | 1.444 | 0.5773 | 0.2021 |
## |.....| 0.000 | 3.001 |...........|...........|
## | 67| -5.253 | 0.3782 | 0.5485 | 0.1920 |
## |.....| 0.000 | 2.982 |...........|...........|
## |SA: X| 0.005233 | 1.460 | 0.5485 | 0.1920 |
## |.....| 0.000 | 2.982 |...........|...........|
## | 68| -5.291 | 0.3899 | 0.5210 | 0.1900 |
## |.....| 0.000 | 2.940 |...........|...........|
## |SA: X| 0.005038 | 1.477 | 0.5210 | 0.1900 |
## |.....| 0.000 | 2.940 |...........|...........|
## | 69| -5.283 | 0.3810 | 0.4950 | 0.1885 |
## |.....| 0.000 | 2.841 |...........|...........|
## |SA: X| 0.005079 | 1.464 | 0.4950 | 0.1885 |
## |.....| 0.000 | 2.841 |...........|...........|
## | 70| -5.257 | 0.3806 | 0.4702 | 0.2103 |
## |.....| 0.000 | 2.798 |...........|...........|
## |SA: X| 0.005209 | 1.463 | 0.4702 | 0.2103 |
## |.....| 0.000 | 2.798 |...........|...........|
##
## | #| tcl | tv | V(eta.cl) | V(eta.v) |
## |.....|cov.eta.v.eta.cl | add.sd |...........|...........|
## |-----+-----------+-----------+-----------+-----------|
## | 71| -5.250 | 0.3843 | 0.4467 | 0.1998 |
## |.....| 0.000 | 2.625 |...........|...........|
## |SA: X| 0.005248 | 1.469 | 0.4467 | 0.1998 |
## |.....| 0.000 | 2.625 |...........|...........|
## | 72| -5.254 | 0.3772 | 0.4244 | 0.1898 |
## |.....| 0.000 | 2.612 |...........|...........|
## |SA: X| 0.005226 | 1.458 | 0.4244 | 0.1898 |
## |.....| 0.000 | 2.612 |...........|...........|
## | 73| -5.207 | 0.3667 | 0.4032 | 0.1985 |
## |.....| 0.000 | 2.663 |...........|...........|
## |SA: X| 0.005478 | 1.443 | 0.4032 | 0.1985 |
## |.....| 0.000 | 2.663 |...........|...........|
## | 74| -5.210 | 0.3643 | 0.3830 | 0.1886 |
## |.....| 0.000 | 2.766 |...........|...........|
## |SA: X| 0.005460 | 1.440 | 0.3830 | 0.1886 |
## |.....| 0.000 | 2.766 |...........|...........|
## | 75| -5.175 | 0.3498 | 0.3639 | 0.1791 |
## |.....| 0.000 | 2.670 |...........|...........|
## |SA: X| 0.005659 | 1.419 | 0.3639 | 0.1791 |
## |.....| 0.000 | 2.670 |...........|...........|
## | 76| -5.222 | 0.3625 | 0.3457 | 0.1924 |
## |.....| 0.000 | 2.643 |...........|...........|
## |SA: X| 0.005396 | 1.437 | 0.3457 | 0.1924 |
## |.....| 0.000 | 2.643 |...........|...........|
## | 77| -5.173 | 0.3598 | 0.2900 | 0.1923 |
## |.....| 0.09112 | 2.643 |...........|...........|
## |SA: X| 0.005666 | 1.433 | 0.2900 | 0.1923 |
## |.....| 0.09112 | 2.643 |...........|...........|
## | 78| -5.181 | 0.3630 | 0.3015 | 0.1812 |
## |.....| 0.1050 | 2.762 |...........|...........|
## |SA: X| 0.005624 | 1.438 | 0.3015 | 0.1812 |
## |.....| 0.1050 | 2.762 |...........|...........|
## | 79| -5.158 | 0.3640 | 0.3013 | 0.1898 |
## |.....| 0.1318 | 2.656 |...........|...........|
## |SA: X| 0.005756 | 1.439 | 0.3013 | 0.1898 |
## |.....| 0.1318 | 2.656 |...........|...........|
## | 80| -5.139 | 0.3687 | 0.2673 | 0.1758 |
## |.....| 0.1239 | 2.838 |...........|...........|
## |SA: X| 0.005862 | 1.446 | 0.2673 | 0.1758 |
## |.....| 0.1239 | 2.838 |...........|...........|
##
## | #| tcl | tv | V(eta.cl) | V(eta.v) |
## |.....|cov.eta.v.eta.cl | add.sd |...........|...........|
## |-----+-----------+-----------+-----------+-----------|
## | 81| -5.134 | 0.3537 | 0.2566 | 0.1781 |
## |.....| 0.1233 | 2.608 |...........|...........|
## |SA: X| 0.005891 | 1.424 | 0.2566 | 0.1781 |
## |.....| 0.1233 | 2.608 |...........|...........|
## | 82| -5.126 | 0.3559 | 0.2796 | 0.1834 |
## |.....| 0.1485 | 2.578 |...........|...........|
## |SA: X| 0.005939 | 1.427 | 0.2796 | 0.1834 |
## |.....| 0.1485 | 2.578 |...........|...........|
## | 83| -5.070 | 0.3555 | 0.2911 | 0.1636 |
## |.....| 0.1552 | 2.623 |...........|...........|
## |SA: X| 0.006281 | 1.427 | 0.2911 | 0.1636 |
## |.....| 0.1552 | 2.623 |...........|...........|
## | 84| -5.079 | 0.3624 | 0.2926 | 0.1595 |
## |.....| 0.1641 | 2.663 |...........|...........|
## |SA: X| 0.006225 | 1.437 | 0.2926 | 0.1595 |
## |.....| 0.1641 | 2.663 |...........|...........|
## | 85| -5.092 | 0.3592 | 0.3014 | 0.1590 |
## |.....| 0.1688 | 2.667 |...........|...........|
## |SA: X| 0.006143 | 1.432 | 0.3014 | 0.1590 |
## |.....| 0.1688 | 2.667 |...........|...........|
## | 86| -5.110 | 0.3674 | 0.2835 | 0.1707 |
## |.....| 0.1704 | 2.681 |...........|...........|
## |SA: X| 0.006037 | 1.444 | 0.2835 | 0.1707 |
## |.....| 0.1704 | 2.681 |...........|...........|
## | 87| -5.072 | 0.3512 | 0.2862 | 0.1627 |
## |.....| 0.1732 | 2.605 |...........|...........|
## |SA: X| 0.006269 | 1.421 | 0.2862 | 0.1627 |
## |.....| 0.1732 | 2.605 |...........|...........|
## | 88| -5.066 | 0.3464 | 0.2828 | 0.1672 |
## |.....| 0.1797 | 2.606 |...........|...........|
## |SA: X| 0.006305 | 1.414 | 0.2828 | 0.1672 |
## |.....| 0.1797 | 2.606 |...........|...........|
## | 89| -5.063 | 0.3424 | 0.2701 | 0.1722 |
## |.....| 0.1845 | 2.709 |...........|...........|
## |SA: X| 0.006329 | 1.408 | 0.2701 | 0.1722 |
## |.....| 0.1845 | 2.709 |...........|...........|
## | 90| -5.025 | 0.3411 | 0.2639 | 0.1602 |
## |.....| 0.1760 | 2.637 |...........|...........|
## |SA: X| 0.006569 | 1.406 | 0.2639 | 0.1602 |
## |.....| 0.1760 | 2.637 |...........|...........|
##
## | #| tcl | tv | V(eta.cl) | V(eta.v) |
## |.....|cov.eta.v.eta.cl | add.sd |...........|...........|
## |-----+-----------+-----------+-----------+-----------|
## | 91| -5.028 | 0.3544 | 0.2618 | 0.1649 |
## |.....| 0.1742 | 2.642 |...........|...........|
## |SA: X| 0.006555 | 1.425 | 0.2618 | 0.1649 |
## |.....| 0.1742 | 2.642 |...........|...........|
## | 92| -5.034 | 0.3464 | 0.2507 | 0.1632 |
## |.....| 0.1723 | 2.727 |...........|...........|
## |SA: X| 0.006511 | 1.414 | 0.2507 | 0.1632 |
## |.....| 0.1723 | 2.727 |...........|...........|
## | 93| -5.017 | 0.3489 | 0.2519 | 0.1614 |
## |.....| 0.1746 | 2.681 |...........|...........|
## |SA: X| 0.006626 | 1.417 | 0.2519 | 0.1614 |
## |.....| 0.1746 | 2.681 |...........|...........|
## | 94| -5.000 | 0.3408 | 0.2444 | 0.1780 |
## |.....| 0.1824 | 2.657 |...........|...........|
## |SA: X| 0.006739 | 1.406 | 0.2444 | 0.1780 |
## |.....| 0.1824 | 2.657 |...........|...........|
## | 95| -5.010 | 0.3381 | 0.2504 | 0.1681 |
## |.....| 0.1831 | 2.707 |...........|...........|
## |SA: X| 0.006669 | 1.402 | 0.2504 | 0.1681 |
## |.....| 0.1831 | 2.707 |...........|...........|
## | 96| -5.026 | 0.3505 | 0.2328 | 0.1716 |
## |.....| 0.1814 | 2.687 |...........|...........|
## |SA: X| 0.006562 | 1.420 | 0.2328 | 0.1716 |
## |.....| 0.1814 | 2.687 |...........|...........|
## | 97| -5.018 | 0.3444 | 0.2029 | 0.1628 |
## |.....| 0.1654 | 2.700 |...........|...........|
## |SA: X| 0.006619 | 1.411 | 0.2029 | 0.1628 |
## |.....| 0.1654 | 2.700 |...........|...........|
## | 98| -5.014 | 0.3457 | 0.2281 | 0.1756 |
## |.....| 0.1852 | 2.722 |...........|...........|
## |SA: X| 0.006644 | 1.413 | 0.2281 | 0.1756 |
## |.....| 0.1852 | 2.722 |...........|...........|
## | 99| -5.012 | 0.3361 | 0.2168 | 0.1671 |
## |.....| 0.1726 | 2.805 |...........|...........|
## |SA: X| 0.006658 | 1.399 | 0.2168 | 0.1671 |
## |.....| 0.1726 | 2.805 |...........|...........|
## | 100| -4.993 | 0.3488 | 0.2234 | 0.1567 |
## |.....| 0.1697 | 2.779 |...........|...........|
## |SA: X| 0.006782 | 1.417 | 0.2234 | 0.1567 |
## |.....| 0.1697 | 2.779 |...........|...........|
##
## | #| tcl | tv | V(eta.cl) | V(eta.v) |
## |.....|cov.eta.v.eta.cl | add.sd |...........|...........|
## |-----+-----------+-----------+-----------+-----------|
## | 101| -5.000 | 0.3477 | 0.2283 | 0.1567 |
## |.....| 0.1713 | 2.805 |...........|...........|
## |EM: X| 0.006739 | 1.416 | 0.2283 | 0.1567 |
## |.....| 0.1713 | 2.805 |...........|...........|
## | 102| -5.004 | 0.3432 | 0.2371 | 0.1581 |
## |.....| 0.1763 | 2.771 |...........|...........|
## |EM: X| 0.006709 | 1.409 | 0.2371 | 0.1581 |
## |.....| 0.1763 | 2.771 |...........|...........|
## | 103| -5.003 | 0.3452 | 0.2390 | 0.1590 |
## |.....| 0.1778 | 2.752 |...........|...........|
## |EM: X| 0.006718 | 1.412 | 0.2390 | 0.1590 |
## |.....| 0.1778 | 2.752 |...........|...........|
## | 104| -5.002 | 0.3452 | 0.2440 | 0.1591 |
## |.....| 0.1800 | 2.757 |...........|...........|
## |EM: X| 0.006725 | 1.412 | 0.2440 | 0.1591 |
## |.....| 0.1800 | 2.757 |...........|...........|
## | 105| -4.997 | 0.3455 | 0.2466 | 0.1620 |
## |.....| 0.1831 | 2.747 |...........|...........|
## |EM: X| 0.006757 | 1.413 | 0.2466 | 0.1620 |
## |.....| 0.1831 | 2.747 |...........|...........|
## | 106| -4.997 | 0.3453 | 0.2477 | 0.1626 |
## |.....| 0.1840 | 2.738 |...........|...........|
## |EM: X| 0.006758 | 1.412 | 0.2477 | 0.1626 |
## |.....| 0.1840 | 2.738 |...........|...........|
## | 107| -4.995 | 0.3456 | 0.2488 | 0.1624 |
## |.....| 0.1840 | 2.727 |...........|...........|
## |EM: X| 0.006769 | 1.413 | 0.2488 | 0.1624 |
## |.....| 0.1840 | 2.727 |...........|...........|
## | 108| -4.994 | 0.3454 | 0.2487 | 0.1625 |
## |.....| 0.1845 | 2.735 |...........|...........|
## |EM: X| 0.006779 | 1.413 | 0.2487 | 0.1625 |
## |.....| 0.1845 | 2.735 |...........|...........|
## | 109| -4.995 | 0.3452 | 0.2473 | 0.1629 |
## |.....| 0.1842 | 2.739 |...........|...........|
## |EM: X| 0.006774 | 1.412 | 0.2473 | 0.1629 |
## |.....| 0.1842 | 2.739 |...........|...........|
## | 110| -4.994 | 0.3462 | 0.2474 | 0.1627 |
## |.....| 0.1841 | 2.734 |...........|...........|
## |EM: X| 0.006778 | 1.414 | 0.2474 | 0.1627 |
## |.....| 0.1841 | 2.734 |...........|...........|
##
## | #| tcl | tv | V(eta.cl) | V(eta.v) |
## |.....|cov.eta.v.eta.cl | add.sd |...........|...........|
## |-----+-----------+-----------+-----------+-----------|
## | 111| -4.993 | 0.3466 | 0.2477 | 0.1623 |
## |.....| 0.1841 | 2.737 |...........|...........|
## |EM: X| 0.006788 | 1.414 | 0.2477 | 0.1623 |
## |.....| 0.1841 | 2.737 |...........|...........|
## | 112| -4.993 | 0.3467 | 0.2477 | 0.1623 |
## |.....| 0.1842 | 2.735 |...........|...........|
## |EM: X| 0.006786 | 1.414 | 0.2477 | 0.1623 |
## |.....| 0.1842 | 2.735 |...........|...........|
## | 113| -4.994 | 0.3464 | 0.2487 | 0.1619 |
## |.....| 0.1845 | 2.730 |...........|...........|
## |EM: X| 0.006779 | 1.414 | 0.2487 | 0.1619 |
## |.....| 0.1845 | 2.730 |...........|...........|
## | 114| -4.994 | 0.3466 | 0.2482 | 0.1626 |
## |.....| 0.1849 | 2.731 |...........|...........|
## |EM: X| 0.006779 | 1.414 | 0.2482 | 0.1626 |
## |.....| 0.1849 | 2.731 |...........|...........|
## | 115| -4.994 | 0.3463 | 0.2482 | 0.1625 |
## |.....| 0.1849 | 2.728 |...........|...........|
## |EM: X| 0.006779 | 1.414 | 0.2482 | 0.1625 |
## |.....| 0.1849 | 2.728 |...........|...........|
## | 116| -4.994 | 0.3460 | 0.2481 | 0.1623 |
## |.....| 0.1849 | 2.726 |...........|...........|
## |EM: X| 0.006779 | 1.413 | 0.2481 | 0.1623 |
## |.....| 0.1849 | 2.726 |...........|...........|
## | 117| -4.995 | 0.3460 | 0.2479 | 0.1621 |
## |.....| 0.1848 | 2.726 |...........|...........|
## |EM: X| 0.006774 | 1.413 | 0.2479 | 0.1621 |
## |.....| 0.1848 | 2.726 |...........|...........|
## | 118| -4.995 | 0.3459 | 0.2478 | 0.1621 |
## |.....| 0.1847 | 2.726 |...........|...........|
## |EM: X| 0.006773 | 1.413 | 0.2478 | 0.1621 |
## |.....| 0.1847 | 2.726 |...........|...........|
## | 119| -4.995 | 0.3461 | 0.2468 | 0.1621 |
## |.....| 0.1843 | 2.729 |...........|...........|
## |EM: X| 0.006771 | 1.414 | 0.2468 | 0.1621 |
## |.....| 0.1843 | 2.729 |...........|...........|
## | 120| -4.995 | 0.3462 | 0.2473 | 0.1621 |
## |.....| 0.1845 | 2.730 |...........|...........|
## |EM: X| 0.006772 | 1.414 | 0.2473 | 0.1621 |
## |.....| 0.1845 | 2.730 |...........|...........|
##
## | #| tcl | tv | V(eta.cl) | V(eta.v) |
## |.....|cov.eta.v.eta.cl | add.sd |...........|...........|
## |-----+-----------+-----------+-----------+-----------|
## | 121| -4.995 | 0.3457 | 0.2481 | 0.1621 |
## |.....| 0.1848 | 2.727 |...........|...........|
## |EM: X| 0.006770 | 1.413 | 0.2481 | 0.1621 |
## |.....| 0.1848 | 2.727 |...........|...........|
## | 122| -4.996 | 0.3459 | 0.2475 | 0.1616 |
## |.....| 0.1843 | 2.730 |...........|...........|
## |EM: X| 0.006768 | 1.413 | 0.2475 | 0.1616 |
## |.....| 0.1843 | 2.730 |...........|...........|
## | 123| -4.995 | 0.3459 | 0.2474 | 0.1613 |
## |.....| 0.1842 | 2.733 |...........|...........|
## |EM: X| 0.006772 | 1.413 | 0.2474 | 0.1613 |
## |.....| 0.1842 | 2.733 |...........|...........|
## | 124| -4.994 | 0.3456 | 0.2478 | 0.1613 |
## |.....| 0.1844 | 2.735 |...........|...........|
## |EM: X| 0.006778 | 1.413 | 0.2478 | 0.1613 |
## |.....| 0.1844 | 2.735 |...........|...........|
## | 125| -4.994 | 0.3456 | 0.2482 | 0.1614 |
## |.....| 0.1847 | 2.731 |...........|...........|
## |EM: X| 0.006775 | 1.413 | 0.2482 | 0.1614 |
## |.....| 0.1847 | 2.731 |...........|...........|
## | 126| -4.994 | 0.3450 | 0.2483 | 0.1615 |
## |.....| 0.1847 | 2.728 |...........|...........|
## |EM: X| 0.006777 | 1.412 | 0.2483 | 0.1615 |
## |.....| 0.1847 | 2.728 |...........|...........|
## | 127| -4.994 | 0.3450 | 0.2480 | 0.1616 |
## |.....| 0.1846 | 2.726 |...........|...........|
## |EM: X| 0.006777 | 1.412 | 0.2480 | 0.1616 |
## |.....| 0.1846 | 2.726 |...........|...........|
## | 128| -4.995 | 0.3442 | 0.2482 | 0.1618 |
## |.....| 0.1848 | 2.724 |...........|...........|
## |EM: X| 0.006773 | 1.411 | 0.2482 | 0.1618 |
## |.....| 0.1848 | 2.724 |...........|...........|
## | 129| -4.995 | 0.3443 | 0.2484 | 0.1621 |
## |.....| 0.1850 | 2.721 |...........|...........|
## |EM: X| 0.006773 | 1.411 | 0.2484 | 0.1621 |
## |.....| 0.1850 | 2.721 |...........|...........|
## | 130| -4.995 | 0.3442 | 0.2487 | 0.1623 |
## |.....| 0.1854 | 2.722 |...........|...........|
## |EM: X| 0.006772 | 1.411 | 0.2487 | 0.1623 |
## |.....| 0.1854 | 2.722 |...........|...........|
##
## | #| tcl | tv | V(eta.cl) | V(eta.v) |
## |.....|cov.eta.v.eta.cl | add.sd |...........|...........|
## |-----+-----------+-----------+-----------+-----------|
## | 131| -4.995 | 0.3439 | 0.2487 | 0.1623 |
## |.....| 0.1854 | 2.720 |...........|...........|
## |EM: X| 0.006772 | 1.410 | 0.2487 | 0.1623 |
## |.....| 0.1854 | 2.720 |...........|...........|
## | 132| -4.995 | 0.3434 | 0.2487 | 0.1622 |
## |.....| 0.1854 | 2.721 |...........|...........|
## |EM: X| 0.006772 | 1.410 | 0.2487 | 0.1622 |
## |.....| 0.1854 | 2.721 |...........|...........|
## | 133| -4.995 | 0.3437 | 0.2485 | 0.1622 |
## |.....| 0.1853 | 2.724 |...........|...........|
## |EM: X| 0.006770 | 1.410 | 0.2485 | 0.1622 |
## |.....| 0.1853 | 2.724 |...........|...........|
## | 134| -4.995 | 0.3439 | 0.2484 | 0.1620 |
## |.....| 0.1851 | 2.728 |...........|...........|
## |EM: X| 0.006769 | 1.410 | 0.2484 | 0.1620 |
## |.....| 0.1851 | 2.728 |...........|...........|
## | 135| -4.996 | 0.3440 | 0.2483 | 0.1618 |
## |.....| 0.1849 | 2.725 |...........|...........|
## |EM: X| 0.006768 | 1.411 | 0.2483 | 0.1618 |
## |.....| 0.1849 | 2.725 |...........|...........|
## | 136| -4.995 | 0.3441 | 0.2481 | 0.1619 |
## |.....| 0.1849 | 2.726 |...........|...........|
## |EM: X| 0.006769 | 1.411 | 0.2481 | 0.1619 |
## |.....| 0.1849 | 2.726 |...........|...........|
## | 137| -4.995 | 0.3442 | 0.2481 | 0.1620 |
## |.....| 0.1849 | 2.728 |...........|...........|
## |EM: X| 0.006771 | 1.411 | 0.2481 | 0.1620 |
## |.....| 0.1849 | 2.728 |...........|...........|
## | 138| -4.995 | 0.3444 | 0.2485 | 0.1622 |
## |.....| 0.1852 | 2.726 |...........|...........|
## |EM: X| 0.006772 | 1.411 | 0.2485 | 0.1622 |
## |.....| 0.1852 | 2.726 |...........|...........|
## | 139| -4.995 | 0.3443 | 0.2484 | 0.1622 |
## |.....| 0.1852 | 2.726 |...........|...........|
## |EM: X| 0.006770 | 1.411 | 0.2484 | 0.1622 |
## |.....| 0.1852 | 2.726 |...........|...........|
## | 140| -4.995 | 0.3443 | 0.2483 | 0.1622 |
## |.....| 0.1851 | 2.723 |...........|...........|
## |EM: X| 0.006769 | 1.411 | 0.2483 | 0.1622 |
## |.....| 0.1851 | 2.723 |...........|...........|
##
## | #| tcl | tv | V(eta.cl) | V(eta.v) |
## |.....|cov.eta.v.eta.cl | add.sd |...........|...........|
## |-----+-----------+-----------+-----------+-----------|
## | 141| -4.995 | 0.3444 | 0.2485 | 0.1620 |
## |.....| 0.1852 | 2.724 |...........|...........|
## |EM: X| 0.006770 | 1.411 | 0.2485 | 0.1620 |
## |.....| 0.1852 | 2.724 |...........|...........|
## | 142| -4.996 | 0.3443 | 0.2489 | 0.1619 |
## |.....| 0.1853 | 2.724 |...........|...........|
## |EM: X| 0.006767 | 1.411 | 0.2489 | 0.1619 |
## |.....| 0.1853 | 2.724 |...........|...........|
## | 143| -4.996 | 0.3442 | 0.2487 | 0.1618 |
## |.....| 0.1852 | 2.726 |...........|...........|
## |EM: X| 0.006762 | 1.411 | 0.2487 | 0.1618 |
## |.....| 0.1852 | 2.726 |...........|...........|
## | 144| -4.997 | 0.3441 | 0.2485 | 0.1617 |
## |.....| 0.1850 | 2.725 |...........|...........|
## |EM: X| 0.006758 | 1.411 | 0.2485 | 0.1617 |
## |.....| 0.1850 | 2.725 |...........|...........|
## | 145| -4.997 | 0.3441 | 0.2486 | 0.1618 |
## |.....| 0.1852 | 2.724 |...........|...........|
## |EM: X| 0.006757 | 1.411 | 0.2486 | 0.1618 |
## |.....| 0.1852 | 2.724 |...........|...........|
## | 146| -4.998 | 0.3442 | 0.2483 | 0.1617 |
## |.....| 0.1851 | 2.723 |...........|...........|
## |EM: X| 0.006754 | 1.411 | 0.2483 | 0.1617 |
## |.....| 0.1851 | 2.723 |...........|...........|
## | 147| -4.998 | 0.3441 | 0.2481 | 0.1615 |
## |.....| 0.1849 | 2.723 |...........|...........|
## |EM: X| 0.006753 | 1.411 | 0.2481 | 0.1615 |
## |.....| 0.1849 | 2.723 |...........|...........|
## | 148| -4.998 | 0.3440 | 0.2478 | 0.1616 |
## |.....| 0.1849 | 2.722 |...........|...........|
## |EM: X| 0.006754 | 1.411 | 0.2478 | 0.1616 |
## |.....| 0.1849 | 2.722 |...........|...........|
## | 149| -4.998 | 0.3440 | 0.2479 | 0.1616 |
## |.....| 0.1849 | 2.719 |...........|...........|
## |EM: X| 0.006754 | 1.411 | 0.2479 | 0.1616 |
## |.....| 0.1849 | 2.719 |...........|...........|
## | 150| -4.997 | 0.3441 | 0.2475 | 0.1617 |
## |.....| 0.1848 | 2.718 |...........|...........|
## |EM: X| 0.006756 | 1.411 | 0.2475 | 0.1617 |
## |.....| 0.1848 | 2.718 |...........|...........|
##
## | #| tcl | tv | V(eta.cl) | V(eta.v) |
## |.....|cov.eta.v.eta.cl | add.sd |...........|...........|
## |-----+-----------+-----------+-----------+-----------|
## | 151| -4.997 | 0.3440 | 0.2478 | 0.1617 |
## |.....| 0.1849 | 2.718 |...........|...........|
## |EM: X| 0.006758 | 1.411 | 0.2478 | 0.1617 |
## |.....| 0.1849 | 2.718 |...........|...........|
## | 152| -4.997 | 0.3440 | 0.2477 | 0.1618 |
## |.....| 0.1850 | 2.718 |...........|...........|
## |EM: X| 0.006756 | 1.411 | 0.2477 | 0.1618 |
## |.....| 0.1850 | 2.718 |...........|...........|
## | 153| -4.998 | 0.3441 | 0.2479 | 0.1618 |
## |.....| 0.1850 | 2.717 |...........|...........|
## |EM: X| 0.006753 | 1.411 | 0.2479 | 0.1618 |
## |.....| 0.1850 | 2.717 |...........|...........|
## | 154| -4.998 | 0.3440 | 0.2479 | 0.1618 |
## |.....| 0.1851 | 2.719 |...........|...........|
## |EM: X| 0.006754 | 1.411 | 0.2479 | 0.1618 |
## |.....| 0.1851 | 2.719 |...........|...........|
## | 155| -4.997 | 0.3440 | 0.2480 | 0.1618 |
## |.....| 0.1851 | 2.718 |...........|...........|
## |EM: X| 0.006755 | 1.411 | 0.2480 | 0.1618 |
## |.....| 0.1851 | 2.718 |...........|...........|
## | 156| -4.997 | 0.3439 | 0.2481 | 0.1620 |
## |.....| 0.1853 | 2.717 |...........|...........|
## |EM: X| 0.006757 | 1.410 | 0.2481 | 0.1620 |
## |.....| 0.1853 | 2.717 |...........|...........|
## | 157| -4.998 | 0.3438 | 0.2486 | 0.1619 |
## |.....| 0.1854 | 2.719 |...........|...........|
## |EM: X| 0.006754 | 1.410 | 0.2486 | 0.1619 |
## |.....| 0.1854 | 2.719 |...........|...........|
## | 158| -4.997 | 0.3440 | 0.2485 | 0.1619 |
## |.....| 0.1854 | 2.719 |...........|...........|
## |EM: X| 0.006755 | 1.411 | 0.2485 | 0.1619 |
## |.....| 0.1854 | 2.719 |...........|...........|
## | 159| -4.998 | 0.3439 | 0.2485 | 0.1620 |
## |.....| 0.1855 | 2.717 |...........|...........|
## |EM: X| 0.006753 | 1.410 | 0.2485 | 0.1620 |
## |.....| 0.1855 | 2.717 |...........|...........|
## | 160| -4.998 | 0.3437 | 0.2487 | 0.1620 |
## |.....| 0.1855 | 2.716 |...........|...........|
## |EM: X| 0.006752 | 1.410 | 0.2487 | 0.1620 |
## |.....| 0.1855 | 2.716 |...........|...........|
##
## | #| tcl | tv | V(eta.cl) | V(eta.v) |
## |.....|cov.eta.v.eta.cl | add.sd |...........|...........|
## |-----+-----------+-----------+-----------+-----------|
## | 161| -4.998 | 0.3437 | 0.2487 | 0.1620 |
## |.....| 0.1856 | 2.716 |...........|...........|
## |EM: X| 0.006753 | 1.410 | 0.2487 | 0.1620 |
## |.....| 0.1856 | 2.716 |...........|...........|
## | 162| -4.998 | 0.3436 | 0.2490 | 0.1620 |
## |.....| 0.1857 | 2.719 |...........|...........|
## |EM: X| 0.006750 | 1.410 | 0.2490 | 0.1620 |
## |.....| 0.1857 | 2.719 |...........|...........|
## | 163| -4.999 | 0.3436 | 0.2488 | 0.1620 |
## |.....| 0.1856 | 2.719 |...........|...........|
## |EM: X| 0.006747 | 1.410 | 0.2488 | 0.1620 |
## |.....| 0.1856 | 2.719 |...........|...........|
## | 164| -4.999 | 0.3436 | 0.2489 | 0.1621 |
## |.....| 0.1857 | 2.717 |...........|...........|
## |EM: X| 0.006744 | 1.410 | 0.2489 | 0.1621 |
## |.....| 0.1857 | 2.717 |...........|...........|
## | 165| -4.999 | 0.3437 | 0.2493 | 0.1622 |
## |.....| 0.1860 | 2.717 |...........|...........|
## |EM: X| 0.006742 | 1.410 | 0.2493 | 0.1622 |
## |.....| 0.1860 | 2.717 |...........|...........|
## | 166| -5.000 | 0.3435 | 0.2498 | 0.1622 |
## |.....| 0.1862 | 2.717 |...........|...........|
## |EM: X| 0.006740 | 1.410 | 0.2498 | 0.1622 |
## |.....| 0.1862 | 2.717 |...........|...........|
## | 167| -5.000 | 0.3436 | 0.2500 | 0.1622 |
## |.....| 0.1862 | 2.717 |...........|...........|
## |EM: X| 0.006738 | 1.410 | 0.2500 | 0.1622 |
## |.....| 0.1862 | 2.717 |...........|...........|
## | 168| -5.000 | 0.3434 | 0.2498 | 0.1621 |
## |.....| 0.1861 | 2.717 |...........|...........|
## |EM: X| 0.006736 | 1.410 | 0.2498 | 0.1621 |
## |.....| 0.1861 | 2.717 |...........|...........|
## | 169| -5.001 | 0.3433 | 0.2496 | 0.1621 |
## |.....| 0.1861 | 2.716 |...........|...........|
## |EM: X| 0.006734 | 1.410 | 0.2496 | 0.1621 |
## |.....| 0.1861 | 2.716 |...........|...........|
## | 170| -5.001 | 0.3433 | 0.2495 | 0.1622 |
## |.....| 0.1861 | 2.716 |...........|...........|
## |EM: X| 0.006734 | 1.410 | 0.2495 | 0.1622 |
## |.....| 0.1861 | 2.716 |...........|...........|
##
## | #| tcl | tv | V(eta.cl) | V(eta.v) |
## |.....|cov.eta.v.eta.cl | add.sd |...........|...........|
## |-----+-----------+-----------+-----------+-----------|
## | 171| -5.000 | 0.3433 | 0.2497 | 0.1623 |
## |.....| 0.1863 | 2.715 |...........|...........|
## |EM: X| 0.006735 | 1.410 | 0.2497 | 0.1623 |
## |.....| 0.1863 | 2.715 |...........|...........|
## | 172| -5.000 | 0.3432 | 0.2496 | 0.1625 |
## |.....| 0.1864 | 2.715 |...........|...........|
## |EM: X| 0.006735 | 1.409 | 0.2496 | 0.1625 |
## |.....| 0.1864 | 2.715 |...........|...........|
## | 173| -5.001 | 0.3432 | 0.2496 | 0.1626 |
## |.....| 0.1864 | 2.715 |...........|...........|
## |EM: X| 0.006734 | 1.409 | 0.2496 | 0.1626 |
## |.....| 0.1864 | 2.715 |...........|...........|
## | 174| -5.001 | 0.3431 | 0.2496 | 0.1626 |
## |.....| 0.1865 | 2.715 |...........|...........|
## |EM: X| 0.006734 | 1.409 | 0.2496 | 0.1626 |
## |.....| 0.1865 | 2.715 |...........|...........|
## | 175| -5.001 | 0.3429 | 0.2498 | 0.1626 |
## |.....| 0.1865 | 2.715 |...........|...........|
## |EM: X| 0.006734 | 1.409 | 0.2498 | 0.1626 |
## |.....| 0.1865 | 2.715 |...........|...........|
## | 176| -5.000 | 0.3430 | 0.2497 | 0.1626 |
## |.....| 0.1866 | 2.715 |...........|...........|
## |EM: X| 0.006735 | 1.409 | 0.2497 | 0.1626 |
## |.....| 0.1866 | 2.715 |...........|...........|
## | 177| -5.000 | 0.3430 | 0.2500 | 0.1625 |
## |.....| 0.1866 | 2.715 |...........|...........|
## |EM: X| 0.006736 | 1.409 | 0.2500 | 0.1625 |
## |.....| 0.1866 | 2.715 |...........|...........|
## | 178| -5.000 | 0.3430 | 0.2501 | 0.1626 |
## |.....| 0.1867 | 2.717 |...........|...........|
## |EM: X| 0.006736 | 1.409 | 0.2501 | 0.1626 |
## |.....| 0.1867 | 2.717 |...........|...........|
## | 179| -5.000 | 0.3430 | 0.2500 | 0.1625 |
## |.....| 0.1866 | 2.717 |...........|...........|
## |EM: X| 0.006737 | 1.409 | 0.2500 | 0.1625 |
## |.....| 0.1866 | 2.717 |...........|...........|
## | 180| -5.000 | 0.3431 | 0.2500 | 0.1625 |
## |.....| 0.1866 | 2.717 |...........|...........|
## |EM: X| 0.006737 | 1.409 | 0.2500 | 0.1625 |
## |.....| 0.1866 | 2.717 |...........|...........|
##
## | #| tcl | tv | V(eta.cl) | V(eta.v) |
## |.....|cov.eta.v.eta.cl | add.sd |...........|...........|
## |-----+-----------+-----------+-----------+-----------|
## | 181| -5.000 | 0.3433 | 0.2497 | 0.1625 |
## |.....| 0.1865 | 2.719 |...........|...........|
## |EM: X| 0.006738 | 1.410 | 0.2497 | 0.1625 |
## |.....| 0.1865 | 2.719 |...........|...........|
## | 182| -5.000 | 0.3434 | 0.2497 | 0.1624 |
## |.....| 0.1864 | 2.719 |...........|...........|
## |EM: X| 0.006739 | 1.410 | 0.2497 | 0.1624 |
## |.....| 0.1864 | 2.719 |...........|...........|
## | 183| -5.000 | 0.3434 | 0.2497 | 0.1624 |
## |.....| 0.1864 | 2.720 |...........|...........|
## |EM: X| 0.006738 | 1.410 | 0.2497 | 0.1624 |
## |.....| 0.1864 | 2.720 |...........|...........|
## | 184| -5.000 | 0.3434 | 0.2496 | 0.1624 |
## |.....| 0.1864 | 2.720 |...........|...........|
## |EM: X| 0.006740 | 1.410 | 0.2496 | 0.1624 |
## |.....| 0.1864 | 2.720 |...........|...........|
## | 185| -5.000 | 0.3432 | 0.2494 | 0.1623 |
## |.....| 0.1863 | 2.722 |...........|...........|
## |EM: X| 0.006739 | 1.409 | 0.2494 | 0.1623 |
## |.....| 0.1863 | 2.722 |...........|...........|
## | 186| -5.000 | 0.3431 | 0.2493 | 0.1623 |
## |.....| 0.1862 | 2.722 |...........|...........|
## |EM: X| 0.006740 | 1.409 | 0.2493 | 0.1623 |
## |.....| 0.1862 | 2.722 |...........|...........|
## | 187| -5.000 | 0.3429 | 0.2494 | 0.1623 |
## |.....| 0.1862 | 2.720 |...........|...........|
## |EM: X| 0.006739 | 1.409 | 0.2494 | 0.1623 |
## |.....| 0.1862 | 2.720 |...........|...........|
## | 188| -5.000 | 0.3429 | 0.2496 | 0.1623 |
## |.....| 0.1863 | 2.719 |...........|...........|
## |EM: X| 0.006739 | 1.409 | 0.2496 | 0.1623 |
## |.....| 0.1863 | 2.719 |...........|...........|
## | 189| -5.000 | 0.3429 | 0.2495 | 0.1622 |
## |.....| 0.1862 | 2.719 |...........|...........|
## |EM: X| 0.006739 | 1.409 | 0.2495 | 0.1622 |
## |.....| 0.1862 | 2.719 |...........|...........|
## | 190| -5.000 | 0.3429 | 0.2496 | 0.1621 |
## |.....| 0.1862 | 2.719 |...........|...........|
## |EM: X| 0.006740 | 1.409 | 0.2496 | 0.1621 |
## |.....| 0.1862 | 2.719 |...........|...........|
##
## | #| tcl | tv | V(eta.cl) | V(eta.v) |
## |.....|cov.eta.v.eta.cl | add.sd |...........|...........|
## |-----+-----------+-----------+-----------+-----------|
## | 191| -5.000 | 0.3430 | 0.2497 | 0.1620 |
## |.....| 0.1862 | 2.720 |...........|...........|
## |EM: X| 0.006740 | 1.409 | 0.2497 | 0.1620 |
## |.....| 0.1862 | 2.720 |...........|...........|
## | 192| -5.000 | 0.3431 | 0.2497 | 0.1620 |
## |.....| 0.1861 | 2.720 |...........|...........|
## |EM: X| 0.006741 | 1.409 | 0.2497 | 0.1620 |
## |.....| 0.1861 | 2.720 |...........|...........|
## | 193| -5.000 | 0.3430 | 0.2497 | 0.1621 |
## |.....| 0.1862 | 2.719 |...........|...........|
## |EM: X| 0.006740 | 1.409 | 0.2497 | 0.1621 |
## |.....| 0.1862 | 2.719 |...........|...........|
## | 194| -5.000 | 0.3430 | 0.2499 | 0.1621 |
## |.....| 0.1863 | 2.720 |...........|...........|
## |EM: X| 0.006739 | 1.409 | 0.2499 | 0.1621 |
## |.....| 0.1863 | 2.720 |...........|...........|
## | 195| -5.000 | 0.3430 | 0.2498 | 0.1620 |
## |.....| 0.1862 | 2.721 |...........|...........|
## |EM: X| 0.006739 | 1.409 | 0.2498 | 0.1620 |
## |.....| 0.1862 | 2.721 |...........|...........|
## | 196| -5.000 | 0.3429 | 0.2497 | 0.1619 |
## |.....| 0.1861 | 2.721 |...........|...........|
## |EM: X| 0.006738 | 1.409 | 0.2497 | 0.1619 |
## |.....| 0.1861 | 2.721 |...........|...........|
## | 197| -5.000 | 0.3429 | 0.2495 | 0.1618 |
## |.....| 0.1860 | 2.721 |...........|...........|
## |EM: X| 0.006738 | 1.409 | 0.2495 | 0.1618 |
## |.....| 0.1860 | 2.721 |...........|...........|
## | 198| -5.000 | 0.3429 | 0.2495 | 0.1619 |
## |.....| 0.1860 | 2.721 |...........|...........|
## |EM: X| 0.006737 | 1.409 | 0.2495 | 0.1619 |
## |.....| 0.1860 | 2.721 |...........|...........|
## | 199| -5.000 | 0.3429 | 0.2496 | 0.1619 |
## |.....| 0.1860 | 2.721 |...........|...........|
## |EM: X| 0.006736 | 1.409 | 0.2496 | 0.1619 |
## |.....| 0.1860 | 2.721 |...........|...........|
## | 200| -5.000 | 0.3430 | 0.2496 | 0.1619 |
## |.....| 0.1861 | 2.723 |...........|...........|
## |EM: X| 0.006735 | 1.409 | 0.2496 | 0.1619 |
## |.....| 0.1861 | 2.723 |...........|...........|
## [====|====|====|====|====|====|====|====|====|====] 0:00:00
##
## [====|====|====|====|====|====|====|====|====|====] 0:00:00
##
## [====|====|====|====|====|====|====|====|====|====] 0:00:00
##
## [====|====|====|====|====|====|====|====|====|====] 0:00:00# the importance-sampling Monte Carlo observed information, same fit
setCov(fit, "imp")## [====|====|====|====|====|====|====|====|====|====] 0:00:00
##
## [====|====|====|====|====|====|====|====|====|====] 0:00:00
##
## [====|====|====|====|====|====|====|====|====|====] 0:00:00
##
## [====|====|====|====|====|====|====|====|====|====] 0:00:00
##
## [====|====|====|====|====|====|====|====|====|====] 0:00:00
##
## [====|====|====|====|====|====|====|====|====|====] 0:00:00
##
## [====|====|====|====|====|====|====|====|====|====] 0:00:00
##
## [====|====|====|====|====|====|====|====|====|====] 0:00:00
##
## [====|====|====|====|====|====|====|====|====|====] 0:00:00
##
## [====|====|====|====|====|====|====|====|====|====] 0:00:00
##
## [====|====|====|====|====|====|====|====|====|====] 0:00:00
##
## [====|====|====|====|====|====|====|====|====|====] 0:00:00
##
## Key: X: Back-transformed parameters; Omegas=chol(solve(omega));
## Diagonals are transformed, as specified by impmapControl(diagXform=)
##
## | #| Function Val. | tcl | tv | add.sd | o1 |
## |.....................| o2 | o3 |...........|...........|
## |-----+---------------+-----------+-----------+-----------+-----------|
## | 1| 1350.5097 | -5.085 | 0.3437 | 2.540 | 1.526 |
## |.....................| -2.645 | 1.547 |...........|...........|
## | X| | 0.006190 | 1.410 | 2.540 | 1.526 |
## |.....................| -2.645 | 1.547 |...........|...........|
## |-----+---------------+-----------+-----------+-----------+-----------|
## calculating covariance matrix
## [====|====|====|====|====|====|====|====|====|====] 0:00:54
## [====|====|====|====|====|====|====|====|====|====
## [====|====|====|====|====|====|====|====|====|====] 0:00:00
##
## [====|====|====|====|====|====|====|====|====|====] 0:00:00
##
## [====|====|====|====|====|====|====|====|====|====] 0:00:00
##
## [====|====|====|====|====|====|====|====|====|====] 0:00:00
##
## [====|====|====|====|====|====|====|====|====|====] 0:00:00
##
## [====|====|====|====|====|====|====|====|====|====] 0:00:00
##
## [====|====|====|====|====|====|====|====|====|====] 0:00:00
##
## [====|====|====|====|====|====|====|====|====|====] 0:00:00
##
## [====|====|====|====|====|====|====|====|====|====] 0:00:00
##
## [====|====|====|====|====|====|====|====|====|====] 0:00:00
##
## [====|====|====|====|====|====|====|====|====|====] 0:00:00The setCov() will calculate the covariance and integrate it into the
fit. Once calculated, it will be saved and you can switch between
covariances by setCov() without the overhead of calculating it again.
Here’s the full list of covMethod tokens you can reach for, and what
each one actually is:
"r,s"– the sandwich estimatorsolve(R) %*% S %*% solve(R), whereRis the Hessian of the objective andSis the sum of each individual’s gradient cross-product at their empirical Bayes estimate. This is the finite-difference default for thefoceifamily."r"/"s"– just the Hessian-based or cross-product-based half of the sandwich, if you want to compare them."analytic"– the exact analytic observed-information covariance, matching NONMEM’s$COV MATRIX=Rbut it is exact rather than finite-differenced, and it covers additive/proportional/combined error, censored M2/M3/M4 observations, an estimatedboxCox()oryeoJohnson()lambda,foce+,matExp()/indLin()models, and mu-referenced covariate parameters. When a model falls outside that scope it says so and falls back to the finite-difference sandwich, rather than failing outright."sa"– the SAEM Louis stochastic-approximation Fisher information (Kuhn & Lavielle 2005): a dedicated covariance phase resimulates the individual parameters at the converged estimate and Monte-Carlo averages the observed-information integrand into a FIM decoupled from the cooling schedule. No longersaem-only."imp"– importance-sampling Monte Carlo observed information, in the style of NONMEMMETHOD=IMP. No longerimp/impmap-only."vi"– the variational covariance fromemvi/fbvi(can’t be calculated outsideemvi/fbvi)."nlme"–nlme’s own standard errors, for when you want them as-is rather than recomputed (can’t be calculate outside bynlme)."linFim"/"fim"– SAEM’s linearized Fisher information, and the (noisier) Fisher information matrix accumulated during estimation itself, both usable as fallbacks or direct requests. (Can’t be calculated outside ofsaem).""– skip the covariance step entirely.
Because every family now recognizes this shared vocabulary, the
default covMethod per family also changed where it made sense to:
the FOCEI family (
focei/foce/laplace/agq) defaults to"r,s",est="saem"keeps"sa"as its default, now with"analytic"and"linFim"as fallbacks when a model is out ofsa’s scope,est="imp"/"impmap"/"qrpem"default to"imp"(the oldimpCov=TRUEargument is gone –covMethod="imp"is just the default now),est="nlme"keepsnlme’s own covariance ("nlme") as the default, but can now also recompute at the converged estimate withcovMethod="analytic"or the finite-difference methods,est="npag"/"npb", which previously reported no covariance at all, now compute one by default ("imp"),est="emvi"/"fbvi"keep their variational covariance ("vi") as the default, and now honor an explicitcovMethodoverride instead of silently overwriting it.
Why this is worth having
None of this changes what a fit estimates. What it changes is how much you can trust – and cross-check – what comes out of the covariance step.
The nonparametric family going from “no covariance at all” to a real
one is the most obvious win, but the quieter one is being able to spot
check an "r,s" finite-difference covariance against the exact
"analytic" one, or against "sa", without paying for a second fit.
If two covariance methods agree on a parameter’s SE, that’s real
signal. If they don’t, that’s worth knowing before you write the
number into a report.
References
Kuhn E, Lavielle M. Maximum likelihood estimation in nonlinear mixed effects models. Comput Stat Data Anal. 2005;49(4):1020-1038.