R Under development (unstable) (2024-06-05 r86695 ucrt) -- "Unsuffered Consequences"
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> library(nlme)
> fm1 <- nlsList(SSasymp, Loblolly)
> fm1
Call:
  Model: height ~ SSasymp(age, Asym, R0, lrc) | Seed 
   Data: Loblolly 

Coefficients:
         Asym        R0       lrc
329  94.12820 -8.250753 -3.217578
327  94.94058 -7.757495 -3.229325
325  89.88487 -8.759017 -3.086219
307 110.69919 -8.169431 -3.390345
331 111.00287 -8.462608 -3.397574
311 109.98575 -8.558543 -3.362518
315 101.05622 -8.443628 -3.232825
321 127.13400 -7.679356 -3.575331
319 101.08748 -8.502343 -3.214021
301  95.66688 -9.078241 -3.116381
323  95.55627 -9.665035 -3.092266
309 113.51390 -7.595622 -3.352815
303 105.71792 -8.906081 -3.222957
305  99.17191 -9.916654 -3.084841

Degrees of freedom: 84 total; 42 residual
Residual standard error: 0.7003965
> system.time(cnL1 <- confint(fm1)) # 0.48 sec
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
   user  system elapsed 
   0.44    0.02    0.45 
> 
> stopifnot(
+     all.equal(as.matrix(coef(fm1)),
+               array(c(94.1282, 94.9406, 89.8849, 110.699, 111.003, 109.986, 101.056,
+                       127.134, 101.087, 95.6669, 95.5563, 113.514, 105.718, 99.1719,
+                       -8.25075, -7.75749, -8.75902, -8.16943, -8.46261, -8.55854, -8.44363,
+                       -7.67936, -8.50234, -9.07824, -9.66503, -7.59562, -8.90608, -9.91665,
+                       -3.21758, -3.22932, -3.08622, -3.39034, -3.39757, -3.36252, -3.23282,
+                       -3.57533, -3.21402, -3.11638, -3.09227, -3.35282, -3.22296, -3.08484),
+                     dim = c(14L, 3L),
+                     dimnames = list(c("329", "327", "325", "307", "331", "311", "315",
+                                       "321", "319", "301", "323", "309", "303", "305"),
+                                     c("Asym", "R0", "lrc"))),
+               tol = 1e-5)
+     ,
+     all.equal(pooledSD(fm1), structure(0.70039649, df = 42), tol = 1e-5)
+     ,
+     84 == sum(vapply(lapply(fm1, fitted), length, 1L)) # total deg.freedom
+    , ## confint() :
+     is.list(cnL1), identical(names(cnL1), names(fm1)),
+     vapply(cnL1, is.matrix, NA),
+     vapply(cnL1, dim, c(NA,0L)) == 3:2,
+     identical(unname(sapply(cnL1, dim)), matrix(3:2, 2, length(fm1))),
+     sapply(cnL1, is.finite)
+     )
> 
> fm2 <- nlme(fm1, random = Asym ~ 1)
> fm2
Nonlinear mixed-effects model fit by maximum likelihood
  Model: height ~ SSasymp(age, Asym, R0, lrc) 
  Data: Loblolly 
  Log-likelihood: -114.743
  Fixed: list(Asym ~ 1, R0 ~ 1, lrc ~ 1) 
      Asym         R0        lrc 
101.448300  -8.627494  -3.233730 

Random effects:
 Formula: Asym ~ 1 | Seed
            Asym  Residual
StdDev: 3.650645 0.7188624

Number of Observations: 84
Number of Groups: 14 
> stopifnot(
+     all.equal(fixef(fm2),
+               c(Asym = 101.4483, R0 = -8.6274937, lrc = -3.2337304), tol = 4e-7)
+     ,
+     all.equal(logLik(fm2),
+               structure(-114.743, class = "logLik", nall = 84, nobs = 84, df = 5),
+               tol = 4e-6)
+     ,
+     all.equal(sigma(fm2), 0.71886244, tol = 1e-6)
+     )
> 
> pm2.0 <- predict(fm2, Loblolly, level=0)## failed in nlme 3.1-123
> stopifnot(all.equal(head(pm2.0),
+ 		    c(3.64694, 11.0597, 27.2258, 40.5006, 51.4012, 60.3522),
+ 		    tol = 1e-5)) # 4e-7 {64b nb-mm4}
> 
> ## same as fm2 but fitted via nlme's formula interface
> fm3 <- nlme(height ~ SSasymp(age, Asym, R0, lrc),
+             data = Loblolly,
+             fixed = Asym + R0 + lrc ~ 1,
+             random = Asym ~ 1, groups = ~Seed)
> ## explicitly specifying 'groups' failed in 3.1-153 with
> ## Error in nlme::nlsList(model = height ~ SSasymp(age, Asym, R0, lrc), data = Loblolly,  : 
> ##   unused argument (groups = ~Seed)
> fm2$origCall <- NULL
> stopifnot(all.equal(fm2, fm3))
> 
> proc.time()
   user  system elapsed 
   0.95    0.09    0.98