@r-universe/webr 2023.6.11 → 2023.6.21

package/dist/vfs/usr/lib/R/tests/reg-examples1.R

@@ -0,0 +1,92 @@
+## For examples skipped in testing because they are 'random'
+
+set.seed(1)
+if(.Platform$OS.type == "windows") options(pager = "console")
+
+pdf("reg-examples-1.pdf", encoding = "ISOLatin1.enc")
+
+
+## base
+example(Cstack_info, run.donttest = TRUE)
+example(DateTimeClasses, run.donttest = TRUE)
+example(Dates, run.donttest = TRUE)
+example(Ops.Date, run.donttest = TRUE)
+example(Random, run.donttest = TRUE)
+head(s <- Sys.getenv(), 12) # from Sys.getenv.Rd
+writeLines(formatDL(s, style = "list")) # from formatDL.Rd
+example(Sys.getpid, run.donttest = TRUE)
+example(Sys.sleep, run.donttest = TRUE)
+example(Sys.time, run.donttest = TRUE)
+example(as.POSIXlt, run.donttest = TRUE)
+example(difftime, run.donttest = TRUE)
+example(format.Date, run.donttest = TRUE)
+example(Reduce, run.donttest = TRUE) # funprog.Rd
+example(gc, run.donttest = TRUE)
+example(memory.profile, run.donttest = TRUE)
+paste("Today is", date()) # from paste.Rd
+trunc(Sys.time(), "day") # from round.POSIXt.Rd
+example(srcref, run.donttest = TRUE)
+example(strptime, run.donttest = TRUE)
+example(sys.parent, run.donttest = TRUE)
+example(system.time, run.donttest = TRUE)
+example(tempfile, run.donttest = TRUE)
+example(weekdays, run.donttest = TRUE)
+library(help = "splines")
+
+## for example(NA)
+if(require("microbenchmark")) {
+  x <- c(NaN, 1:10000)
+  print(microbenchmark(any(is.na(x)), anyNA(x)))
+} else { ## much less accurate
+  x <- c(NaN, 1e6)
+  nSim <- 2^13
+  print(rbind(is.na = system.time(replicate(nSim, any(is.na(x)))),
+              anyNA = system.time(replicate(nSim, anyNA(x)))))
+}
+
+## utils
+example(news, run.donttest = TRUE)
+example(packageDescription, run.donttest = TRUE)
+example(sessionInfo, run.donttest = TRUE)
+
+## datasets
+example(JohnsonJohnson, run.donttest = TRUE)
+example(ability.cov, run.donttest = TRUE)
+example(npk, run.donttest = TRUE)
+
+## grDevices
+example(grSoftVersion, run.donttest = TRUE)
+if(.Platform$OS.type == "windows") {
+    example(windowsFonts, run.donttest = TRUE)
+} else {
+    example(X11Fonts, run.donttest = TRUE)
+    example(quartzFonts, run.donttest = TRUE)
+}
+
+library(tools)
+example(Rd_db, run.donttest = TRUE)
+example(file_ext, run.donttest = TRUE)
+example(makevars_user, run.donttest = TRUE)
+## results are location- and OS-specific
+example(parseLatex, run.donttest = TRUE) # charset-specific
+
+## part of example(buildVignettes) at one time
+gVigns <- pkgVignettes("grid")
+str(gVigns) # contains paths
+
+vind <- system.file(package = "grid", "doc", "index.html")
+if(nzchar(vind)) { # so vignettes have been installed
+    `%=f=%` <- function(a, b) normalizePath(a) == normalizePath(b)
+    with(gVigns,
+         stopifnot(engines == "utils::Sweave",
+                   pkgdir %=f=% system.file(package="grid"),
+                   dir    %=f=% system.file(package = "grid", "doc"),
+                   (n. <- length(docs)) >= 12, # have 13
+                   n. == length(names), n. == length(engines),
+                   length(msg) == 0) ) # as it is a 'base' package
+    stopifnot("grid" %in% gVigns$names, inherits(gVigns, "pkgVignettes"))
+}
+
+## This might leave collation changed, so do not put other things after it.
+example(icuSetCollate, run.donttest = TRUE)
+proc.time()

package/dist/vfs/usr/lib/R/tests/reg-examples2.R

@@ -0,0 +1,38 @@
+## For examples skipped in testing because they are 'random'
+
+## some should still be skipped when  --with-recommended-packages=no :
+## (This is not really right as could be installed elsewhere.)
+base.and.rec <- .packages(all.available = TRUE, lib = .Library)
+
+set.seed(1)
+if(.Platform$OS.type == "windows") options(pager = "console")
+
+pdf("reg-examples-2.pdf", encoding = "ISOLatin1.enc")
+
+
+## stats
+example(SSasympOrig, run.donttest = TRUE)
+example(SSlogis, run.donttest = TRUE)
+example(constrOptim, run.donttest = TRUE)
+example(cancor, run.donttest = TRUE)
+example(aov, run.donttest = TRUE)
+# signs for promax rotation are arbitrary
+example(factanal, run.donttest = TRUE)
+example(family, run.donttest = TRUE)
+example(fft, run.donttest = TRUE)
+example(glm, run.donttest = ("MASS" %in% base.and.rec))
+example(glm.control, run.donttest = TRUE)
+# from extractAIC
+extractAIC(glm.D93)
+example(influence.measures, run.donttest = TRUE)
+example(lm, run.donttest = TRUE)
+example(ls.diag, run.donttest = TRUE)
+example(model.tables, run.donttest = TRUE)
+example(nlminb, run.donttest = TRUE)
+example(optim, run.donttest = TRUE)
+example(prcomp, run.donttest = TRUE)
+example(step, run.donttest = TRUE)
+example(summary.manova, run.donttest = TRUE)
+example(uniroot, run.donttest = TRUE)
+
+proc.time()

package/dist/vfs/usr/lib/R/tests/reg-examples3.Rout.save

@@ -0,0 +1,546 @@
+
+R Under development (unstable) (2022-03-19 r81942) -- "Unsuffered Consequences"
+Copyright (C) 2022 The R Foundation for Statistical Computing
+Platform: x86_64-pc-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> ## For examples skipped in testing because they need recommended packages.
+> 
+> ## This is skipped entirely on a Unix-alike if recommended packages are,
+> ## so for Windows
+> if(!require("MASS")) q()
+Loading required package: MASS
+> 
+> pdf("reg-examples-3.pdf", encoding = "ISOLatin1.enc")
+> 
+> ## From datasets
+> if(require("survival")) {
++   model3 <- clogit(case ~ spontaneous+induced+strata(stratum), data = infert)
++   print(summary(model3))
++   detach("package:survival", unload = TRUE)  # survival (conflicts)
++ }
+Loading required package: survival
+Call:
+coxph(formula = Surv(rep(1, 248L), case) ~ spontaneous + induced + 
+    strata(stratum), data = infert, method = "exact")
+
+  n= 248, number of events= 83 
+
+              coef exp(coef) se(coef)     z Pr(>|z|)    
+spontaneous 1.9859    7.2854   0.3524 5.635 1.75e-08 ***
+induced     1.4090    4.0919   0.3607 3.906 9.38e-05 ***
+---
+Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
+
+            exp(coef) exp(-coef) lower .95 upper .95
+spontaneous     7.285     0.1373     3.651    14.536
+induced         4.092     0.2444     2.018     8.298
+
+Concordance= 0.776  (se = 0.044 )
+Likelihood ratio test= 53.15  on 2 df,   p=3e-12
+Wald test            = 31.84  on 2 df,   p=1e-07
+Score (logrank) test = 48.44  on 2 df,   p=3e-11
+
+> 
+> 
+> ## From grDevices
+> x1  <- matrix(rnorm(1e3), ncol = 2)
+> x2  <- matrix(rnorm(1e3, mean = 3, sd = 1.5), ncol = 2)
+> x   <- rbind(x1, x2)
+> 
+> dcols <- densCols(x)
+> graphics::plot(x, col = dcols, pch = 20, main = "n = 1000")
+> 
+> 
+> ## From graphics:
+> ## A largish data set
+> set.seed(123)
+> n <- 10000
+> x1  <- matrix(rnorm(n), ncol = 2)
+> x2  <- matrix(rnorm(n, mean = 3, sd = 1.5), ncol = 2)
+> x   <- rbind(x1, x2)
+> 
+> oldpar <- par(mfrow = c(2, 2))
+> smoothScatter(x, nrpoints = 0)
+> smoothScatter(x)
+> 
+> ## a different color scheme:
+> Lab.palette <- colorRampPalette(c("blue", "orange", "red"), space = "Lab")
+> smoothScatter(x, colramp = Lab.palette)
+> 
+> ## somewhat similar, using identical smoothing computations,
+> ## but considerably *less* efficient for really large data:
+> plot(x, col = densCols(x), pch = 20)
+> 
+> ## use with pairs:
+> par(mfrow = c(1, 1))
+> y <- matrix(rnorm(40000), ncol = 4) + 3*rnorm(10000)
+> y[, c(2,4)] <-  -y[, c(2,4)]
+> pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0, add = TRUE))
+> 
+> par(oldpar)
+> 
+> 
+> ## From stats
+> # alias.Rd
+> op <- options(contrasts = c("contr.helmert", "contr.poly"))
+> npk.aov <- aov(yield ~ block + N*P*K, npk)
+> alias(npk.aov)
+Model :
+yield ~ block + N * P * K
+
+Complete :
+         (Intercept) block1 block2 block3 block4 block5 N1    P1    K1    N1:P1
+N1:P1:K1     0           1    1/3    1/6  -3/10   -1/5      0     0     0     0
+         N1:K1 P1:K1
+N1:P1:K1     0     0
+
+> options(op)  # reset
+> 
+> # as.hclust.Rd
+> if(require("cluster", quietly = TRUE)) {# is a recommended package
++   set.seed(123)
++   x <- matrix(rnorm(30), ncol = 3)
++   hc <- hclust(dist(x), method = "complete")
++   ag <- agnes(x, method = "complete")
++   hcag <- as.hclust(ag)
++   ## The dendrograms order slightly differently:
++   op <- par(mfrow = c(1,2))
++   plot(hc) ;  mtext("hclust", side = 1)
++   plot(hcag); mtext("agnes",  side = 1)
++   detach("package:cluster")
++ }
+> 
+> # confint.Rd
+> counts <- c(18,17,15,20,10,20,25,13,12)
+> outcome <- gl(3, 1, 9); treatment <- gl(3, 3)
+> glm.D93 <- glm(counts ~ outcome + treatment, family = poisson())
+> confint(glm.D93)
+Waiting for profiling to be done...
+                 2.5 %      97.5 %
+(Intercept)  2.6958215  3.36655581
+outcome2    -0.8577018 -0.06255840
+outcome3    -0.6753696  0.08244089
+treatment2  -0.3932548  0.39325483
+treatment3  -0.3932548  0.39325483
+> confint.default(glm.D93)  # based on asymptotic normality}
+                 2.5 %      97.5 %
+(Intercept)  2.7095672  3.37947764
+outcome2    -0.8505027 -0.05800787
+outcome3    -0.6707552  0.08478093
+treatment2  -0.3919928  0.39199279
+treatment3  -0.3919928  0.39199279
+> 
+> # contrasts.Rd
+> utils::example(factor)
+
+factor> (ff <- factor(substring("statistics", 1:10, 1:10), levels = letters))
+ [1] s t a t i s t i c s
+Levels: a b c d e f g h i j k l m n o p q r s t u v w x y z
+
+factor> as.integer(ff)      # the internal codes
+ [1] 19 20  1 20  9 19 20  9  3 19
+
+factor> (f. <- factor(ff))  # drops the levels that do not occur
+ [1] s t a t i s t i c s
+Levels: a c i s t
+
+factor> ff[, drop = TRUE]   # the same, more transparently
+ [1] s t a t i s t i c s
+Levels: a c i s t
+
+factor> factor(letters[1:20], labels = "letter")
+ [1] letter1  letter2  letter3  letter4  letter5  letter6  letter7  letter8 
+ [9] letter9  letter10 letter11 letter12 letter13 letter14 letter15 letter16
+[17] letter17 letter18 letter19 letter20
+20 Levels: letter1 letter2 letter3 letter4 letter5 letter6 letter7 ... letter20
+
+factor> class(ordered(4:1)) # "ordered", inheriting from "factor"
+[1] "ordered" "factor" 
+
+factor> z <- factor(LETTERS[3:1], ordered = TRUE)
+
+factor> ## and "relational" methods work:
+factor> stopifnot(sort(z)[c(1,3)] == range(z), min(z) < max(z))
+
+factor> ## Don't show: 
+factor> of <- ordered(ff)
+
+factor> stopifnot(identical(range(of, rev(of)), of[3:2]),
+factor+ 	  identical(max(of), of[2]))
+
+factor> ## End(Don't show)
+factor> 
+factor> ## suppose you want "NA" as a level, and to allow missing values.
+factor> (x <- factor(c(1, 2, NA), exclude = NULL))
+[1] 1    2    <NA>
+Levels: 1 2 <NA>
+
+factor> is.na(x)[2] <- TRUE
+
+factor> x  # [1] 1    <NA> <NA>
+[1] 1    <NA> <NA>
+Levels: 1 2 <NA>
+
+factor> is.na(x)
+[1] FALSE  TRUE FALSE
+
+factor> # [1] FALSE  TRUE FALSE
+factor> 
+factor> ## More rational, since R 3.4.0 :
+factor> factor(c(1:2, NA), exclude =  "" ) # keeps <NA> , as
+[1] 1    2    <NA>
+Levels: 1 2 <NA>
+
+factor> factor(c(1:2, NA), exclude = NULL) # always did
+[1] 1    2    <NA>
+Levels: 1 2 <NA>
+
+factor> ## exclude = <character>
+factor> z # ordered levels 'A < B < C'
+[1] C B A
+Levels: A < B < C
+
+factor> factor(z, exclude = "C") # does exclude
+[1] <NA> B    A   
+Levels: A < B
+
+factor> factor(z, exclude = "B") # ditto
+[1] C    <NA> A   
+Levels: A < C
+
+factor> ## Now, labels maybe duplicated:
+factor> ## factor() with duplicated labels allowing to "merge levels"
+factor> x <- c("Man", "Male", "Man", "Lady", "Female")
+
+factor> ## Map from 4 different values to only two levels:
+factor> (xf <- factor(x, levels = c("Male", "Man" , "Lady",   "Female"),
+factor+                  labels = c("Male", "Male", "Female", "Female")))
+[1] Male   Male   Male   Female Female
+Levels: Male Female
+
+factor> #> [1] Male   Male   Male   Female Female
+factor> #> Levels: Male Female
+factor> 
+factor> ## Using addNA()
+factor> Month <- airquality$Month
+
+factor> table(addNA(Month))
+
+   5    6    7    8    9 <NA> 
+  31   30   31   31   30    0 
+
+factor> table(addNA(Month, ifany = TRUE))
+
+ 5  6  7  8  9 
+31 30 31 31 30 
+> fff <- ff[, drop = TRUE]  # reduce to 5 levels.
+> contrasts(fff) <- contr.sum(5)[, 1:2]; contrasts(fff)
+  [,1] [,2]       [,3]       [,4]
+a    1    0 -0.2471257  0.2688164
+c    0    1 -0.2471257  0.2688164
+i    0    0 -0.1498721 -0.8817814
+s    0    0  0.8912491  0.0753323
+t   -1   -1 -0.2471257  0.2688164
+> 
+> ## using sparse contrasts: % useful, once model.matrix() works with these :
+> ffs <- fff
+> contrasts(ffs) <- contr.sum(5, sparse = TRUE)[, 1:2]; contrasts(ffs)
+  [,1] [,2]       [,3]       [,4]
+a    1    0 -0.2471257  0.2688164
+c    0    1 -0.2471257  0.2688164
+i    0    0 -0.1498721 -0.8817814
+s    0    0  0.8912491  0.0753323
+t   -1   -1 -0.2471257  0.2688164
+> stopifnot(all.equal(ffs, fff))
+> contrasts(ffs) <- contr.sum(5, sparse = TRUE); contrasts(ffs)
+5 x 4 sparse Matrix of class "dgCMatrix"
+             
+a  1  .  .  .
+c  .  1  .  .
+i  .  .  1  .
+s  .  .  .  1
+t -1 -1 -1 -1
+> 
+> # glm.Rd
+> utils::data(anorexia, package = "MASS")
+> 
+> anorex.1 <- glm(Postwt ~ Prewt + Treat + offset(Prewt),
++                 family = gaussian, data = anorexia)
+> summary(anorex.1)
+
+Call:
+glm(formula = Postwt ~ Prewt + Treat + offset(Prewt), family = gaussian, 
+    data = anorexia)
+
+Coefficients:
+            Estimate Std. Error t value Pr(>|t|)    
+(Intercept)  49.7711    13.3910   3.717 0.000410 ***
+Prewt        -0.5655     0.1612  -3.509 0.000803 ***
+TreatCont    -4.0971     1.8935  -2.164 0.033999 *  
+TreatFT       4.5631     2.1333   2.139 0.036035 *  
+---
+Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
+
+(Dispersion parameter for gaussian family taken to be 48.69504)
+
+    Null deviance: 4525.4  on 71  degrees of freedom
+Residual deviance: 3311.3  on 68  degrees of freedom
+AIC: 489.97
+
+Number of Fisher Scoring iterations: 2
+
+> 
+> # logLik.Rd
+> utils::data(Orthodont, package = "nlme")
+> fm1 <- lm(distance ~ Sex * age, Orthodont)
+> logLik(fm1)
+'log Lik.' -239.1209 (df=5)
+> logLik(fm1, REML = TRUE)
+'log Lik.' -241.7796 (df=5)
+> 
+> # nls.Rd
+> od <- options(digits=5)
+> ## The muscle dataset in MASS is from an experiment on muscle
+> ## contraction on 21 animals.  The observed variables are Strip
+> ## (identifier of muscle), Conc (Cacl concentration) and Length
+> ## (resulting length of muscle section).
+> utils::data(muscle, package = "MASS")
+> 
+> ## The non linear model considered is
+> ##       Length = alpha + beta*exp(-Conc/theta) + error
+> ## where theta is constant but alpha and beta may vary with Strip.
+> 
+> with(muscle, table(Strip)) # 2, 3 or 4 obs per strip
+Strip
+S01 S02 S03 S04 S05 S06 S07 S08 S09 S10 S11 S12 S13 S14 S15 S16 S17 S18 S19 S20 
+  4   4   4   3   3   3   2   2   2   2   3   2   2   2   2   4   4   3   3   3 
+S21 
+  3 
+> 
+> ## We first use the plinear algorithm to fit an overall model,
+> ## ignoring that alpha and beta might vary with Strip.
+> 
+> musc.1 <- nls(Length ~ cbind(1, exp(-Conc/th)), muscle,
++               start = list(th = 1), algorithm = "plinear")
+> ## IGNORE_RDIFF_BEGIN
+> summary(musc.1)
+
+Formula: Length ~ cbind(1, exp(-Conc/th))
+
+Parameters:
+      Estimate Std. Error t value Pr(>|t|)    
+th       0.608      0.115    5.31  1.9e-06 ***
+.lin1   28.963      1.230   23.55  < 2e-16 ***
+.lin2  -34.227      3.793   -9.02  1.4e-12 ***
+---
+Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
+
+Residual standard error: 4.67 on 57 degrees of freedom
+
+Number of iterations to convergence: 5 
+Achieved convergence tolerance: 9.32e-07
+
+> ## IGNORE_RDIFF_END
+> 
+> ## Then we use nls' indexing feature for parameters in non-linear
+> ## models to use the conventional algorithm to fit a model in which
+> ## alpha and beta vary with Strip.  The starting values are provided
+> ## by the previously fitted model.
+> ## Note that with indexed parameters, the starting values must be
+> ## given in a list (with names):
+> b <- coef(musc.1)
+> musc.2 <- nls(Length ~ a[Strip] + b[Strip]*exp(-Conc/th), muscle,
++               start = list(a = rep(b[2], 21), b = rep(b[3], 21), th = b[1]))
+> ## IGNORE_RDIFF_BEGIN
+> summary(musc.2)
+
+Formula: Length ~ a[Strip] + b[Strip] * exp(-Conc/th)
+
+Parameters:
+    Estimate Std. Error t value Pr(>|t|)    
+a1    23.454      0.796   29.46  5.0e-16 ***
+a2    28.302      0.793   35.70  < 2e-16 ***
+a3    30.801      1.716   17.95  1.7e-12 ***
+a4    25.921      3.016    8.60  1.4e-07 ***
+a5    23.201      2.891    8.02  3.5e-07 ***
+a6    20.120      2.435    8.26  2.3e-07 ***
+a7    33.595      1.682   19.98  3.0e-13 ***
+a8    39.053      3.753   10.41  8.6e-09 ***
+a9    32.137      3.318    9.69  2.5e-08 ***
+a10   40.005      3.336   11.99  1.0e-09 ***
+a11   36.190      3.109   11.64  1.6e-09 ***
+a12   36.911      1.839   20.07  2.8e-13 ***
+a13   30.635      1.700   18.02  1.6e-12 ***
+a14   34.312      3.495    9.82  2.0e-08 ***
+a15   38.395      3.375   11.38  2.3e-09 ***
+a16   31.226      0.886   35.26  < 2e-16 ***
+a17   31.230      0.821   38.02  < 2e-16 ***
+a18   19.998      1.011   19.78  3.6e-13 ***
+a19   37.095      1.071   34.65  < 2e-16 ***
+a20   32.594      1.121   29.07  6.2e-16 ***
+a21   30.376      1.057   28.74  7.5e-16 ***
+b1   -27.300      6.873   -3.97  0.00099 ***
+b2   -26.270      6.754   -3.89  0.00118 ** 
+b3   -30.901      2.270  -13.61  1.4e-10 ***
+b4   -32.238      3.810   -8.46  1.7e-07 ***
+b5   -29.941      3.773   -7.94  4.1e-07 ***
+b6   -20.622      3.647   -5.65  2.9e-05 ***
+b7   -19.625      8.085   -2.43  0.02661 *  
+b8   -45.780      4.113  -11.13  3.2e-09 ***
+b9   -31.345      6.352   -4.93  0.00013 ***
+b10  -38.599      3.955   -9.76  2.2e-08 ***
+b11  -33.921      3.839   -8.84  9.2e-08 ***
+b12  -38.268      8.992   -4.26  0.00053 ***
+b13  -22.568      8.194   -2.75  0.01355 *  
+b14  -36.167      6.358   -5.69  2.7e-05 ***
+b15  -32.952      6.354   -5.19  7.4e-05 ***
+b16  -47.207      9.540   -4.95  0.00012 ***
+b17  -33.875      7.688   -4.41  0.00039 ***
+b18  -15.896      6.222   -2.55  0.02051 *  
+b19  -28.969      7.235   -4.00  0.00092 ***
+b20  -36.917      8.033   -4.60  0.00026 ***
+b21  -26.508      7.012   -3.78  0.00149 ** 
+th     0.797      0.127    6.30  8.0e-06 ***
+---
+Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
+
+Residual standard error: 1.11 on 17 degrees of freedom
+
+Number of iterations to convergence: 8 
+Achieved convergence tolerance: 2.17e-06
+
+> ## IGNORE_RDIFF_END
+> options(od)
+> 
+> # princomp.Rd
+> ## Robust:
+> (pc.rob <- princomp(stackloss, covmat = MASS::cov.rob(stackloss)))
+Call:
+princomp(x = stackloss, covmat = MASS::cov.rob(stackloss))
+
+Standard deviations:
+   Comp.1    Comp.2    Comp.3    Comp.4 
+7.8322873 4.0077676 1.9114016 0.7624211 
+
+ 4  variables and  21 observations.
+> 
+> # termplot.R
+> library(MASS)
+> hills.lm <- lm(log(time) ~ log(climb)+log(dist), data = hills)
+> termplot(hills.lm, partial.resid = TRUE, smooth = panel.smooth,
++         terms = "log(dist)", main = "Original")
+> termplot(hills.lm, transform.x = TRUE,
++          partial.resid = TRUE, smooth = panel.smooth,
++ 	 terms = "log(dist)", main = "Transformed")
+> 
+> # xtabs.Rd
+> if(require("Matrix")) {
++  ## similar to "nlme"s  'ergoStool' :
++  d.ergo <- data.frame(Type = paste0("T", rep(1:4, 9*4)),
++                       Subj = gl(9, 4, 36*4))
++  print(xtabs(~ Type + Subj, data = d.ergo)) # 4 replicates each
++  set.seed(15) # a subset of cases:
++  print(xtabs(~ Type + Subj, data = d.ergo[sample(36, 10), ], sparse = TRUE))
++ 
++  ## Hypothetical two-level setup:
++  inner <- factor(sample(letters[1:25], 100, replace = TRUE))
++  inout <- factor(sample(LETTERS[1:5], 25, replace = TRUE))
++  fr <- data.frame(inner = inner, outer = inout[as.integer(inner)])
++  print(xtabs(~ inner + outer, fr, sparse = TRUE))
++ }
+Loading required package: Matrix
+    Subj
+Type 1 2 3 4 5 6 7 8 9
+  T1 4 4 4 4 4 4 4 4 4
+  T2 4 4 4 4 4 4 4 4 4
+  T3 4 4 4 4 4 4 4 4 4
+  T4 4 4 4 4 4 4 4 4 4
+4 x 9 sparse Matrix of class "dgCMatrix"
+    Subj
+Type 1 2 3 4 5 6 7 8 9
+  T1 . 1 . . . 1 . . .
+  T2 . . . . . . . 1 1
+  T3 . . 1 1 1 . 1 1 .
+  T4 . 1 . . . . . . .
+25 x 4 sparse Matrix of class "dgCMatrix"
+     outer
+inner A B C E
+    a . . . 3
+    b . . . 6
+    c . . 5 .
+    d . 1 . .
+    e . . 3 .
+    f . . 5 .
+    g . . 3 .
+    h 6 . . .
+    i 8 . . .
+    j . 1 . .
+    k . . . 6
+    l . 2 . .
+    m . . . 7
+    n . . 3 .
+    o . 3 . .
+    p . 3 . .
+    q . . . 7
+    r . . . 2
+    s . 6 . .
+    t . . . 5
+    u 4 . . .
+    v . . 3 .
+    w . 3 . .
+    x . . 3 .
+    y 2 . . .
+> 
+> 
+> ## From splines
+> library(splines)
+> Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, sparse = TRUE)))
+34 x 36 sparse Matrix of class "dgCMatrix"
+                                                                             
+ [1,] 1 4 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+ [2,] . 1 4 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+ [3,] . . 1 4 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+ [4,] . . . 1 4 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+ [5,] . . . . 1 4 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+ [6,] . . . . . 1 4 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+ [7,] . . . . . . 1 4 1 . . . . . . . . . . . . . . . . . . . . . . . . . . .
+ [8,] . . . . . . . 1 4 1 . . . . . . . . . . . . . . . . . . . . . . . . . .
+ [9,] . . . . . . . . 1 4 1 . . . . . . . . . . . . . . . . . . . . . . . . .
+[10,] . . . . . . . . . 1 4 1 . . . . . . . . . . . . . . . . . . . . . . . .
+[11,] . . . . . . . . . . 1 4 1 . . . . . . . . . . . . . . . . . . . . . . .
+[12,] . . . . . . . . . . . 1 4 1 . . . . . . . . . . . . . . . . . . . . . .
+[13,] . . . . . . . . . . . . 1 4 1 . . . . . . . . . . . . . . . . . . . . .
+[14,] . . . . . . . . . . . . . 1 4 1 . . . . . . . . . . . . . . . . . . . .
+[15,] . . . . . . . . . . . . . . 1 4 1 . . . . . . . . . . . . . . . . . . .
+[16,] . . . . . . . . . . . . . . . 1 4 1 . . . . . . . . . . . . . . . . . .
+[17,] . . . . . . . . . . . . . . . . 1 4 1 . . . . . . . . . . . . . . . . .
+[18,] . . . . . . . . . . . . . . . . . 1 4 1 . . . . . . . . . . . . . . . .
+[19,] . . . . . . . . . . . . . . . . . . 1 4 1 . . . . . . . . . . . . . . .
+[20,] . . . . . . . . . . . . . . . . . . . 1 4 1 . . . . . . . . . . . . . .
+[21,] . . . . . . . . . . . . . . . . . . . . 1 4 1 . . . . . . . . . . . . .
+[22,] . . . . . . . . . . . . . . . . . . . . . 1 4 1 . . . . . . . . . . . .
+[23,] . . . . . . . . . . . . . . . . . . . . . . 1 4 1 . . . . . . . . . . .
+[24,] . . . . . . . . . . . . . . . . . . . . . . . 1 4 1 . . . . . . . . . .
+[25,] . . . . . . . . . . . . . . . . . . . . . . . . 1 4 1 . . . . . . . . .
+[26,] . . . . . . . . . . . . . . . . . . . . . . . . . 1 4 1 . . . . . . . .
+[27,] . . . . . . . . . . . . . . . . . . . . . . . . . . 1 4 1 . . . . . . .
+[28,] . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 4 1 . . . . . .
+[29,] . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 4 1 . . . . .
+[30,] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 4 1 . . . .
+[31,] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 4 1 . . .
+[32,] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 4 1 . .
+[33,] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 4 1 .
+[34,] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 4 1
+>