Last updated on 2024-11-03 11:49:20 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 4.6.24 | 24.03 | 146.42 | 170.45 | OK | |
| r-devel-linux-x86_64-debian-gcc | 4.6.24 | 0.62 | 2.07 | 2.69 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 4.6.24 | 273.94 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 4.6.24 | 265.34 | OK | |||
| r-devel-windows-x86_64 | 4.6.24 | 24.00 | 171.00 | 195.00 | OK | |
| r-patched-linux-x86_64 | 4.6.24 | 25.08 | 136.69 | 161.77 | OK | |
| r-release-linux-x86_64 | 4.6.24 | 20.33 | 117.70 | 138.03 | ERROR | |
| r-release-macos-arm64 | 4.6.24 | 87.00 | NOTE | |||
| r-release-macos-x86_64 | 4.6.24 | 144.00 | NOTE | |||
| r-release-windows-x86_64 | 4.6.24 | 25.00 | 176.00 | 201.00 | OK | |
| r-oldrel-macos-arm64 | 4.6.24 | 90.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 4.6.24 | 178.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 4.6.24 | 32.00 | 212.00 | 244.00 | OK |
Version: 4.6.24
Check: whether package can be installed
Result: ERROR
Installation failed.
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 4.6.24
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking: 'lme4', 'pbkrtest'
Flavor: r-release-linux-x86_64
Version: 4.6.24
Check: examples
Result: ERROR
Running examples in ‘doBy-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ls-means
> ### Title: Compute LS-means (aka population means or marginal means)
> ### Aliases: ls-means LSmeans LSmeans.default LSmeans.lmerMod popMeans
> ### popMeans.default popMeans.lmerMod
> ### Keywords: utilities
>
> ### ** Examples
>
>
> ## Two way anova:
>
> data(warpbreaks)
>
> m0 <- lm(breaks ~ wool + tension, data=warpbreaks)
> m1 <- lm(breaks ~ wool * tension, data=warpbreaks)
> LSmeans(m0)
estimate std.error statistic df p.value
[1,] 28.1481 1.5809 17.8052 50.0000 0
> LSmeans(m1)
estimate std.error statistic df p.value
[1,] 28.1481 1.4888 18.9068 48.0000 0
>
> ## same as:
> K <- LE_matrix(m0);K
(Intercept) woolB tensionM tensionH
[1,] 1 0.5 0.3333333 0.3333333
> linest(m0, K)
estimate std.error statistic df p.value
[1,] 28.1481 1.5809 17.8052 50.0000 0
> K <- LE_matrix(m1);K
(Intercept) woolB tensionM tensionH woolB:tensionM woolB:tensionH
[1,] 1 0.5 0.3333333 0.3333333 0.1666667 0.1666667
> linest(m1, K)
estimate std.error statistic df p.value
[1,] 28.1481 1.4888 18.9068 48.0000 0
>
> LE_matrix(m0, effect="wool")
(Intercept) woolB tensionM tensionH
[1,] 1 0 0.3333333 0.3333333
[2,] 1 1 0.3333333 0.3333333
> LSmeans(m0, effect="wool")
estimate std.error statistic df p.value
[1,] 31.0370 2.2357 13.8824 50.0000 0
[2,] 25.2593 2.2357 11.2981 50.0000 0
>
> LE_matrix(m1, effect="wool")
(Intercept) woolB tensionM tensionH woolB:tensionM woolB:tensionH
[1,] 1 0 0.3333333 0.3333333 0.0000000 0.0000000
[2,] 1 1 0.3333333 0.3333333 0.3333333 0.3333333
> LSmeans(m1, effect="wool")
estimate std.error statistic df p.value
[1,] 31.0370 2.1055 14.7412 48.0000 0
[2,] 25.2593 2.1055 11.9970 48.0000 0
>
> LE_matrix(m0, effect=c("wool", "tension"))
(Intercept) woolB tensionM tensionH
[1,] 1 0 0 0
[2,] 1 1 0 0
[3,] 1 0 1 0
[4,] 1 1 1 0
[5,] 1 0 0 1
[6,] 1 1 0 1
> LSmeans(m0, effect=c("wool", "tension"))
estimate std.error statistic df p.value
[1,] 39.2778 3.1618 12.4227 50.0000 0
[2,] 33.5000 3.1618 10.5953 50.0000 0
[3,] 29.2778 3.1618 9.2599 50.0000 0
[4,] 23.5000 3.1618 7.4325 50.0000 0
[5,] 24.5556 3.1618 7.7664 50.0000 0
[6,] 18.7778 3.1618 5.9390 50.0000 0
>
> LE_matrix(m1, effect=c("wool", "tension"))
(Intercept) woolB tensionM tensionH woolB:tensionM woolB:tensionH
[1,] 1 0 0 0 0 0
[2,] 1 1 0 0 0 0
[3,] 1 0 1 0 0 0
[4,] 1 1 1 0 1 0
[5,] 1 0 0 1 0 0
[6,] 1 1 0 1 0 1
> LSmeans(m1, effect=c("wool", "tension"))
estimate std.error statistic df p.value
[1,] 44.5556 3.6468 12.2178 48.0000 0
[2,] 28.2222 3.6468 7.7390 48.0000 0
[3,] 24.0000 3.6468 6.5812 48.0000 0
[4,] 28.7778 3.6468 7.8913 48.0000 0
[5,] 24.5556 3.6468 6.7335 48.0000 0
[6,] 18.7778 3.6468 5.1492 48.0000 0
>
>
> ## Regression; two parallel regression lines:
>
> data(Puromycin)
>
> m0 <- lm(rate ~ state + log(conc), data=Puromycin)
> ## Can not use LSmeans / LE_matrix here because of
> ## the log-transformation. Instead we must do:
> Puromycin$lconc <- log( Puromycin$conc )
> m1 <- lm(rate ~ state + lconc, data=Puromycin)
>
> LE_matrix(m1)
(Intercept) stateuntreated lconc
[1,] 1 0.5 -1.905247
> LSmeans(m1)
estimate std.error statistic df p.value
[1,] 126.2787 2.3738 53.1965 20.0000 0
>
> LE_matrix(m1, effect="state")
(Intercept) stateuntreated lconc
[1,] 1 0 -1.905247
[2,] 1 1 -1.905247
> LSmeans(m1, effect="state")
estimate std.error statistic df p.value
[1,] 138.8689 3.2868 42.2509 20.0000 0
[2,] 113.6884 3.4332 33.1140 20.0000 0
>
> LE_matrix(m1, effect="state", at=list(lconc=3))
(Intercept) stateuntreated lconc
[1,] 1 0 3
[2,] 1 1 3
> LSmeans(m1, effect="state", at=list(lconc=3))
estimate std.error statistic df p.value
[1,] 298.6019 9.3499 31.9363 20.0000 0
[2,] 273.4214 9.6975 28.1950 20.0000 0
>
> ## Non estimable contrasts
>
> ## ## Make balanced dataset
> dat.bal <- expand.grid(list(AA=factor(1:2), BB=factor(1:3),
+ CC=factor(1:3)))
> dat.bal$y <- rnorm(nrow(dat.bal))
>
> ## ## Make unbalanced dataset
> # 'BB' is nested within 'CC' so BB=1 is only found when CC=1
> # and BB=2,3 are found in each CC=2,3,4
> dat.nst <- dat.bal
> dat.nst$CC <-factor(c(1, 1, 2, 2, 2, 2, 1, 1, 3, 3,
+ 3, 3, 1, 1, 4, 4, 4, 4))
>
> mod.bal <- lm(y ~ AA + BB * CC, data=dat.bal)
> mod.nst <- lm(y ~ AA + BB : CC, data=dat.nst)
>
> LSmeans(mod.bal, effect=c("BB", "CC"))
estimate std.error statistic df p.value
[1,] -0.22141 0.67494 -0.32804 8.00000 0.7513
[2,] 0.37983 0.67494 0.56276 8.00000 0.5890
[3,] -0.24548 0.67494 -0.36371 8.00000 0.7255
[4,] 0.61288 0.67494 0.90805 8.00000 0.3904
[5,] 0.13520 0.67494 0.20031 8.00000 0.8462
[6,] 0.95081 0.67494 1.40874 8.00000 0.1966
[7,] -1.41797 0.67494 -2.10090 8.00000 0.0688
[8,] 0.54000 0.67494 0.80007 8.00000 0.4468
[9,] 0.46382 0.67494 0.68721 8.00000 0.5114
> LSmeans(mod.nst, effect=c("BB", "CC"))
estimate std.error statistic df p.value
[1,] -0.34217 0.43697 -0.78304 10.00000 0.4518
[2,] NA NA NA NA NA
[3,] NA NA NA NA NA
[4,] NA NA NA NA NA
[5,] 0.37983 0.75686 0.50185 10.00000 0.6266
[6,] -0.24548 0.75686 -0.32434 10.00000 0.7524
[7,] NA NA NA NA NA
[8,] 0.13520 0.75686 0.17863 10.00000 0.8618
[9,] 0.95081 0.75686 1.25626 10.00000 0.2376
[10,] NA NA NA NA NA
[11,] 0.54000 0.75686 0.71347 10.00000 0.4919
[12,] NA NA NA NA NA
> LSmeans(mod.nst, at=list(BB=1, CC=1))
estimate std.error statistic df p.value
[1,] -0.34217 0.43697 -0.78304 10.00000 0.4518
>
> LSmeans(mod.nst, at=list(BB=1, CC=2))
estimate std.error statistic df p.value
[1,] NA NA NA NA NA
> ## Above: NA's are correct; not an estimable function
>
> if( require( lme4 )){
+ warp.mm <- lmer(breaks ~ -1 + tension + (1|wool), data=warpbreaks)
+ LSmeans(warp.mm, effect="tension")
+ class(warp.mm)
+ fixef(warp.mm)
+ coef(summary(warp.mm))
+ vcov(warp.mm)
+ if (require(pbkrtest))
+ vcovAdj(warp.mm)
+ }
Loading required package: lme4
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘lme4’
>
> LSmeans(warp.mm, effect="tension")
Error: object 'warp.mm' not found
Execution halted
Flavor: r-release-linux-x86_64
Version: 4.6.24
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘doby.rmd’ using knitr
** Processing: figure/unnamed-chunk-27-1.png
504x504 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 32155 bytes
Input file size = 32269 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25263
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25263
Output IDAT size = 25263 bytes (6892 bytes decrease)
Output file size = 25341 bytes (6928 bytes = 21.47% decrease)
** Processing: figure/unnamed-chunk-28-1.png
504x504 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 24608 bytes
Input file size = 24722 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19536
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19536
Output IDAT size = 19536 bytes (5072 bytes decrease)
Output file size = 19614 bytes (5108 bytes = 20.66% decrease)
** Processing: figure/unnamed-chunk-29-1.png
504x504 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 18315 bytes
Input file size = 18417 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14654
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14654
Output IDAT size = 14654 bytes (3661 bytes decrease)
Output file size = 14732 bytes (3685 bytes = 20.01% decrease)
** Processing: figure/unnamed-chunk-31-1.png
504x504 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 18551 bytes
Input file size = 19433 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16965
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 16961
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 13764
zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 13760
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 13760
Output IDAT size = 13760 bytes (4791 bytes decrease)
Output file size = 13838 bytes (5595 bytes = 28.79% decrease)
** Processing: figure/unnamed-chunk-33-1.png
504x504 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 26183 bytes
Input file size = 26297 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 24104
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 24104
Output IDAT size = 24104 bytes (2079 bytes decrease)
Output file size = 24182 bytes (2115 bytes = 8.04% decrease)
** Processing: figure/unnamed-chunk-37-1.png
504x504 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8484 bytes
Input file size = 9354 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7340
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 7335
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 7335
Output IDAT size = 7335 bytes (1149 bytes decrease)
Output file size = 7413 bytes (1941 bytes = 20.75% decrease)
** Processing: figure/unnamed-chunk-38-1.png
504x504 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 46287 bytes
Input file size = 46425 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 43654
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 43207
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 43207
Output IDAT size = 43207 bytes (3080 bytes decrease)
Output file size = 43285 bytes (3140 bytes = 6.76% decrease)
--- finished re-building ‘doby.rmd’
--- re-building ‘linest_lsmeans.rnw’ using knitr
Quitting from lines 513-516 [unnamed-chunk-26] (linest_lsmeans.rnw)
Error: processing vignette 'linest_lsmeans.rnw' failed with diagnostics:
there is no package called ‘lme4’
--- failed re-building ‘linest_lsmeans.rnw’
--- re-building ‘section_fun.rmd’ using knitr
--- finished re-building ‘section_fun.rmd’
SUMMARY: processing the following file failed:
‘linest_lsmeans.rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-linux-x86_64
Version: 4.6.24
Check: HTML version of manual
Result: NOTE
Skipping checking math rendering: package 'V8' unavailable
Flavor: r-release-linux-x86_64
Version: 4.6.24
Check: installed package size
Result: NOTE
installed size is 5.8Mb
sub-directories of 1Mb or more:
data 4.7Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64