Dear package developers,
What is the best way to provide examples in help pages that should only be run
under certain conditions --
e.g., whether another package is installed? The code that is run conditionally
is then an expression, so
only the results of the last statement are displayed; and even if we
force-print results, the output is
separated from the code that produces it.
The best I have been able to come up with is to use withAutoprint(), such as we
see here:
---------------------------------------------------------------------------
> example(hpd.summary)
hpd.sm> if(require("coda")) withAutoprint({
hpd.sm+ # Create an emmGrid object from a system file
hpd.sm+ cbpp.rg <- do.call(emmobj,
hpd.sm+ readRDS(system.file("extdata", "cbpplist", package = "emmeans")))
hpd.sm+ cbpp.emm <- emmeans(cbpp.rg, "period")
hpd.sm+ hpd.summary(cbpp.emm) # or just summary(cbpp.emm) as it gets
redirected
hpd.sm+
hpd.sm+ # Test for any two-fold difference
hpd.sm+ summary(pairs(cbpp.emm), type = "response", delta = log(2))
hpd.sm+ }, spaced = TRUE)
Loading required package: coda
> cbpp.rg <- do.call(emmobj, readRDS(system.file("extdata", "cbpplist", package
> = "emmeans")))
> cbpp.emm <- emmeans(cbpp.rg, "period")
> hpd.summary(cbpp.emm)
period emmean lower.HPD upper.HPD
1 -1.43 -1.96 -0.894
2 -2.39 -3.13 -1.823
3 -2.52 -3.19 -1.862
4 -2.97 -3.88 -1.998
Point estimate displayed: median
Results are given on the logit (not the response) scale.
HPD interval probability: 0.95
> summary(pairs(cbpp.emm), type = "response", delta = log(2))
contrast odds.ratio lower.HPD upper.HPD p.equiv odds.eq
period1 / period2 2.60 1.264 4.34 0.210 0.2658
period1 / period3 2.90 1.266 5.42 0.114 0.1287
period1 / period4 4.64 1.595 9.76 0.026 0.0267
period2 / period3 1.14 0.486 2.36 0.918 11.1951
period2 / period4 1.78 0.580 4.35 0.604 1.5253
period3 / period4 1.55 0.437 4.01 0.700 2.3333
Point estimate displayed: median
'p.equiv' and 'odds.eq' based on posterior P(|lin. pred.| < 0.6931)
Results are back-transformed from the log odds ratio scale
HPD interval probability: 0.95
---------------------------------------------------------------------------
This "works" in that we can see the code and the output, but it is unduly
messy: The example code is displayed twice, the call to withAutoprint() adds
clutter, comments are suppressed, and the part last part no longer has the
example prompt string ("hpd.sm>" in this illustration).
Along these lines, I have a suggestion for enhancement of the example()
function. That function allows for the example code to be marked-up with
conditional blocks such as \dontrun{}. My suggestion is to provide an
additional conditional markup option, perhaps \runif{expr}{...}, that runs the
code in the second pair of braces exactly like any other example code when expr
is true, and behaves like \dontrun{} otherwise.
Thanks
Russ Lenth
Univ of Iowa
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