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* checking for file ‘survcomp/DESCRIPTION’ ... OK
* preparing ‘survcomp’:
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\T1/ptm/m/n/10 Kains \T1/fi4/m/n/10 <benjamin.haibe.kains@utoronto.ca>\T1/ptm/m
/n/10 , Markus Schroeder \T1/fi4/m/n/10 <markus.schroeder@ucdconnect.ie>\T1/ptm
/m/n/10 , Catha-
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[]\T1/ptm/m/n/10 - Com-pu-ta-tional Bi-ol-ogy and Func-tional Ge-nomics Lab-o-r
a-tory, Dana-Farber Can-cer In-sti-tute, Boston,
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[]\T1/ptm/m/n/10 The func-tion com-bines sev-eral es-ti-ma-tors us-ing meta-ana
lytical for-mula to com-pute a meta-estimate.
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[]\T1/fi4/m/n/10 concordance.index(x, surv.time, surv.event, cl, weights, comp
pairs=10, strat, alpha = 0.05, outx = TRUE, method = c("conservative", "noether
", "nam"), alternative = c("two.sided", "less", "greater"), na.rm = FALSE)[]
[10]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of \T1/fi4/m/n/10 "two.sided"
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[]\T1/fi4/m/n/10 D.index(x, surv.time, surv.event, weights, strat, alpha = 0.0
5, method.test = c("logrank", "likelihood.ratio", "wald"), na.rm = FALSE, ...)[
]
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\T1/ptm/m/n/10 and ran-dom ef-fects meta-analysis for two-sample com-par-isons
and cu-mu-la-tive meta-analyses. Draws
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[]\T1/fi4/m/n/9 forestplot.surv(labeltext=labeltext, mean=r.mean, lower=r.lowe
r, upper=r.upper, zero=0.5,[]
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[] \T1/fi4/m/n/9 align=c("l"), graphwidth=unit(2, "inches"), x.ticks=seq(0.
3,0.8,0.1), xlab=paste( "Forestplot Example", myspace, sep=""),[]
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[] \T1/fi4/m/n/9 col=meta.colors(box="royalblue", line="darkblue", zero="da
rkred"), box.size=bs, clip=c(0.3,0.8))[]
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[]\T1/fi4/m/n/10 hazard.ratio(x, surv.time, surv.event, weights, strat, alpha
= 0.05, method.test = c("logrank", "likelihood.ratio", "wald"), na.rm = FALSE,
...)[]
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[]\T1/fi4/m/n/10 km.coxph.plot(formula.s, data.s, weight.s, x.label, y.label,
main.title, sub.title, leg.text, leg.pos = "bottomright", leg.bty = "o", leg.in
set = 0.05, o.text, v.line, h.line, .col = 1:4, .lty = 1, .lwd = 1, show.n.risk
= FALSE, n.risk.step, n.risk.cex = 0.85, verbose = TRUE, ...)[]
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[]\T1/fi4/m/n/9 metaplot.surv(mn=c(0.4,0.5,0.6), lower=c(0.35,0.4,0.57), upper
=c(0.45,0.6,0.63), labels=c("A","B","C"), xlim=c(0.2,0.8), boxsize=0.5, zero=0.
5, col=rmeta::meta.colors(box="royalblue",line="darkblue",zero="firebrick"))[]
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[]\T1/fi4/m/n/10 mrmr.cindex(x, surv.time, surv.event, cl, weights, comppairs=
10, strat, alpha = 0.05, outx = TRUE, method = c("conservative", "noether", "na
m"), alternative = c("two.sided", "less", "greater"), na.rm = FALSE)[]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of \T1/fi4/m/n/10 "two.sided"
[34]
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[]\T1/fi4/m/n/9 mrmr.cindex(x=xx, surv.time=stime, surv.event=sevent, strat=st
rat, weights=weight, method="noether", comppairs=comppairs)[]
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[]\T1/fi4/m/n/10 mrmr.cindex.ensemble(x, surv.time, surv.event, cl, weights, c
omppairs=10, strat, alpha = 0.05, outx = TRUE, method = c("conservative", "noet
her", "nam"), alternative = c("two.sided", "less", "greater"), maxparents, maxn
sol, nboot = 200, na.rm = FALSE)[]
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e-sis, must be one of \T1/fi4/m/n/10 "two.sided"
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[]\T1/ptm/m/n/10 This dataset con-tains a sub-set of the gene ex-pres-sion, an-
no-ta-tions and clin-i-cal data from the TRANS-
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[]\T1/fi4/m/n/10 exprs(transbig7g)\T1/ptm/m/n/10 : Ma-trix con-tain-ing gene ex
-pres-sions as mea-sured by Affymetrix hgu133a
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Output written on Rd2.pdf (51 pages, 184675 bytes).
Transcript written on Rd2.log.
Saving output to ‘/private/tmp/Rtmpx7vEEd/Rbuild8fda60ceba7b/survcomp/build/survcomp.pdf’ ...
Done
* creating vignettes ... OK
* cleaning src
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* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘survcomp_1.20.0.tar.gz’
