Last updated on 2025-01-15 12:48:34 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.9-0 | 33.03 | 492.04 | 525.07 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 2.9-0 | 19.95 | 303.04 | 322.99 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 2.9-0 | 748.51 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 2.9-0 | 533.10 | ERROR | |||
| r-devel-windows-x86_64 | 2.9-0 | 35.00 | 520.00 | 555.00 | NOTE | |
| r-patched-linux-x86_64 | 2.9-0 | 40.45 | 458.58 | 499.03 | OK | |
| r-release-linux-x86_64 | 2.9-0 | 32.18 | 458.73 | 490.91 | OK | |
| r-release-macos-arm64 | 2.9-0 | 191.00 | OK | |||
| r-release-macos-x86_64 | 2.9-0 | 311.00 | OK | |||
| r-release-windows-x86_64 | 2.9-0 | 33.00 | 514.00 | 547.00 | OK | |
| r-oldrel-macos-arm64 | 2.9-0 | 159.00 | OK | |||
| r-oldrel-macos-x86_64 | 2.9-0 | 353.00 | OK | |||
| r-oldrel-windows-x86_64 | 2.9-0 | 42.00 | 676.00 | 718.00 | OK |
clang-ASAN gcc-ASAN noSuggests
Version: 2.9-0
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
Baker2009.Rd: metabin
Dogliotti2014.Rd: metabin
Dong2013.Rd: metabin
Franchini2012.Rd: metacont
Gurusamy2011.Rd: metabin
Linde2015.Rd: metabin
Stowe2010.Rd: metacont
Woods2010.Rd: metabin
dietaryfat.Rd: metainc
forest.netbind.Rd: forest.meta
forest.netcomb.Rd: forest.meta
forest.netcomparison.Rd: forest.meta
forest.netcomplex.Rd: forest.meta
forest.netmeta.Rd: forest.meta
forest.netsplit.Rd: forest.meta
funnel.netmeta.Rd: funnel.meta, metabias
metabias.netmeta.Rd: metabias
netmeta.Rd: metabin, metacont, metainc, metagen
netpairwise.Rd: metagen
pairwise.Rd: metabin, metacont, metainc, metagen
radial.netmeta.Rd: radial.meta, funnel.meta, metabias
smokingcessation.Rd: metabin
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
Version: 2.9-0
Check: Rd cross-references
Result: NOTE
Undeclared package ‘crossnma’ in Rd xrefs
Unknown package ‘hasseDiagram’ in Rd xrefs
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 2.9-0
Check: examples
Result: ERROR
Running examples in ‘netmeta-Ex.R’ failed
The error most likely occurred in:
> ### Name: netposet
> ### Title: Partial order of treatments in network meta-analysis
> ### Aliases: netposet print.netposet
>
> ### ** Examples
>
> ## Not run:
> ##D # Use depression dataset
> ##D #
> ##D data(Linde2015)
> ##D
> ##D # Define order of treatments
> ##D #
> ##D trts <- c("TCA", "SSRI", "SNRI", "NRI",
> ##D "Low-dose SARI", "NaSSa", "rMAO-A", "Hypericum", "Placebo")
> ##D
> ##D # Outcome labels
> ##D #
> ##D outcomes <- c("Early response", "Early remission")
> ##D
> ##D # (1) Early response
> ##D #
> ##D p1 <- pairwise(treat = list(treatment1, treatment2, treatment3),
> ##D event = list(resp1, resp2, resp3), n = list(n1, n2, n3),
> ##D studlab = id, data = Linde2015, sm = "OR")
> ##D #
> ##D net1 <- netmeta(p1, common = FALSE,
> ##D seq = trts, ref = "Placebo", small.values = "undesirable")
> ##D
> ##D # (2) Early remission
> ##D #
> ##D p2 <- pairwise(treat = list(treatment1, treatment2, treatment3),
> ##D event = list(remi1, remi2, remi3), n = list(n1, n2, n3),
> ##D studlab = id, data = Linde2015, sm = "OR")
> ##D #
> ##D net2 <- netmeta(p2, common = FALSE,
> ##D seq = trts, ref = "Placebo", small.values = "undesirable")
> ##D
> ##D # Partial order of treatment rankings (two outcomes)
> ##D #
> ##D po <- netposet(netrank(net1), netrank(net2), outcomes = outcomes)
> ##D
> ##D # Hasse diagram
> ##D #
> ##D hasse(po)
> ##D
> ##D
> ##D #
> ##D # Outcome labels
> ##D #
> ##D outcomes <- c("Early response", "Early remission",
> ##D "Lost to follow-up", "Lost to follow-up due to AEs",
> ##D "Adverse events (AEs)")
> ##D
> ##D # (3) Loss to follow-up
> ##D #
> ##D p3 <- pairwise(treat = list(treatment1, treatment2, treatment3),
> ##D event = list(loss1, loss2, loss3), n = list(n1, n2, n3),
> ##D studlab = id, data = Linde2015, sm = "OR")
> ##D #
> ##D net3 <- netmeta(p3, common = FALSE,
> ##D seq = trts, ref = "Placebo", small.values = "desirable")
> ##D
> ##D # (4) Loss to follow-up due to adverse events
> ##D #
> ##D p4 <- pairwise(treat = list(treatment1, treatment2, treatment3),
> ##D event = list(loss.ae1, loss.ae2, loss.ae3), n = list(n1, n2, n3),
> ##D studlab = id, data = subset(Linde2015, id != 55), sm = "OR")
> ##D #
> ##D net4 <- netmeta(p4, common = FALSE,
> ##D seq = trts, ref = "Placebo", small.values = "desirable")
> ##D
> ##D # (5) Adverse events
> ##D #
> ##D p5 <- pairwise(treat = list(treatment1, treatment2, treatment3),
> ##D event = list(ae1, ae2, ae3), n = list(n1, n2, n3),
> ##D studlab = id, data = Linde2015, sm = "OR")
> ##D #
> ##D net5 <- netmeta(p5, common = FALSE,
> ##D seq = trts, ref = "Placebo", small.values = "desirable")
> ##D
> ##D # Partial order of treatment rankings (all five outcomes)
> ##D #
> ##D po.ranks <- netposet(netrank(net1), netrank(net2),
> ##D netrank(net3), netrank(net4), netrank(net5), outcomes = outcomes)
> ##D
> ##D # Same result
> ##D #
> ##D po.nets <- netposet(net1, net2, net3, net4, net5,
> ##D outcomes = outcomes)
> ##D #
> ##D all.equal(po.ranks, po.nets)
> ##D
> ##D # Print matrix with P-scores (random effects model)
> ##D #
> ##D po.nets$P.random
> ##D
> ##D # Hasse diagram for all outcomes (random effects model)
> ##D #
> ##D hasse(po.ranks)
> ##D
> ##D # Hasse diagram for outcomes early response and early remission
> ##D #
> ##D po12 <- netposet(netrank(net1), netrank(net2),
> ##D outcomes = outcomes[1:2])
> ##D hasse(po12)
> ##D
> ##D # Scatter plot
> ##D #
> ##D oldpar <- par(pty = "s")
> ##D plot(po12)
> ##D par(oldpar)
> ## End(Not run)
>
> # Example using ranking matrix with P-scores
> #
> # Ribassin-Majed L, Marguet S, Lee A.W., et al. (2017):
> # What is the best treatment of locally advanced nasopharyngeal
> # carcinoma? An individual patient data network meta-analysis.
> # Journal of Clinical Oncology, 35, 498-505
> #
> outcomes <- c("OS", "PFS", "LC", "DC")
> treatments <- c("RT", "IC-RT", "IC-CRT", "CRT",
+ "CRT-AC", "RT-AC", "IC-RT-AC")
> #
> # P-scores (from Table 1)
> #
> pscore.os <- c(15, 33, 63, 70, 96, 28, 45) / 100
> pscore.pfs <- c( 4, 46, 79, 52, 94, 36, 39) / 100
> pscore.lc <- c( 9, 27, 47, 37, 82, 58, 90) / 100
> pscore.dc <- c(16, 76, 95, 48, 72, 32, 10) / 100
> #
> pscore.matrix <- data.frame(pscore.os, pscore.pfs, pscore.lc, pscore.dc)
> rownames(pscore.matrix) <- treatments
> colnames(pscore.matrix) <- outcomes
> pscore.matrix
OS PFS LC DC
RT 0.15 0.04 0.09 0.16
IC-RT 0.33 0.46 0.27 0.76
IC-CRT 0.63 0.79 0.47 0.95
CRT 0.70 0.52 0.37 0.48
CRT-AC 0.96 0.94 0.82 0.72
RT-AC 0.28 0.36 0.58 0.32
IC-RT-AC 0.45 0.39 0.90 0.10
> #
> po <- netposet(pscore.matrix)
> po12 <- netposet(pscore.matrix[, 1:2])
> po
RT IC-RT IC-CRT CRT CRT-AC RT-AC IC-RT-AC
RT 0 0 0 0 0 0 0
IC-RT 1 0 0 0 0 0 0
IC-CRT 0 1 0 0 0 0 0
CRT 1 0 0 0 0 0 0
CRT-AC 0 0 0 1 0 1 0
RT-AC 1 0 0 0 0 0 0
IC-RT-AC 0 0 0 0 0 0 0
> po12
RT IC-RT IC-CRT CRT CRT-AC RT-AC IC-RT-AC
RT 0 0 0 0 0 0 0
IC-RT 0 0 0 0 0 1 0
IC-CRT 0 1 0 0 0 0 1
CRT 0 1 0 0 0 0 1
CRT-AC 0 0 1 1 0 0 0
RT-AC 1 0 0 0 0 0 0
IC-RT-AC 0 0 0 0 0 1 0
> #
> hasse(po)
Error: Package 'hasseDiagram' missing.
Please use the following R commands for installation:
install.packages("BiocManager")
BiocManager::install()
BiocManager::install("Rgraphviz")
install.packages("hasseDiagram")
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 2.9-0
Check: Rd cross-references
Result: NOTE
Unknown package ‘hasseDiagram’ in Rd xrefs
Flavor: r-devel-linux-x86_64-fedora-gcc