Last updated on 2020-08-07 01:50:26 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| betaper | 1 | 11 | |
| rareNMtests | 12 | ||
| Taxonstand | 12 |
Current CRAN status: ERROR: 1, OK: 11
Version: 1.1-1
Check: examples
Result: ERROR
Running examples in ‘betaper-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: adonis_pertables
> ### Title: Function to assess the efects of taxonomic uncertainty on
> ### permutational multivariate analysis of variance using distance
> ### matrices
> ### Aliases: adonis_pertables print.adonis_pertables plot.adonis_pertables
> ### Keywords: multivariate
>
> ### ** Examples
>
>
>
>
> data(Amazonia)
> data(soils)
>
> # Define a new index that includes the terms used in the \code{Amazonia} dataset to define
> # undetermined taxa at different taxonomic levels
>
> index.Amazon <- c(paste("sp.", rep(1:20), sep=""), "Indet.", "indet.")
>
> # Generate a pertables object (i.e. a list of biological data tables simulated from taxonomic
> # uncertainty)
> ## Not run:
> ##D Amazonia100 <- pertables(Amazonia, index=index.Amazon, nsim=100)
> ##D
> ##D # Assess the effects of taxonomic uncertainty on a PERMANOVA (i.e., adonis) test:
> ##D
> ##D Amazonia.adonis <- adonis_pertables(Amazonia100 ~ Ca + K + Mg + Na, data=soils)
> ##D
> ##D Amazonia.adonis
> ##D
> ##D plot(Amazonia.adonis)
> ## End(Not run)
> # Fast example for Rcheck
>
> Amazonia_subset <- Amazonia[1:50,]
> Amazonia4.p2<- pertables.p2(Amazonia_subset, index=index.Amazon, nsim=4, ncl=2)
>
> Amazonia.adonis <- adonis_pertables(Amazonia4.p2 ~ Ca + K + Mg + Na, data=soils)
>
> Amazonia.adonis
Permutation tests for multivariate analysis of variance using distance matrices
Call:
adonis_pertables(formula = Amazonia4.p2 ~ Ca + K + Mg + Na, data = soils)
Permutation: free
Number of permutations: 5
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F) Pr(tax)
Ca 1 0.40368 0.40368 1.3171 0.13150 0.66667 < 2.2e-16 ***
K 1 0.71782 0.71782 2.3420 0.23382 0.33333 < 2.2e-16 ***
Mg 1 0.31974 0.31974 1.0432 0.10415 0.50000 < 2.2e-16 ***
Na 1 0.40264 0.40264 1.3137 0.13116 0.33333 < 2.2e-16 ***
Residuals 4 1.22602 0.30650 0.39937
Total 8 3.06990 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Confidence intervals of R-squared under different taxonomic scenarios
Ca K Mg Na
0% 0.1094928 0.1485037 0.08348150 0.09163682
0.5% 0.1095575 0.1490302 0.08352862 0.09165293
2.5% 0.1098160 0.1511358 0.08371712 0.09171741
50% 0.1175286 0.1853076 0.09604214 0.09618701
97.5% 0.1239531 0.1959178 0.11849458 0.10335729
99.5% 0.1241280 0.1964951 0.11934000 0.10359694
100% 0.1241718 0.1966395 0.11955135 0.10365686
Confidence intervals of p-values under different taxonomic scenarios
Ca K Mg Na
0% 0.6666667 0.1666667 0.5000 0.6666667
0.5% 0.6666667 0.1666667 0.5025 0.6666667
2.5% 0.6666667 0.1666667 0.5125 0.6666667
50% 0.6666667 0.1666667 0.7500 0.8333333
97.5% 0.8208333 0.1666667 0.9875 1.0000000
99.5% 0.8308333 0.1666667 0.9975 1.0000000
100% 0.8333333 0.1666667 1.0000 1.0000000
>
> plot(Amazonia.adonis)
Error in hist.default(z, plot = FALSE, breaks = seq(min(z), max(z), by = diff.z/30)) :
invalid number of 'breaks'
Calls: plot -> plot.adonis_pertables -> hist -> hist.default
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Current CRAN status: NOTE: 12
Version: 1.1
Check: DESCRIPTION meta-information
Result: NOTE
Malformed Description field: should contain one or more complete sentences.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.1
Check: R code for possible problems
Result: NOTE
BiogTest.individual: no visible global function definition for 'combn'
BiogTest.individual: no visible global function definition for 'runif'
BiogTest.individual: no visible global function definition for 'rlnorm'
BiogTest.individual: no visible global function definition for
'rnbinom'
BiogTest.sample: no visible global function definition for 'combn'
BiogTest.sample: no visible global function definition for 'runif'
BiogTest.sample: no visible global function definition for 'rlnorm'
BiogTest.sample: no visible global function definition for 'rnbinom'
BiogTest.sample: no visible global function definition for 'aggregate'
EcoTest.individual: no visible global function definition for 'xtabs'
plot.BiogTest: no visible global function definition for 'quantile'
plot.BiogTest: no visible global function definition for 'combn'
plot.EcoTest: no visible global function definition for 'quantile'
Undefined global functions or variables:
aggregate combn quantile rlnorm rnbinom runif xtabs
Consider adding
importFrom("stats", "aggregate", "quantile", "rlnorm", "rnbinom",
"runif", "xtabs")
importFrom("utils", "combn")
to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Current CRAN status: OK: 12