Validation Report - bayestestR@0.15.2
Context
This report is fully automated and builds on rhub/ref-image image. Documents the installation of this package on an open source R environment, focusing on:
- Installation environment description
- Testing coverage
It is limited to assess whether unit tests and documentation are present and can execute without error. An assessment would be required that the tests and documentation are meaningful.
Package bayestestR
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 1 |
| news_current | TRUE |
| exported_namespace | 92 |
| has_vignettes | 2 |
| export_help | 92 |
| has_website | TRUE |
| has_maintainer | Dominique Makowski dom.makowski@gmail.com |
| bugs_status | subscript out of bounds |
| has_bug_reports_url | 1 |
| downloads_1yr | 799601 |
| reverse_dependencies | 30 |
| has_examples | 0.9636364 |
| dependencies | 6 |
| license | GPL-3 |
Package general assessment: Coverage, check results, size, download the last year, reverse dependencies and number of dependencies.
Dependencies
Overall the package has these dependencies:
| package | type | |
|---|---|---|
| 1 | insight (>= 1.0.1) | Imports |
| 2 | datawizard (>= 1.0.0) | Imports |
| 3 | graphics | Imports |
| 4 | methods | Imports |
| 5 | stats | Imports |
| 6 | utils | Imports |
Package dependencies
Reverse dependencies
Overall the package has 30 reverse dependencies:
BayesERtools, bayesMeanScale, brmsmargins, clinicalsignificance, correlation, datawizard, easystats, eDNAjoint, effectsize, emmeans, fbst, ggeffects, insight, modelbased, multifear, multilevelcoda, neatStats, nichetools, ordbetareg, parameters, pcvr, performance, psycho, report, rstanbdp, see, sjPlot, snSMART, SSVS, statsExpressions
Namespace
Overall the package has 92 exported objects. 92 are documented:
area_under_curve auc
TRUE TRUE
bayesfactor bayesfactor_inclusion
TRUE TRUE
bayesfactor_models bayesfactor_parameters
TRUE TRUE
bayesfactor_pointnull bayesfactor_restricted
TRUE TRUE
bayesfactor_rope bayesian_as_frequentist
TRUE TRUE
bcai bci
TRUE TRUE
bf_inclusion bf_models
TRUE TRUE
bf_parameters bf_pointnull
TRUE TRUE
bf_restricted bf_rope
TRUE TRUE
bic_to_bf check_prior
TRUE TRUE
ci contr.bayes
TRUE TRUE
contr.equalprior contr.equalprior_deviations
TRUE TRUE
contr.equalprior_pairs contr.orthonorm
TRUE TRUE
convert_bayesian_as_frequentist convert_p_to_pd
TRUE TRUE
convert_pd_to_p density_at
TRUE TRUE
describe_posterior describe_prior
TRUE TRUE
diagnostic_draws diagnostic_posterior
TRUE TRUE
distribution distribution_beta
TRUE TRUE
distribution_binom distribution_binomial
TRUE TRUE
distribution_cauchy distribution_chisq
TRUE TRUE
distribution_chisquared distribution_custom
TRUE TRUE
distribution_gamma distribution_gaussian
TRUE TRUE
distribution_mixture_normal distribution_nbinom
TRUE TRUE
distribution_normal distribution_poisson
TRUE TRUE
distribution_student distribution_student_t
TRUE TRUE
distribution_t distribution_tweedie
TRUE TRUE
distribution_uniform effective_sample
TRUE TRUE
equivalence_test estimate_density
TRUE TRUE
eti hdi
TRUE TRUE
map_estimate mcse
TRUE TRUE
mediation model_to_priors
TRUE TRUE
overlap p_direction
TRUE TRUE
p_map p_pointnull
TRUE TRUE
p_rope p_significance
TRUE TRUE
p_to_bf p_to_pd
TRUE TRUE
pd pd_to_p
TRUE TRUE
point_estimate print_html
TRUE TRUE
print_md reshape_draws
TRUE TRUE
reshape_iterations rnorm_perfect
TRUE TRUE
rope rope_range
TRUE TRUE
sensitivity_to_prior sexit
TRUE TRUE
sexit_thresholds si
TRUE TRUE
simulate_correlation simulate_difference
TRUE TRUE
simulate_prior simulate_simpson
TRUE TRUE
simulate_ttest spi
TRUE TRUE
unupdate weighted_posteriors
TRUE TRUE Examples
There are 53 help pages with examples, from 55 (96.36 %).
NEWS
The package has NEWS file and it is current.
License
The package uses .
Installation environment
System Info
| Field | Value |
|---|---|
| Image | rhub/ref-image |
| OS | Ubuntu 24.04.1 LTS |
| Platform | x86_64-pc-linux-gnu |
| System | x86_64, linux-gnu |
| Execution Time | 2025-02-15 03:41:45 UTC |
System information. Table about the system used to check the package.
R Session Info
Information about the R environment and capabilities:
R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: UTC
tzcode source: system (glibc)
attached base packages:
[1] tools stats graphics grDevices utils datasets methods
[8] base
loaded via a namespace (and not attached):
[1] riskreports_0.0.0.9003 compiler_4.4.2 fastmap_1.2.0
[4] cli_3.6.4 htmltools_0.5.8.1 yaml_2.3.10
[7] rmarkdown_2.29 knitr_1.49 jsonlite_1.8.9
[10] xfun_0.50 digest_0.6.37 rlang_1.1.5
[13] evaluate_1.0.3 Platform used:
OS.type file.sep dynlib.ext GUI endian pkgType path.sep
"unix" "/" ".so" "X11" "little" "source" ":"
r_arch
"" R’s capabilities:
jpeg png tiff tcltk X11 aqua
TRUE TRUE TRUE TRUE FALSE FALSE
http/ftp sockets libxml fifo cledit iconv
TRUE TRUE FALSE TRUE FALSE TRUE
NLS Rprof profmem cairo ICU long.double
TRUE TRUE TRUE TRUE TRUE TRUE
libcurl
TRUE External software:
zlib
"1.3"
bzlib
"1.0.8, 13-Jul-2019"
xz
"5.4.5"
libdeflate
"1.19"
PCRE
"10.42 2022-12-11"
ICU
"74.2"
TRE
"TRE 0.8.0 R_fixes (BSD)"
iconv
"glibc 2.39"
readline
"8.2"
BLAS
"/usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3" Graphics external software:
cairo cairoFT pango
"1.18.0" "" "1.52.1"
libpng jpeg libtiff
"1.6.43" "8.0" "LIBTIFF, Version 4.5.1" Numerical characteristics of the machine:
double.eps double.neg.eps double.xmin
2.220446e-16 1.110223e-16 2.225074e-308
double.xmax double.base double.digits
1.797693e+308 2.000000e+00 5.300000e+01
double.rounding double.guard double.ulp.digits
5.000000e+00 0.000000e+00 -5.200000e+01
double.neg.ulp.digits double.exponent double.min.exp
-5.300000e+01 1.100000e+01 -1.022000e+03
double.max.exp integer.max sizeof.long
1.024000e+03 2.147484e+09 8.000000e+00
sizeof.longlong sizeof.longdouble sizeof.pointer
8.000000e+00 1.600000e+01 8.000000e+00
sizeof.time_t longdouble.eps longdouble.neg.eps
8.000000e+00 1.084202e-19 5.421011e-20
longdouble.digits longdouble.rounding longdouble.guard
6.400000e+01 5.000000e+00 0.000000e+00
longdouble.ulp.digits longdouble.neg.ulp.digits longdouble.exponent
-6.300000e+01 -6.400000e+01 1.500000e+01
longdouble.min.exp longdouble.max.exp
-1.638200e+04 1.638400e+04 Random number generation process:
[1] "Mersenne-Twister" "Inversion" "Rejection" Information about the environment
Environmental and options variables affect how package checks and software in it might behave. Here is the environmental variables when running this report
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FALSE
ACCEPT_EULA Y
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HOMEBREW_CLEANUP_PERIODIC_FULL_DAYS
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HOMEBREW_NO_AUTO_UPDATE
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LOGGER_LOG_LEVEL DEBUG
MAKE make
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PERFLOG_LOCATION_SETTING
RUNNER_PERFLOG
PHARMAPKGS_EXCLUDED_METRICS
assess_covr_coverage,assess_r_cmd_check
PHARMAPKGS_LIMIT 1000
PHARMAPKGS_PLATFORM ubuntu-22.04
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PHARMAPKGS_REMOTE_REPO
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PKGCACHE_HTTP_VERSION 2
PKGLOAD_PARENT_TEMPDIR
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POWERSHELL_DISTRIBUTION_CHANNEL
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YES
PWD /home/runner/work/pharmapkgs/pharmapkgs
QUARTO_BIN_PATH /opt/quarto/bin
QUARTO_DENO /opt/quarto/bin/tools/x86_64/deno
QUARTO_DOCUMENT_PATH /home/runner/work/pharmapkgs/pharmapkgs/inst/report
QUARTO_PROFILE
QUARTO_PROJECT_DIR /home/runner/work/pharmapkgs/pharmapkgs
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QUARTO_ROOT /
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R_DOC_DIR /opt/R/4.4.2/lib/R/doc
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R_PLATFORM x86_64-pc-linux-gnu
R_PRINTCMD /usr/bin/lpr
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TZ UTC
USER runner
VCPKG_INSTALLATION_ROOT
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XDG_CONFIG_HOME /home/runner/.config
XDG_RUNTIME_DIR /run/user/1001These are the options set to generate the report:
$add.smooth
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$bitmapType
[1] "cairo"
$browser
[1] "xdg-open"
$browserNLdisabled
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$callr.condition_handler_cli_message
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else {
cli_server_default(msg)
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}
<bytecode: 0x55f361c69910>
<environment: namespace:cli>
$catch.script.errors
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"contr.treatment" "contr.poly"
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<bytecode: 0x55f361c98ae0>
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$matprod
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$rl_word_breaks
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$rlang_trace_top_env
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$scipen
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$show.coef.Pvalues
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$show.signif.stars
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$str
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$str$list.len
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$str$drop.deparse.attr
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$str$formatNum
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<environment: 0x55f361141520>
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$try.outFile
A connection with
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$ts.eps
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$unzip
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$width
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