Validation Report - contingencytables@3.0.1
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 contingencytables
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 1 |
| news_current | TRUE |
| exported_namespace | 194 |
| has_vignettes | 0 |
| export_help | 194 |
| has_website | TRUE |
| has_maintainer | Waldir Leoncio w.l.netto@medisin.uio.no |
| bugs_status | subscript out of bounds |
| has_bug_reports_url | 1 |
| downloads_1yr | 5569 |
| reverse_dependencies | 0 |
| has_examples | 0.9519231 |
| dependencies | 3 |
| 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 | MASS | Imports |
| 2 | boot | Imports |
| 3 | methods | Imports |
Package dependencies
Reverse dependencies
Overall the package has 0 reverse dependencies:
Namespace
Overall the package has 194 exported objects. 194 are documented:
Adjusted_inv_sinh_CI_OR_2x2
TRUE
Adjusted_inv_sinh_CI_ratio_2x2
TRUE
Adjusted_log_CI_2x2
TRUE
AgrestiCaffo_CI_2x2
TRUE
AgrestiCoull_CI_1x2
TRUE
Arcsine_CI_1x2
TRUE
BaptistaPike_exact_conditional_CI_2x2
TRUE
BaptistaPike_midP_CI_2x2
TRUE
bentur_2009
TRUE
Bhapkar_test_paired_cxc
TRUE
Blaker_exact_CI_1x2
TRUE
Blaker_exact_test_1x2
TRUE
Blaker_midP_CI_1x2
TRUE
Blaker_midP_test_1x2
TRUE
BonettPrice_hybrid_Wilson_score_CI_CC_paired_2x2
TRUE
BonettPrice_hybrid_Wilson_score_CI_paired_2x2
TRUE
Bonferroni_type_CIs_paired_cxc
TRUE
Bonferroni_type_CIs_rxc
TRUE
Brant_test_2xc
TRUE
BreslowDay_homogeneity_test_stratified_2x2
TRUE
calc_prob
TRUE
calc_Pvalue_4x2
TRUE
calc_Pvalue_5x2
TRUE
calculate_limit_lower
TRUE
calculate_limit_upper
TRUE
cavo_2012
TRUE
Chacko_test_1xc
TRUE
ClopperPearson_exact_CI_1x2
TRUE
ClopperPearson_exact_CI_1x2_beta_version
TRUE
ClopperPearson_midP_CI_1x2
TRUE
Cochran_Q_test_stratified_2x2
TRUE
CochranArmitage_CI_rx2
TRUE
CochranArmitage_exact_cond_midP_tests_rx2
TRUE
CochranArmitage_MH_tests_rx2
TRUE
CochranMantelHaenszel_test_stratified_2x2
TRUE
Cornfield_exact_conditional_CI_2x2
TRUE
Cornfield_midP_CI_2x2
TRUE
Cumulative_models_for_2xc
TRUE
Cumulative_models_for_rxc
TRUE
doll_hill_1950
TRUE
Exact_binomial_test_1x2
TRUE
Exact_cond_midP_linear_rank_tests_2xc
TRUE
Exact_cond_midP_tests_rxc
TRUE
Exact_cond_midP_unspecific_ordering_rx2
TRUE
Exact_multinomial_test_1xc
TRUE
Exact_unconditional_test_2x2
TRUE
ezra_2010
TRUE
fischer_1999
TRUE
Fisher_exact_test_2x2
TRUE
Fisher_midP_test_2x2
TRUE
FisherFreemanHalton_asymptotic_test_rxc
TRUE
fleiss_2003
TRUE
FleissEveritt_test_paired_cxc
TRUE
FleissLevinPaik_test_paired_cxc
TRUE
fontanella_2008
TRUE
gamma_coefficient_rxc
TRUE
gamma_coefficient_rxc_bca
TRUE
Gart_adjusted_logit_CI_2x2
TRUE
Gold_Wald_CIs_1xc
TRUE
Goodman_Wald_CIs_1xc
TRUE
Goodman_Wald_CIs_for_diffs_1xc
TRUE
Goodman_Wilson_score_CIs_1xc
TRUE
hine_1989
TRUE
hypothetical
TRUE
Independence_smoothed_logit_CI_2x2
TRUE
indredavik_2008
TRUE
Inv_sinh_CI_OR_2x2
TRUE
Inv_sinh_CI_ratio_2x2
TRUE
InverseVariance_estimate_stratified_2x2
TRUE
Jeffreys_CI_1x2
TRUE
JonckheereTerpstra_test_rxc
TRUE
Katz_log_CI_2x2
TRUE
Kendalls_tau_b_rxc
TRUE
Kendalls_tau_b_rxc_bca
TRUE
Koopman_asymptotic_score_CI_2x2
TRUE
KruskalWallis_asymptotic_test_rxc
TRUE
lampasona_2013
TRUE
ligarden_2010
TRUE
linear_by_linear_test_rxc
TRUE
list_functions
TRUE
LR_CI_1x2
TRUE
LR_test_1x2
TRUE
LR_test_1xc
TRUE
LR_test_2x2
TRUE
lydersen_2012a
TRUE
MantelHaenszel_estimate_stratified_2x2
TRUE
MantelHaenszel_test_2xc
TRUE
McNemar_asymptotic_test_CC_paired_2x2
TRUE
McNemar_asymptotic_test_paired_2x2
TRUE
McNemar_exact_cond_test_paired_2x2
TRUE
McNemar_exact_unconditional_test_paired_2x2
TRUE
McNemar_midP_test_paired_2x2
TRUE
McNemarBowker_test_paired_cxc
TRUE
Mee_asymptotic_score_CI_2x2
TRUE
MidP_binomial_test_1x2
TRUE
MidP_multinomial_test_1xc
TRUE
MiettinenNurminen_asymptotic_score_CI_difference_2x2
TRUE
MiettinenNurminen_asymptotic_score_CI_OR_2x2
TRUE
MiettinenNurminen_asymptotic_score_CI_ratio_2x2
TRUE
mills_graubard_1987
TRUE
ML_estimates
TRUE
ML_estimates_and_CIs_stratified_2x2
TRUE
MOVER_R_Wilson_CI_OR_2x2
TRUE
MOVER_R_Wilson_CI_ratio_2x2
TRUE
MOVER_Wilson_score_CI_paired_2x2
TRUE
Newcombe_hybrid_score_CI_2x2
TRUE
Newcombe_square_and_add_CI_paired_2x2
TRUE
Pearson_chi_squared_test_1xc
TRUE
Pearson_chi_squared_test_2x2
TRUE
Pearson_chi_squared_test_CC_2x2
TRUE
Pearson_correlation_coefficient_rxc
TRUE
Pearson_correlation_coefficient_rxc_bca
TRUE
Pearson_LR_homogeneity_test_stratified_2x2
TRUE
Pearson_LR_test_common_effect_stratified_2x2
TRUE
Pearson_LR_tests_cum_OR_2xc
TRUE
Pearson_LR_tests_rxc
TRUE
Pearson_LR_tests_unspecific_ordering_rx2
TRUE
Pearson_residuals_rxc
TRUE
perondi_2004
TRUE
peterson_2007
TRUE
Peto_homogeneity_test_stratified_2x2
TRUE
Peto_OR_estimate_stratified_2x2
TRUE
PriceBonett_approximate_Bayes_CI_2x2
TRUE
QuesenberryHurst_Wilson_score_CIs_1xc
TRUE
RBG_test_and_CI_stratified_2x2
TRUE
ritland_2007
TRUE
Scheffe_type_CIs_paired_cxc
TRUE
Scheffe_type_CIs_rxc
TRUE
Score_test_1x2
TRUE
Score_test_and_CI_marginal_mean_scores_paired_cxc
TRUE
Score_test_CC_1x2
TRUE
Score_test_for_effect_in_the_probit_model_2xc
TRUE
score_test_statistic
TRUE
singh_2010
TRUE
snp6498169
TRUE
Spearman_correlation_coefficient_rxc
TRUE
Spearman_correlation_coefficient_rxc_bca
TRUE
stratified_2x2_tables
TRUE
Stuart_test_paired_cxc
TRUE
table_7.3
TRUE
table_7.4
TRUE
table_7.5
TRUE
table_7.6
TRUE
table_7.7
TRUE
table_7.8
TRUE
table_7.9
TRUE
Tang_asymptotic_score_CI_paired_2x2
TRUE
Tango_asymptotic_score_CI_paired_2x2
TRUE
tea
TRUE
the_1x2_table_CIs
TRUE
the_1x2_table_tests
TRUE
the_1xc_table_CIs
TRUE
the_1xc_table_tests
TRUE
the_2x2_table_CIs_difference
TRUE
the_2x2_table_CIs_OR
TRUE
the_2x2_table_CIs_ratio
TRUE
the_2x2_table_tests
TRUE
the_2xc_table
TRUE
the_paired_2x2_table_CIs_difference
TRUE
the_paired_2x2_table_CIs_OR
TRUE
the_paired_2x2_table_CIs_ratio
TRUE
the_paired_2x2_table_tests
TRUE
the_paired_cxc_table_nominal
TRUE
the_paired_cxc_table_ordinal
TRUE
the_rx2_table
TRUE
the_rxc_table
TRUE
Transformed_Blaker_exact_CI_paired_2x2
TRUE
Transformed_Clopper_Pearson_exact_CI_paired_2x2
TRUE
Transformed_Clopper_Pearson_midP_CI_paired_2x2
TRUE
Transformed_Wilson_score_CI_paired_2x2
TRUE
Trend_estimate_CI_tests_rx2
TRUE
Uncorrected_asymptotic_score_CI_2x2
TRUE
Wald_CI_1x2
TRUE
Wald_CI_2x2
TRUE
Wald_CI_AgrestiMin_paired_2x2
TRUE
Wald_CI_BonettPrice_paired_2x2
TRUE
Wald_CI_CC_1x2
TRUE
Wald_CI_CC_2x2
TRUE
Wald_CI_diff_CC_paired_2x2
TRUE
Wald_CI_diff_paired_2x2
TRUE
Wald_CI_OR_Laplace_paired_2x2
TRUE
Wald_CI_OR_paired_2x2
TRUE
Wald_CI_ratio_paired_2x2
TRUE
Wald_test_1x2
TRUE
Wald_test_and_CI_common_diff_stratified_2x2
TRUE
Wald_test_and_CI_common_ratio_stratified_2x2
TRUE
Wald_test_and_CI_marginal_mean_ranks_paired_cxc
TRUE
Wald_test_and_CI_marginal_mean_scores_paired_cxc
TRUE
Wald_test_CC_1x2
TRUE
Wilson_score_CI_1x2
TRUE
Wilson_score_CI_CC_1x2
TRUE
Woolf_logit_CI_2x2
TRUE
Woolf_test_and_CI_stratified_2x2
TRUE
Z_unpooled_test_2x2
TRUE Examples
There are 198 help pages with examples, from 208 (95.19 %).
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 | 2025-02-17 03:49:29 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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/usr/local/share/vcpkg
XDG_CONFIG_HOME /home/runner/.config
XDG_RUNTIME_DIR /run/user/1001These are the options set to generate the report:
$add.smooth
[1] TRUE
$bitmapType
[1] "cairo"
$browser
[1] "xdg-open"
$browserNLdisabled
[1] FALSE
$callr.condition_handler_cli_message
function (msg)
{
custom_handler <- getOption("cli.default_handler")
if (is.function(custom_handler)) {
custom_handler(msg)
}
else {
cli_server_default(msg)
}
}
<bytecode: 0x561f86390910>
<environment: namespace:cli>
$catch.script.errors
[1] FALSE
$CBoundsCheck
[1] FALSE
$check.bounds
[1] FALSE
$citation.bibtex.max
[1] 1
$continue
[1] "+ "
$contrasts
unordered ordered
"contr.treatment" "contr.poly"
$covr.record_tests
[1] TRUE
$defaultPackages
[1] "datasets" "utils" "grDevices" "graphics" "stats" "methods"
$demo.ask
[1] "default"
$deparse.cutoff
[1] 60
$device
function (width = 7, height = 7, ...)
{
grDevices::pdf(NULL, width, height, ...)
}
<bytecode: 0x561f85acf310>
<environment: namespace:knitr>
$device.ask.default
[1] FALSE
$digits
[1] 7
$dvipscmd
[1] "dvips"
$echo
[1] FALSE
$editor
[1] "vi"
$encoding
[1] "native.enc"
$example.ask
[1] "default"
$expressions
[1] 5000
$help.search.types
[1] "vignette" "demo" "help"
$help.try.all.packages
[1] FALSE
$htmltools.preserve.raw
[1] TRUE
$HTTPUserAgent
[1] "R/4.4.2 R (4.4.2 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions"
$internet.info
[1] 2
$keep.parse.data
[1] TRUE
$keep.parse.data.pkgs
[1] FALSE
$keep.source
[1] FALSE
$keep.source.pkgs
[1] FALSE
$knitr.in.progress
[1] TRUE
$locatorBell
[1] TRUE
$mailer
[1] "mailto"
$matprod
[1] "default"
$max.contour.segments
[1] 25000
$max.print
[1] 99999
$menu.graphics
[1] TRUE
$na.action
[1] "na.omit"
$Ncpus
[1] 1
$nwarnings
[1] 50
$OutDec
[1] "."
$pager
[1] "/opt/R/4.4.2/lib/R/bin/pager"
$papersize
[1] "letter"
$PCRE_limit_recursion
[1] NA
$PCRE_study
[1] FALSE
$PCRE_use_JIT
[1] TRUE
$pdfviewer
[1] "/usr/bin/xdg-open"
$pkgType
[1] "source"
$printcmd
[1] "/usr/bin/lpr"
$prompt
[1] "> "
$repos
CRAN
"https://cran.rstudio.com"
$rl_word_breaks
[1] " \t\n\"\\'`><=%;,|&{()}"
$rlang_trace_top_env
<environment: R_GlobalEnv>
$scipen
[1] 0
$show.coef.Pvalues
[1] TRUE
$show.error.messages
[1] TRUE
$show.signif.stars
[1] TRUE
$showErrorCalls
[1] TRUE
$showNCalls
[1] 50
$showWarnCalls
[1] FALSE
$str
$str$strict.width
[1] "no"
$str$digits.d
[1] 3
$str$vec.len
[1] 4
$str$list.len
[1] 99
$str$deparse.lines
NULL
$str$drop.deparse.attr
[1] TRUE
$str$formatNum
function (x, ...)
format(x, trim = TRUE, drop0trailing = TRUE, ...)
<environment: 0x561f85868520>
$str.dendrogram.last
[1] "`"
$texi2dvi
[1] "/usr/bin/texi2dvi"
$tikzMetricsDictionary
[1] "validation_report_contingencytables_v3.0.1-tikzDictionary"
$timeout
[1] 60
$try.outFile
A connection with
description ""
class "file"
mode "w+b"
text "binary"
opened "opened"
can read "yes"
can write "yes"
$ts.eps
[1] 1e-05
$ts.S.compat
[1] FALSE
$unzip
[1] "/usr/bin/unzip"
$useFancyQuotes
[1] FALSE
$verbose
[1] FALSE
$warn
[1] 0
$warning.length
[1] 1000
$warnPartialMatchArgs
[1] FALSE
$warnPartialMatchAttr
[1] FALSE
$warnPartialMatchDollar
[1] FALSE
$width
[1] 80