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IndrajeetPatil / statsExpressions

Tidy data frames and expressions with statistical summaries 📜
https://indrajeetpatil.github.io/statsExpressions/
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ggbarstats - paired - subtitle/caption not shown #8

Closed xmarti6 closed 4 years ago

xmarti6 commented 4 years ago

Seems like stats are not shown when paired option is enabled (using ggstatsplot "v0.1.2") Cheers


dfEx<-data.frame(cat1= rep(c("A","B"),10), cat2=c(rep("C",10),rep("D",10)))
ggstatsplot::ggbarstats(
data=dfEx,
x=cat1,
y=cat2,
paired=T,
nboot=10
)
#> Registered S3 methods overwritten by 'broom.mixed':
#>   method         from 
#>   augment.lme    broom
#>   augment.merMod broom
#>   glance.lme     broom
#>   glance.merMod  broom
#>   glance.stanreg broom
#>   tidy.brmsfit   broom
#>   tidy.gamlss    broom
#>   tidy.lme       broom
#>   tidy.merMod    broom
#>   tidy.rjags     broom
#>   tidy.stanfit   broom
#>   tidy.stanreg   broom
#> Registered S3 methods overwritten by 'car':
#>   method                          from
#>   influence.merMod                lme4
#>   cooks.distance.influence.merMod lme4
#>   dfbeta.influence.merMod         lme4
#>   dfbetas.influence.merMod        lme4
#> # A tibble: 2 x 11
#>   cat2  counts  perc N     A     B     statistic p.value parameter method
#>   <fct>  <int> <dbl> <chr> <chr> <chr>     <dbl>   <dbl>     <dbl> <chr> 
#> 1 D         10    50 (n =~ 50.0~ 50.0~         0       1         1 Chi-s~
#> 2 C         10    50 (n =~ 50.0~ 50.0~         0       1         1 Chi-s~
#> # ... with 1 more variable: significance <chr>

Created on 2019-10-08 by the reprex package (v0.3.0)

IndrajeetPatil commented 4 years ago

Thanks, I can confirm that this is a bug coming from upstream in statsExpressions:

set.seed(123)

dfEx <-
  data.frame(cat1 = rep(c("A", "B"), 10), 
             cat2 = c(rep("C", 10), rep("D", 10)))

statsExpressions::expr_contingency_tab(
  data = dfEx,
  x = cat1,
  y = cat2,
  paired = T,
  nboot = 10
)
#> Error in if (const(t, min(1e-08, mean(t, na.rm = TRUE)/1e+06))) {: missing value where TRUE/FALSE needed

Traceback

Error in if (const(t, min(1e-08, mean(t, na.rm = TRUE)/1e+06))) { : 
  missing value where TRUE/FALSE needed 
6.
boot.ci(Boot, conf = conf, type = type) 
5.
rcompanion::cohenG(x = x_arg, ci = TRUE, conf = conf.level, type = conf.type, 
    R = nboot, histogram = FALSE, digits = 5) 
4.
eval(lhs, parent, parent) 
3.
eval(lhs, parent, parent) 
2.
rcompanion::cohenG(x = x_arg, ci = TRUE, conf = conf.level, type = conf.type, 
    R = nboot, histogram = FALSE, digits = 5)$Global.statistics %>% 
    rcompanion_cleaner(object = ., estimate.col = "Value") %>% 
    dplyr::filter(.data = ., Statistic == "g") at helpers_contingency_tabs_expressions.R#245
1.
statsExpressions::expr_contingency_tab(data = dfEx, x = cat1, 
    y = cat2, paired = T, nboot = 10)

Created on 2019-10-09 by the reprex package (v0.3.0)

Session info ``` r devtools::session_info() #> - Session info ---------------------------------------------------------- #> setting value #> version R version 3.6.1 (2019-07-05) #> os Windows 10 x64 #> system x86_64, mingw32 #> ui RTerm #> language (EN) #> collate English_United States.1252 #> ctype English_United States.1252 #> tz Europe/Berlin #> date 2019-10-09 #> #> - Packages -------------------------------------------------------------- #> package * version date lib #> abind 1.4-5 2016-07-21 [1] #> assertthat 0.2.1 2019-03-21 [1] #> backports 1.1.5 2019-10-02 [1] #> BayesFactor 0.9.12-4.2 2018-05-19 [1] #> bayestestR 0.3.0 2019-09-22 [1] #> boot 1.3-23 2019-07-05 [1] #> broom 0.5.2.9002 2019-08-15 [1] #> broom.mixed 0.2.4.9000 2019-08-07 [1] #> broomExtra 0.0.5.9000 2019-09-22 [1] #> callr 3.3.2 2019-09-22 [1] #> car 3.0-3 2019-05-27 [1] #> carData 3.0-2 2018-09-30 [1] #> cellranger 1.1.0 2016-07-27 [1] #> cli 1.1.0 2019-03-19 [1] #> cluster 2.1.0 2019-06-19 [2] #> coda 0.19-3 2019-07-05 [1] #> codetools 0.2-16 2018-12-24 [1] #> coin 1.3-1 2019-08-28 [1] #> colorspace 1.4-1 2019-03-18 [1] #> crayon 1.3.4 2017-09-16 [1] #> curl 4.2 2019-09-24 [1] #> data.table 1.12.4 2019-10-03 [1] #> DEoptimR 1.0-8 2016-11-19 [1] #> desc 1.2.0 2019-04-03 [1] #> DescTools 0.99.29 2019-09-26 [1] #> devtools 2.2.1 2019-09-24 [1] #> digest 0.6.21 2019-09-20 [1] #> dplyr 0.8.3 2019-07-04 [1] #> ellipsis 0.3.0 2019-09-20 [1] #> emmeans 1.4.1 2019-09-12 [1] #> EMT 1.1 2013-01-29 [1] #> estimability 1.3 2018-02-11 [1] #> evaluate 0.14 2019-05-28 [1] #> expm 0.999-4 2019-03-21 [1] #> ez 4.4-0 2016-11-02 [1] #> fit.models 0.5-14 2017-04-06 [1] #> forcats 0.4.0 2019-02-17 [1] #> foreign 0.8-71 2018-07-20 [2] #> fs 1.3.1 2019-05-06 [1] #> furrr 0.1.0 2018-05-16 [1] #> future 1.14.0 2019-07-02 [1] #> generics 0.0.2 2019-03-05 [1] #> ggplot2 3.2.1 2019-08-10 [1] #> globals 0.12.4 2018-10-11 [1] #> glue 1.3.1 2019-03-12 [1] #> groupedstats 0.0.9.9000 2019-10-01 [1] #> gtable 0.3.0 2019-03-25 [1] #> gtools 3.8.1 2018-06-26 [1] #> haven 2.1.1 2019-07-04 [1] #> highr 0.8 2019-03-20 [1] #> hms 0.5.1 2019-08-23 [1] #> htmltools 0.4.0 2019-10-04 [1] #> insight 0.5.0.9000 2019-09-16 [1] #> knitr 1.25 2019-09-18 [1] #> lattice 0.20-38 2018-11-04 [2] #> lazyeval 0.2.2 2019-03-15 [1] #> libcoin 1.0-5 2019-08-27 [1] #> lifecycle 0.1.0 2019-08-01 [1] #> listenv 0.7.0 2018-01-21 [1] #> lme4 1.1-21 2019-03-05 [1] #> lmtest 0.9-37 2019-04-30 [1] #> magrittr 1.5 2014-11-22 [1] #> MASS 7.3-51.4 2019-03-31 [1] #> Matrix 1.2-17 2019-03-22 [1] #> MatrixModels 0.4-1 2015-08-22 [1] #> matrixStats 0.55.0 2019-09-07 [1] #> mc2d 0.1-18 2017-03-06 [1] #> mcmc 0.9-6 2019-03-10 [1] #> MCMCpack 1.4-4 2018-09-14 [1] #> memoise 1.1.0 2017-04-21 [1] #> mgcv 1.8-29 2019-09-20 [1] #> minqa 1.2.4 2014-10-09 [1] #> mnormt 1.5-5 2016-10-15 [1] #> modelr 0.1.5 2019-08-08 [1] #> modeltools 0.2-22 2018-07-16 [1] #> multcomp 1.4-10 2019-03-05 [1] #> multcompView 0.1-7 2015-07-31 [1] #> munsell 0.5.0 2018-06-12 [1] #> mvtnorm 1.0-11 2019-06-19 [1] #> nlme 3.1-140 2019-05-12 [2] #> nloptr 1.2.1 2018-10-03 [1] #> nortest 1.0-4 2015-07-30 [1] #> openxlsx 4.1.0.1 2019-05-28 [1] #> parameters 0.2.0 2019-09-26 [1] #> pbapply 1.4-2 2019-08-31 [1] #> pcaPP 1.9-73 2018-01-14 [1] #> performance 0.3.0 2019-08-05 [1] #> pillar 1.4.2 2019-06-29 [1] #> pkgbuild 1.0.5 2019-08-26 [1] #> pkgconfig 2.0.3 2019-09-22 [1] #> pkgload 1.0.2 2018-10-29 [1] #> plyr 1.8.4 2016-06-08 [1] #> prettyunits 1.0.2 2015-07-13 [1] #> processx 3.4.1 2019-07-18 [1] #> ps 1.3.0 2018-12-21 [1] #> psych 1.8.12 2019-01-12 [1] #> purrr 0.3.2 2019-03-15 [1] #> quantreg 5.51 2019-08-07 [1] #> R6 2.4.0 2019-02-14 [1] #> rcompanion 2.3.7 2019-09-29 [1] #> Rcpp 1.0.2 2019-07-25 [1] #> readxl 1.3.1 2019-03-13 [1] #> remotes 2.1.0 2019-06-24 [1] #> reshape 0.8.8 2018-10-23 [1] #> reshape2 1.4.3 2017-12-11 [1] #> rio 0.5.16 2018-11-26 [1] #> rlang 0.4.0 2019-06-25 [1] #> rmarkdown 1.16 2019-10-01 [1] #> robust 0.4-18.1 2019-07-02 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3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> local #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> CRAN (R 3.6.1) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> CRAN (R 3.5.2) #> CRAN (R 3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.5.1) #> CRAN (R 3.5.0) #> CRAN (R 3.6.1) #> CRAN (R 3.5.1) #> CRAN (R 3.5.2) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.5.1) #> CRAN (R 3.5.2) #> CRAN (R 3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.5.0) #> CRAN (R 3.6.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.0) #> CRAN (R 3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.0) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.0) #> CRAN (R 3.5.0) #> local #> CRAN (R 3.6.0) #> CRAN (R 3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.5.2) #> CRAN (R 3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> Github (r-lib/usethis@a2342b8) #> CRAN (R 3.6.1) #> CRAN (R 3.5.1) #> R-Forge (R 3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.5.3) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.0) #> #> [1] C:/Users/inp099/Documents/R/win-library/3.6 #> [2] C:/Program Files/R/R-3.6.1/library ```
IndrajeetPatil commented 4 years ago 
dfEx <- 
data.frame(cat1 = rep(c("A", "B"), 10),
           cat2 = c(rep("C", 10), rep("D", 10)))

# subtitle
  statsExpressions::expr_contingency_tab(
    data = dfEx,
    x = cat1,
    y = cat2,
    paired = TRUE,
    nboot = 10,
    messages = FALSE
  )

#> paste(NULL, chi["McNemar"]^2, "(", "1", ") = ", "0.00", ", ", 
#>     italic("p"), " = ", "1.000", ", ", widehat(italic("g"))["Cohen"], 
#>     " = ", "0.00", ", CI"["95%"], " [", "-0.27", ", ", "0.39", 
#>     "]", ", ", italic("n")["pairs"], " = ", 20L)

Created on 2019-12-27 by the reprex package (v0.3.0)

Session info ``` r devtools::session_info() #> - Session info --------------------------------------------------------------- #> setting value #> version R version 3.6.1 (2019-07-05) #> os Windows 10 x64 #> system x86_64, mingw32 #> ui RTerm #> language (EN) #> collate English_United States.1252 #> ctype English_United States.1252 #> tz Europe/Berlin #> date 2019-12-27 #> #> - Packages ------------------------------------------------------------------- #> package * version date lib #> abind 1.4-5 2016-07-21 [1] #> assertthat 0.2.1 2019-03-21 [1] #> backports 1.1.5 2019-10-02 [1] #> base64enc 0.1-3 2015-07-28 [1] #> BayesFactor 0.9.12-4.2 2018-05-19 [1] #> bayestestR 0.4.0 2019-10-20 [1] #> boot 1.3-24 2019-12-20 [1] #> broom 0.5.3.9000 2019-12-15 [1] #> broom.mixed 0.2.4.9000 2019-08-07 [1] #> broomExtra 1.0.0.9000 2019-12-17 [1] #> callr 3.4.0 2019-12-09 [1] #> car 3.0-6 2019-12-23 [1] #> carData 3.0-3 2019-11-16 [1] #> cellranger 1.1.0 2016-07-27 [1] #> cli 2.0.0.9000 2019-12-23 [1] #> cluster 2.1.0 2019-06-19 [2] #> coda 0.19-3 2019-07-05 [1] #> codetools 0.2-16 2018-12-24 [1] #> coin 1.3-1 2019-08-28 [1] #> colorspace 1.4-1 2019-03-18 [1] #> crayon 1.3.4 2017-09-16 [1] #> curl 4.3 2019-12-02 [1] #> data.table 1.12.8 2019-12-09 [1] #> DEoptimR 1.0-8 2016-11-19 [1] #> desc 1.2.0 2019-11-11 [1] #> DescTools 0.99.31 2019-12-02 [1] #> devtools 2.2.1 2019-09-24 [1] #> digest 0.6.23 2019-11-23 [1] #> dplyr 0.8.99.9000 2019-12-24 [1] #> ellipsis 0.3.0 2019-09-20 [1] #> emmeans 1.4.3.01 2019-11-28 [1] #> EMT 1.1 2013-01-29 [1] #> estimability 1.3 2018-02-11 [1] #> evaluate 0.14 2019-05-28 [1] #> expm 0.999-4 2019-03-21 [1] #> ez 4.4-0 2016-11-02 [1] #> fansi 0.4.0 2018-11-05 [1] #> fit.models 0.5-14 2017-04-06 [1] #> forcats 0.4.0 2019-02-17 [1] #> foreign 0.8-71 2018-07-20 [2] #> fs 1.3.1 2019-05-06 [1] #> generics 0.0.2 2019-03-05 [1] #> ggplot2 3.2.1 2019-08-10 [1] #> glue 1.3.1 2019-03-12 [1] #> groupedstats 0.1.0.9000 2019-11-26 [1] #> gtable 0.3.0 2019-03-25 [1] #> gtools 3.8.1 2018-06-26 [1] #> haven 2.2.0 2019-11-08 [1] #> highr 0.8 2019-03-20 [1] #> hms 0.5.2 2019-10-30 [1] #> htmltools 0.4.0 2019-10-04 [1] #> insight 0.7.1.1 2019-12-26 [1] #> jsonlite 1.6 2018-12-07 [1] #> knitr 1.26 2019-11-12 [1] #> lattice 0.20-38 2018-11-04 [2] #> lazyeval 0.2.2 2019-03-15 [1] #> libcoin 1.0-5 2019-08-27 [1] #> lifecycle 0.1.0 2019-08-01 [1] #> lme4 1.1-21 2019-03-05 [1] #> lmtest 0.9-37 2019-04-30 [1] #> lobstr 1.1.1 2019-07-02 [1] #> magrittr 1.5 2014-11-22 [1] #> MASS 7.3-51.5 2019-12-20 [1] #> Matrix 1.2-18 2019-11-27 [1] #> MatrixModels 0.4-1 2015-08-22 [1] #> matrixStats 0.55.0 2019-09-07 [1] #> mc2d 0.1-18 2017-03-06 [1] #> memoise 1.1.0 2017-04-21 [1] #> mgcv 1.8-31 2019-11-09 [1] #> minqa 1.2.4 2014-10-09 [1] #> mnormt 1.5-5 2016-10-15 [1] #> modelr 0.1.5 2019-08-08 [1] #> modeltools 0.2-22 2018-07-16 [1] #> multcomp 1.4-11 2019-12-10 [1] #> multcompView 0.1-8 2019-12-19 [1] #> munsell 0.5.0 2018-06-12 [1] #> mvtnorm 1.0-11 2019-06-19 [1] #> nlme 3.1-140 2019-05-12 [2] #> nloptr 1.2.1 2018-10-03 [1] #> nortest 1.0-4 2015-07-30 [1] #> openxlsx 4.1.4 2019-12-06 [1] #> parameters 0.3.0.1 2019-12-24 [1] #> pbapply 1.4-2 2019-08-31 [1] #> pcaPP 1.9-73 2018-01-14 [1] #> performance 0.4.2.1 2019-12-24 [1] #> pillar 1.4.3 2019-12-24 [1] #> pkgbuild 1.0.6 2019-10-09 [1] #> pkgconfig 2.0.3 2019-09-22 [1] #> pkgload 1.0.2 2018-10-29 [1] #> plyr 1.8.5 2019-12-10 [1] #> prettyunits 1.0.2 2015-07-13 [1] #> processx 3.4.1 2019-07-18 [1] #> ps 1.3.0 2018-12-21 [1] #> psych 1.9.12 2019-12-20 [1] #> purrr 0.3.3 2019-10-18 [1] #> R6 2.4.1 2019-11-12 [1] #> rcompanion 2.3.9 2019-12-27 [1] #> Rcpp 1.0.3 2019-11-08 [1] #> readxl 1.3.1 2019-03-13 [1] #> remotes 2.1.0 2019-06-24 [1] #> repr 1.0.2 2019-12-16 [1] #> reshape 0.8.8 2018-10-23 [1] #> reshape2 1.4.3 2017-12-11 [1] #> rio 0.5.16 2018-11-26 [1] #> rlang 0.4.2.9000 2019-12-24 [1] #> rmarkdown 2.0 2019-12-12 [1] #> robust 0.4-18.2 2019-12-26 [1] #> robustbase 0.93-5 2019-05-12 [1] #> rprojroot 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CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.0) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.5.1) #> CRAN (R 3.6.1) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.5.1) #> CRAN (R 3.5.0) #> CRAN (R 3.6.1) #> CRAN (R 3.5.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.5.1) #> CRAN (R 3.5.2) #> CRAN (R 3.6.1) #> Github (easystats/parameters@78e4442) #> CRAN (R 3.6.1) #> CRAN (R 3.5.0) #> local #> Github (r-lib/pillar@e2e7926) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.5.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.2) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> local #> CRAN (R 3.6.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> Github (r-lib/rlang@ce4f717) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> local #> CRAN (R 3.6.0) #> CRAN (R 3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.5.2) #> Github (tidyverse/tibble@6e7a544) #> CRAN (R 3.6.1) #> Github (r-lib/tidyselect@6b8f176) #> CRAN (R 3.6.1) #> Github (r-lib/usethis@23dd62c) #> Github (r-lib/vctrs@fa48942) #> CRAN (R 3.5.1) #> R-Forge (R 3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.5.3) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.0) #> #> [1] C:/Users/inp099/Documents/R/win-library/3.6 #> [2] C:/Program Files/R/R-3.6.1/library ```
sakinahsalsa commented 6 months ago

The same issue reoccur in ggstatsplot v0.12.1.