Format Ttest Output by R for Tex

Format ttest output by r for tex

Give Pander a try, it’s an all round good table formatting package for R, and supports the t.test result type. I’m not sure whether it leaves out too much information for your taste, though.

result = t.test(…)
pander(result)

Pander produces Markdown rather than LaTeX tables, so the result needs to be transformed into LaTeX using pandoc.

Alternatively, you can use broom to generate a regular table form your t.test result, and stargaze that:

stargazer(tidy(result))

Broom also knows the glance function for a reduced output, however, for t.test the result is the same.

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Extending stargazer for other types is effectively not possible, since everything is hard-coded in the function. The only thing you can do is put the data of interest into a data.frame and pass that to stargazer. You may want to play with this approach a bit. Here’s a basic example of what you could do:

stargazer_htest = function (data, ...) {
    summary = data.frame(`Test statistic` = data$statistic,
                         DF = data$parameter,
                         `p value` = data$p.value,
                         `Alternative hypothesis` = data$alternative,
                         check.names = FALSE)
    stargazer(summary, flip = TRUE, summary = FALSE,
              notes = paste(data$method, data$data.name, sep = ': '), ...)
}

And then use it like this:

stargazer_htest(t.test(extra ~ group, data = sleep))

To produce the following output:

… Note the completely wonky alignment and the wrong formatting of negative numbers. I gave up trying to get this to work: I would suggest dropping stargazer, it doesn’t like customisation.

In summary, the stargazer output isn’t nearly as “beautiful” or “easy to use” as they claim: their table formatting is cluttered and runs afoul of best practices for table formatting (which are summarised in the booktabs package documentation). The function is impossible to customise meaningfully for own types and instead offers a jungle of parameters. Oh, and despite their claim of supporting “a large number of models”, they don’t even support the base R hypothesis tests.

At the risk of sounding divisive, stargazer is a pretty terrible package.

R: t.test output for LaTex

This does the trick.

library(schoRsch)
library(xtable)

T.Test <- t.test(extra ~ group, data = sleep)
xtable(
  t_out(toutput=T.Test, n.equal = TRUE, welch.df.exact = TRUE, welch.n = NA,
    d.corr = TRUE, print = TRUE)
    )

                      Test                            Results
1 Welch Two Sample t-test: t(17.78) = -1.86, p = .079, d = NA
% latex table generated in R 3.1.1 by xtable 1.7-3 package
% Mon Aug 25 21:01:13 2014
\begin{table}[ht]
\centering
\begin{tabular}{rll}
  \hline
 & Test & Results \\ 
  \hline
1 & Welch Two Sample t-test: & t(17.78) = -1.86, p = .079, d = NA \\ 
   \hline
\end{tabular}
\end{table}

Creating function with output table from t-test in R

the input arguments for your function should a) not have the same name and b) should not contain $. Other than that your function works fine:

t_table <- function(col1, col2) {

  t.test(col1, col2) %>%
    broom::tidy() %>%
    mutate(Cohens_d = cohensD(col1, col2)) %>% # calc. cohen's d
    mutate_at(vars(- c(p.value,method,alternative)), round, 2)
}

set.seed(1)
t_table(rnorm(100), rnorm(100)+1/2)
  estimate estimate1 estimate2 statistic     p.value parameter conf.low conf.high                  method alternative Cohens_d
1    -0.35      0.11      0.46     -2.69 0.007745151    197.19    -0.61     -0.09 Welch Two Sample t-test   two.sided     0.38

Is it possible to extract the full output for the statistical tests performed in gtsummary?

This should be possible, but unfortunately it is not current possible with the aov() results. I will make it possible in the next release, and you can follow this GitHub Issue to track the progress of the release. https://github.com/ddsjoberg/gtsummary/issues/956

Here is an example using a t-test, where it currently is possible.

library(gtsummary)
packageVersion("gtsummary")
#> [1] '1.4.2'

tbl <-
  trial %>%
  select(age, trt) %>%
  tbl_summary(by = trt,
              missing = "no") %>%
  add_p(all_continuous() ~ "t.test")

# report any statistics in `tbl$table_body` with `inline_text()`
tbl$table_body
#> # A tibble: 1 x 18
#>   variable test_name var_type   var_label row_type label stat_1 stat_2 test_result
#>   <chr>    <chr>     <chr>      <chr>     <chr>    <chr> <chr>  <chr>  <list>     
#> 1 age      t.test    continuous Age       label    Age   46 (3~ 48 (3~ <named lis~
#> # ... with 9 more variables: estimate <dbl>, statistic <dbl>, parameter <dbl>,
#> #   conf.low <dbl>, conf.high <dbl>, p.value <dbl>, estimate1 <dbl>,
#> #   estimate2 <dbl>, alternative <chr>

# the columns about the t-test come from `t.test(...) %>% broom::tidy()`
t.test(age ~  trt, data = trial) %>% broom::tidy()
#> # A tibble: 1 x 10
#>   estimate estimate1 estimate2 statistic p.value parameter conf.low conf.high
#>      <dbl>     <dbl>     <dbl>     <dbl>   <dbl>     <dbl>    <dbl>     <dbl>
#> 1   -0.438      47.0      47.4    -0.209   0.834      184.    -4.57      3.69
#> # ... with 2 more variables: method <chr>, alternative <chr>

# t-statistic
inline_text(tbl, variable = "age", column = "statistic") %>% style_sigfig()
#>       t 
#> "-0.21"
# degrees of freedom
inline_text(tbl, variable = "age", column = "parameter") %>% style_number()
#>    df 
#> "184"

^{Created on 2021-08-10 by the reprex package (v2.0.1)}

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