After tidying up your analyses with the broom package, go ahead and grab the pixiedust. Customize your table output and write it to markdown, HTML, LaTeX, or even just the console. pixiedust makes it easy to customize the appearance of your tables in all of these formats by adding any number of "sprinkles", much in the same way you can add layers to a ggplot.
fit <- lm(mpg ~ qsec + factor(am) + wt + factor(gear), data = mtcars)
library(pixiedust)
dust(fit) %>%
sprinkle(col = 2:4, round = 3) %>%
sprinkle(col = 5, fn = quote(pvalString(value))) %>%
sprinkle_colnames(term = "Term",
estimate = "Estimate",
std.error = "SE",
statistic = "T-statistic",
p.value = "P-value")
#> Term Estimate SE T-statistic P-value
#> 1 (Intercept) 9.365 8.373 1.118 0.27
#> 2 qsec 1.245 0.383 3.252 0.003
#> 3 factor(am)1 3.151 1.941 1.624 0.12
#> 4 wt -3.926 0.743 -5.286 < 0.001
#> 5 factor(gear)4 -0.268 1.655 -0.162 0.87
#> 6 factor(gear)5 -0.27 2.063 -0.131 0.9Tables can be customized by row, column, or even by a single cell by adding sprinkles to the dust object. The table below shows the currently planned and implemented sprinkles. In the "implemented" column, an 'x' indicates a customization that has been implemented, while a blank cell suggests that the customization is planned but has not yet been implemented. In the remaining columns, an 'x' indicates that the sprinkle is already implemented for the output format; an 'o' indicates that implementation is planned but not yet completed; and a blank cell indicates that the sprinkle will not be implemented (usually because the output format doesn't support the option).
| sprinkle | implemented | console | markdown | html | latex |
|---|---|---|---|---|---|
| bg | x | x | x | ||
| bg_pattern | x | x | x | ||
| bg_pattern_by | x | x | x | ||
| bold | x | x | x | x | x |
| bookdown | x | x | |||
| border_collapse | x | x | x | ||
| border | x | x | x | ||
| border_thickness | x | x | x | ||
| border_units | x | x | x | ||
| border_style | x | x | x | ||
| border_color | x | x | x | ||
| caption | x | x | x | x | x |
| colnames | x | x | x | x | x |
| float | x | x | |||
| fn | x | x | x | x | x |
| font_color | x | x | x | ||
| font_family | x | x | |||
| font_size | x | x | x | ||
| font_size_units | x | x | x | ||
| halign | x | x | x | ||
| height | x | x | x | ||
| height_units | x | x | x | ||
| hhline | x | x | |||
| italic | x | x | x | x | x |
| label | x | x | x | ||
| longtable | x | x | x | x | x |
| merge | x | x | x | x | x |
| na_string | x | x | x | x | x |
| padding | x | x | |||
| replace | x | x | x | x | x |
| round | x | x | x | x | x |
| rotate_degree | x | x | x | ||
| valign | x | x | x | ||
| width | x | x | x | ||
| width_units | x | x | x |
To demonstrate, let's look at a simple linear model. We build the model and generate the standard summary.
fit <- lm(mpg ~ qsec + factor(am) + wt + factor(gear), data = mtcars)
summary(fit)
#>
#> Call:
#> lm(formula = mpg ~ qsec + factor(am) + wt + factor(gear), data = mtcars)
#>
#> Residuals:
#> Min 1Q Median 3Q Max
#> -3.5064 -1.5220 -0.7517 1.3841 4.6345
#>
#> Coefficients:
#> Estimate Std. Error t value Pr(>|t|)
#> (Intercept) 9.3650 8.3730 1.118 0.27359
#> qsec 1.2449 0.3828 3.252 0.00317 **
#> factor(am)1 3.1505 1.9405 1.624 0.11654
#> wt -3.9263 0.7428 -5.286 1.58e-05 ***
#> factor(gear)4 -0.2682 1.6555 -0.162 0.87257
#> factor(gear)5 -0.2697 2.0632 -0.131 0.89698
#> ---
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
#>
#> Residual standard error: 2.55 on 26 degrees of freedom
#> Multiple R-squared: 0.8498, Adjusted R-squared: 0.8209
#> F-statistic: 29.43 on 5 and 26 DF, p-value: 6.379e-10While the summary is informative and useful, it is full of "stats-speak" and isn't necessarily in a format that is suitable for publication or submission to a client. The broom package provides the summary in tidy format that, serendipitously, it a lot closer to what we would want for formal reports.
library(broom)
tidy(fit)
#> term estimate std.error statistic p.value
#> 1 (Intercept) 9.3650443 8.3730161 1.1184792 2.735903e-01
#> 2 qsec 1.2449212 0.3828479 3.2517387 3.168128e-03
#> 3 factor(am)1 3.1505178 1.9405171 1.6235455 1.165367e-01
#> 4 wt -3.9263022 0.7427562 -5.2861251 1.581735e-05
#> 5 factor(gear)4 -0.2681630 1.6554617 -0.1619868 8.725685e-01
#> 6 factor(gear)5 -0.2697468 2.0631829 -0.1307430 8.969850e-01It has been observed by some, however, that even this summary isn't quite ready for publication. There are too many decimal places, the p-value employ scientific notation, and column titles like "statistic" don't specify what type of statistic. These kinds of details aren't the purview of broom, however, as broom is focused on tidying the results of a model for further analysis (particularly with respect to comparing slightly varying models).
The pixiedust package diverts from broom's mission here and provides the ability to customize the broom output for presentation. The initial dust object returns a table that is largely similar to the broom output. Truthfully, it may be less desirable because it has converted all of those numerical values into character strings. This has the consequence of losing the numerical formatting employed by printing a data frame.
library(pixiedust)
dust(fit)
#> term estimate std.error statistic
#> 1 (Intercept) 9.36504430865836 8.37301612033658 1.11847919245161
#> 2 qsec 1.24492121340088 0.382847869162145 3.2517386504602
#> 3 factor(am)1 3.15051775932893 1.94051711270669 1.62354546563854
#> 4 wt -3.9263021501002 0.742756198609962 -5.2861250534807
#> 5 factor(gear)4 -0.268163000929796 1.65546166120695 -0.161986838604456
#> 6 factor(gear)5 -0.269746805223248 2.0631829212229 -0.130743039043461
#> p.value
#> 1 0.273590282784449
#> 2 0.00316812765022556
#> 3 0.116536745986852
#> 4 1.58173505907644e-05
#> 5 0.872568516561885
#> 6 0.896984955536724Where pixiedust shows its strength is the ease of which these tables can be customized. The code below rounds the columns estimate, std.error, and statistic to three decimal places each, and then formats the p.value into a format that happens to be one that I like.
x <- dust(fit) %>%
sprinkle(col = 2:4, round = 3) %>%
sprinkle(col = 5, fn = quote(pvalString(value)))
x
#> term estimate std.error statistic p.value
#> 1 (Intercept) 9.365 8.373 1.118 0.27
#> 2 qsec 1.245 0.383 3.252 0.003
#> 3 factor(am)1 3.151 1.941 1.624 0.12
#> 4 wt -3.926 0.743 -5.286 < 0.001
#> 5 factor(gear)4 -0.268 1.655 -0.162 0.87
#> 6 factor(gear)5 -0.27 2.063 -0.131 0.9Now we're almost there! Let's change up the column names, and while we're add it, let's add some "bold" markers to the statistically significant terms in order to make them stand out some (I say "bold" because the console output doesn't show up in bold, but with the markdown tags for bold text. In a rendered table, the text would actually be rendered in bold).
x <- x %>%
sprinkle(col = c("estimate", "p.value"),
row = c(2, 4),
bold = TRUE) %>%
sprinkle_colnames(term = "Term",
estimate = "Estimate",
std.error = "SE",
statistic = "T-statistic",
p.value = "P-value")
x
#> Term Estimate SE T-statistic P-value
#> 1 (Intercept) 9.365 8.373 1.118 0.27
#> 2 qsec **1.245** 0.383 3.252 **0.003**
#> 3 factor(am)1 3.151 1.941 1.624 0.12
#> 4 wt **-3.926** 0.743 -5.286 **< 0.001**
#> 5 factor(gear)4 -0.268 1.655 -0.162 0.87
#> 6 factor(gear)5 -0.27 2.063 -0.131 0.9We're just getting started! While there are a number of customizations already available or planned, here are some other ideas that I hope to implement in the future.
- Support for multi-row table headings
- Support for
longtables in LaTeX (and a similar rendering in markdown and HTML). - An option to use
broom'sglanceoutput in the table foot. - Multicolumn and multirow support
- Perhaps an
htmlTablesengine - An engine for
flexTables(ReporteRspackage) - Option to add variable labels to
broomoutput (if labels were given using theHmisc::labelfunctions - Option to add factor levels as a separate column to
broomoutput - Functionality to define your own default settings.
Are there other features you want or need? Please submit an issue, or contribute functionality yourself.
| Version | Release Description | Target Date | Actual Date |
|---|---|---|---|
| 0.1.0 | Console, markdown and HTML output for simple table | 1 Aug 2015 | 3 Aug 2015 |
| 0.2.0 | Multirow table headers; footers; multipage tables | 20 Aug 2015 | 18 Aug 2015 |
| 0.3.0 | Multicolumn and multirow cells in HTML | 15 Sep 2015 | 15 Sept 2015 |
| 0.4.0 | Glance statistics in table footer | 1 Oct 2015 | 25 Sept 2015 |
Add variable labels and levels to broom output |
|||
| 0.5.0 | LaTeX output for simple table | 15 Oct 2015 | 15 Oct 2015 |
| Adjustable cell heights and widths in LaTeX tables | |||
Add medley for batch customizations |
|||
| 0.6.0 | Borders and backgrounds for LaTeX tables | 1 Dec 2015 | 9 Dec 2015 |
| Multicolumn and multirow support for LaTeX tables | |||
| Longtable support for LaTeX tables | |||
| Rotated text for LaTeX tables | |||
| 1.0.0 | Release of basic, stable package | 1 June 2015 |
bold version numbers indicate a planned release to CRAN.
The markdown output from pixiedust is somewhat limited due to the limitations of Rmarkdown itself. If/when more features become available for Rmarkdown output, I'll be sure to include them. But what can you do if you really want all of the flexibility of the HTML tables but need the MS Word document?
With a little help from the Grmd package, you can have the best of both worlds. Grmd isn't available on CRAN yet, but if you're willing to install it from GitHub, you can render a docx file. Install Grmd with
devtools::install_github("gforge/Grmd")
Then use in your YAML header
---
output: Grmd::docx_document
---
When you knit your document, it knits as an HTML file, but I've had no problems with the rendering when I right-click the file and open with MS Word.
Read more at http://gforge.se/2014/07/fast-track-publishing-using-rmarkdown/