Regression tables in Markdown format (for flexible use in R Markdown v2)

Question

The new version of R Markdown is based on pandoc, so you can easyly change the output format.

My Problem is to get markdown formated tables from e.g. regression models, because LATEX and HTML tables do not survive the pandoc conversion.

I know packages that generate LATEX/HTML output from a variety of models (stargazer, texreg, asprtable...) and I'm aware of functions/packages, that generate markdown tables from data frames and matrices but not from other objects.

Any suggestions?

Try `pander` that I started for exactly this purpose: http://rapporter.github.io/pander/ And Roman is currently working on implementing bunch of new S3 methods in GSoC 2014, so lots of models are already included -- but pls feel free to propose further feature requests on [GH](https://github.com/Rapporter/pander). — daroczig, Jun 21 '14 at 15:26
Thanks that fits some of my needs! Is there a way in pander to show results from a _series_ of regression models? — sammerk, Jun 23 '14 at 03:53
@user3762565 yes, see e.g. https://github.com/Rapporter/pander/pull/80 — daroczig, Jun 23 '14 at 13:31

score 18 · Accepted Answer · edited May 23 '17 at 12:25

18

My above comment in more details:

Define a few models for reproducible example:

lm0 <- lm(hp ~ wt, mtcars)
lm1 <- lm(qsec ~ hp, mtcars)
lm2 <- lm(qsec ~ wt, mtcars)

Create a comparative table from those:

require(memisc)
mtable123 <- mtable('Model 1' = lm0,
            'Model 2' = lm1,
            'Model 3' = lm2,
            summary.stats = c('R-squared','F','p','N'))

Render markdown table with a simple call to pander:
```
pander(mtable123)
```

Enjoy the result:

--------------------------------------------------
     &nbsp;        Model 1    Model 2    Model 3  
----------------- ---------- ---------- ----------
 **(Intercept)**   -1.821\   20.556***\ 18.875***\
                   (32.325)   (0.542)    (1.103)  

     **wt**       46.160***\     \       -0.319\  
                   (9.625)               (0.328)  

     **hp**           \      -0.018***\     \     
                              (0.003)             

  **R-squared**     0.434      0.502      0.031   

      **F**         22.999     30.190     0.945   

      **p**         0.000      0.000      0.339   

      **N**           32         32         32    
--------------------------------------------------

Thanks for Roman Tsegelskyi for implementing this nice feature in GSoC 2014.

edited May 23 '17 at 12:25

Community

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answered Jun 23 '14 at 15:12

daroczig

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is it possible to change the format of the table? For example, increase font size? – Ignacio Sep 15 '14 at 19:44
@Ignacio it's markdown, thus there is no font size. If you want to convert the document to LaTex/pdf/html or other document formats, then of course there are some options. What format would you like to change? – daroczig Sep 15 '14 at 21:01
I'm doing a presentation with R Markdown v2 and ioslides. The font that I get in the tables by default is a little too small. Thanks! – Ignacio Sep 16 '14 at 11:38
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@Ignacio I see, thanks for the details. Well, it's definitely not a *markdown* question and rather not relevant in this thread, so if I were you, I'd start a new question on SO. Otherwise search for the following keywords: custom CSS with knitr. – daroczig Sep 16 '14 at 12:51
I tried this solution but I got this error message: "Error in sink(file) : sink stack is full", ..., anyone had this problem? I found a related post, but the solution was to pass the model instead of the model's summary [link](http://stackoverflow.com/questions/24359744/r-pander-sink-stack-full-when-printing-summary-lm), but such a solution only works for one model in the table and not for several model using mtable. Any ideas? – Hernando Casas Sep 30 '14 at 17:54
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@HernandoCasas please verify that you are using the most [recent version](http://rapporter.github.io/pander/#installation) of `pander`, as it's very outdated on CRAN. I will push an update there in the next few weeks. – daroczig Sep 30 '14 at 20:18
Many thx @daroczig that was indeed the problem. It works interactively, but within r code chunk it shows this error: could not find function "asis_output" This is the example: ````{r results='asis'} lm0 <- lm(hp ~ wt, mtcars) lm1 <- lm(qsec ~ hp, mtcars) lm2 <- lm(qsec ~ wt, mtcars) require(memisc) mtable123 <- mtable('Model 1' = lm0, 'Model 2' = lm1, 'Model 3' = lm2, summary.stats = c('R-squared','F','p','N')) require(pander) pander(mtable123) ``` ` – Hernando Casas Sep 30 '14 at 21:07
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@HernandoCasas are you knitting from RStudio? Probably it starts a vanilla R session without loading `knitr` or something. I've just pushed a possible update to GH, please reinstall the dev version of `pander` and let me know if it works. – daroczig Sep 30 '14 at 21:47
great! thanks a lot @daroczig. That was the problem; `knitr` was not loaded. Sorry for that!, maybe your update is to require `knitr` at the time of loading `pander`?, that would work and it would be helpful for other users to avoid such mistakes in the future. – Hernando Casas Oct 01 '14 at 05:25
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@HernandoCasas yeah, that's what I [did](https://github.com/Rapporter/pander/commit/2c84c6a4650e037b01a2e68647ccd0acce5d9f4e) yesterday :) And due to a recent [update](http://blog.rapporter.net/2014/09/pander-tables-inside-of-knitr.html) in `pander`, there's no need to specify `results='asis'` any more in your chunk options when calling `pander`. – daroczig Oct 01 '14 at 08:34
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I seem to be getting: "Warning in pander.default(m): No pander.method for "memisc_mtable"" when I try to do as you suggest. – Will Nov 12 '17 at 01:51
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@Will the most recent version of the `pander` package dropped support for `mtable` but there are plans to re-integrate it at https://github.com/Rapporter/pander/issues/304 – daroczig Nov 12 '17 at 13:24

score 6 · Answer 2 · answered Jun 23 '14 at 13:02

6

Just generate the HTML or LATEX tables. All you have to do is to just add results='asis' to the code chunk. It will leave the output as it is.

For example this code using xtable works for me.

```{r,results='asis'}
x<-rnorm(100)
y<-rnorm(100)
lm <- lm(y~x)
library(xtable)
print(xtable(summary(lm)),type='html')
```

answered Jun 23 '14 at 13:02

Koundy

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could you include a minimal working example, together with explanation on how to compile it? – PatrickT Apr 21 '18 at 16:14

RRuiz · Answer 3 · 2018-11-25T17:36:16.250

4

Here what I did some hours ago:

Some data:

```{r}
lm1 <- lm(qsec ~ hp, mtcars)
lm2 <- lm(qsec ~ wt, mtcars)
```

We use the package sjPlot

```{r}
library(sjPlot)
tab_model(lm1,lm2, file="output.html")# You have to save the table in html format.
```

The next part needs to be outside the chunk in markdown:

htmltools::includeHTML("output.html")

edited Nov 25 '18 at 17:36

answered Jan 05 '17 at 22:53

RRuiz

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That does not work for me, could you insert a minimal example, please :) – Tito Sanz Apr 29 '18 at 11:40
Fixed. Sorry for the mistake – RRuiz Apr 29 '18 at 19:02
'sjt.lm' is deprecated. Use 'tab_model' instead. – RRuiz Nov 25 '18 at 17:36

score 2 · Answer 4 · answered Feb 03 '17 at 02:28

Another way to use sjPlot (great library for easy presentation of regression output) is to use the no.output feature:

     library(sjmisc)
     library(sjPlot)
     library(magrittr)

     lm(qsec ~ wt, mtcars) %>% 
       sjt.lm(no.output = TRUE, show.se = TRUE) %>% 
       return() %>% .[["knitr"]] %>% asis_output

score 1 · Answer 5 · answered Oct 01 '18 at 22:03

1

I'm updating this with an example that uses the popular (and newer) knitr and kableExtra packages.

library(knitr)
library(xtable)

lm(hp ~ wt, mtcars) %>%
summary() %>%
xtable() %>%
kable()

Now you can access all the cool table-formatting features available in Hao Zhu's kableExtra package.

answered Oct 01 '18 at 22:03

John J.

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Can this do model comparison? – gregmacfarlane Nov 28 '18 at 15:45

score 1 · Answer 6 · answered Oct 16 '18 at 05:35

1

The huxtable package can now print nicely formatted regression table. See the documentaton https://hughjonesd.github.io/huxtable/huxreg.html

answered Oct 16 '18 at 05:35

cderv

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Regression tables in Markdown format (for flexible use in R Markdown v2)

6 Answers6

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