I've been using xtable package for a long time, and looking forward to writting my first package in R... so I reckon that if I have some "cool" idea that's worth carying out, there's a great chance that somebody got there before me... =)
I'm interested in functions/packages specialized for LaTeX table creation (through R, of course). I bumped on quantreg package which has latex.table function. Any suggestion for similar function(s)/package(s)?
P.S.
I'm thinking about building a webapp in which users can define their own presets/templates of tables, choose style, statistics, etc. It's an early thought, though... =)
I sometimes divide the task of creating LaTeX tables into two parts:
I'll write the table environment, caption, and tabular environment commands directly in my LaTeX document.
I'll export just the body of the table from R using a custom function.
The R export part involves several steps:
Starting with a matrix of the whole table including any headings:
Add any LaTeX specific formatting to the table. E.g., enclose digits in dollar symbols to ensure that negative numbers display correctly.
Collapse rows into a single character value by replacing separate columns with the ampersand (&) and adding ends-of-row symbols "\\"
Add any horizontal lines to be displayed in the table. I use the booktabs LaTeX package.
Export the resulting character vector using the write function
The exported text file is then imported using the input command in LaTeX. I ensure that the file name corresponds to the table label.
I have used this approach in the context of writing journal articles.
In these cases, there are a lot of different types of tables (e.g., multi-page tables, landscape tables, tables requiring extended margins, tables requiring particular alignment, tables where I want to change the wording of the table title). In this setting, I've mostly found it easier to just export the data from R. In this way, the result is reproducible research, but it is easier to tweak aspects of table design in the LaTeX document. And in the context of journal articles, there are usually not too many tables and rather specific formatting requirements.
However, I imagine if I were producing large numbers of batch reports, I'd consider exporting more aspects directly from R.
Beyond xtable and Hmisc as listed by Rob, there are also at least
apsrtable which formats latex tables from one or more model objects
p2lh which exports R to LaTeX and HTML
RcmdrPlugin.Export which graphically exports output to LaTeX or HTML
reporttools which generates LaTeX tables of descriptive statistics
This was just based on a quick search. So there may be more for you to look at before you try to hook it into a webapp. Good luck.
In addition to the packages mentioned above, there is the stargazer package. It works well with objects from many commonly used functions and packages (lm, glm, svyglm, plm, survival, AER, pscl, and others), as well as with zelig objects.
Apart from xtable, there's the latex function in the Hmisc package.
Related
In our production environment, we use gtsummary package to summarize large data, then convert to gt object to add title and subtitle. The visual quality of the resulting table is unparalleled.
However, in many instances we need this summary table accompanied by a companion data table that carries detail of a handful of outliers or similar specifics that clarify the overall. In a sense, this companion data is a table-based footnote, or clarifying support information.
Because we emit large numbers of these summaries, I am looking for a way to keep them together in the same emitted single-page pdf.
I've tried to solve this with the following:
tbl_merge, tbl_stack in gtsummary: gtsummary tables, not gt objects, requires shared rows or columns.
gridExtra: gt objects cannot be converted to grobs
pdf() or print to device: gtsave or print(gt) does not output to device.
Does anyone know if there is there a way to embed one table as a png object in the footnote of the other? Or is there another alternative?
Found a really clean solution to this problem using the gt package. We needed to avoid converting tables into images, which strips the content of much functionality including machine search.
The solution: Tranform the supplemental table into html using as_raw_html(), then insert into the primary table as source_note using tab_source_note(source_note = html(suppTable).
This retains all formatting, including titles and footnotes for each of the tables.
I have several formatted tables (and some graphs) in a single excel book, and I want to use Rmarkdown to grab those tables and graphs and add them to the knitted word document as images. I cannot simply copy the cell range with Readxl or other packages because all cells lose their formatting, and I need the tables in the document to look exactly the same as in the spreadsheet.
Alternatively, I am considering recreating the tables in R, but again the new tables will not have the formatting (though I imagine kable could allow me to recreate all the formatting). This is certainly not ideal, however, since I'm creating the tables twice, so hopefully the copy ability is doable somehow. I know Rmarkdown can use Python, Javascript, and many other languages, so maybe one of those languages is capable of this.
Is there a way to do this?
I want to replicate in texreg the functionality contained in stargazer via the arguments omit and omit.labels (see here). Unfortunately, I cannot use the stargazer package as it does not support the model I am using and is not extensible. Since texreg is easily extensible I can get it to work with my models. I can also easily omit some output from texreg with the omit.coef argument. What I can't seem to figure out is how to insert labels for the omitted coefficients. Does this exist in texreg? Does anyone have experience trying to write this functionality into an extract function? Alternatively, has anyone figured out how to extend stargazer to work with a custom model?
Context: I am writing a presentation in knitr and need to convert the output of some estimators into latex which will then get converted to pdf for my beamer presentation. The output has a bunch of covariates and thus is too long to display nicely in beamer. I want to truncate the output by omitting some covariates and inserting in their place a line indicating whether these covariates have been included in the model or not, e.g. collapse the variables "County Population", "County Income", etc. into a line that reads "County controls" and then have "Yes" or "No" to indicate whether these controls were included in the estimate or not. Ideally, someone could help me figure out a way to do this in texreg. If not, I would be open to other packages/approaches, e.g. xtable.
A possible option is the github version of huxtable. (I am the author.) This has a huxreg function which creates a table from a bunch of regressions, much like texreg: it'll work for anything that has a broom::tidy method defined for it. You can then edit the table much like a normal data frame, just rbind in the rows you want.
You'll need to install using devtools::install_github, if you want to try this route.
There are a range of tools available for creating publication quality tables using R, Sweave, and LaTeX.
In particular, there are helper functions like latex in the Hmisc package, and xtable in the xtable package. I've also often written my own code so that I could have complete control over table formatting (e.g., see this example).
However, when preparing publication quality tables a range of issues often arise:
how and when to apply numeric formatting
how to precisely control alignment of columns and cells
how to precisely control cell borders
how to convert variable labels to variable names
and so on
Beyond the high level issues of specifying the desired table format, there are issues of implementation.
When should a helper function such as xtable be used?
Which helper function should be used in a given situation?
How can the default output of helper functions be customised to particular requirements?
Question
It seems to me that the above issues are deserving of a detailed textbook-style introduction.
Are there any online or offline resources that provide a detailed overview of how to produce publication quality tables using R, Sweave, and LaTeX, and that address the issues discussed above?
Just to tie this up with a nice little bow at the time of current writing, the best existant tutorials on publication-quality tables and usage scenarios appear to be an amalgamation of these documents:
A Sweave example (source)
The Joy of Sweave: A Beginner's Guide to Reproducible Research with Sweave (source)
Latex and R via Sweave: An example document how to use Sweave (source)
Sweave = R · LaTeX2 (source)
The xtable gallery (source)
The Sweave Homepage
LaTeX documentation
Going beyond the scope of what currently exists, you may want to ask the author of The Joy of Sweave for a document on publication-quality tables specifically. It seems like he's gone above and beyond this problem in his research. In addition to the questions you've raised, this space specifically could use a style guide that, flatly, does not currently exist.
And, as mentioned in the question errata, this is a perfect example of a question for https://tex.stackexchange.com/. I encourage you to continue to ask specific questions there when you run into any difficulties in your current projects.
The package stargazer can create publication-quality - incl. using templates designed to resemble existing academic journals - from commonly used R statistical functions and packages (lm, glm, plm, svyglm, survival, pscl, AER, and others). Also good for creating summary statistics tables, and can directly output data frame content as well.
There is a tabular function in the tables package which addresses formatting, alignment and label operations. The package has a vignette which is a good starting point.
xtable has worked fine for me so far.
In combination with siunitx, and when necessary, longtable, it can produce pretty effective tables, in my opinion. With packages like booktabs and caption, the aesthetics can be pleasing too.
I am not sure this level of detail was asked for by the OP, but for what it's worth, the basic implementation could be something along these lines: https://tex.stackexchange.com/questions/41067/caption-for-longtable-in-sweave/41183#41183 (my own answer to another question).
I highly recommend ConTeXt which makes use of the TABLE package. There is a Table overview in contextgarden and an exhaustive manual.
There are a range of tools available for creating publication quality tables using R, Sweave, and LaTeX.
In particular, there are helper functions like latex in the Hmisc package, and xtable in the xtable package. I've also often written my own code so that I could have complete control over table formatting (e.g., see this example).
However, when preparing publication quality tables a range of issues often arise:
how and when to apply numeric formatting
how to precisely control alignment of columns and cells
how to precisely control cell borders
how to convert variable labels to variable names
and so on
Beyond the high level issues of specifying the desired table format, there are issues of implementation.
When should a helper function such as xtable be used?
Which helper function should be used in a given situation?
How can the default output of helper functions be customised to particular requirements?
Question
It seems to me that the above issues are deserving of a detailed textbook-style introduction.
Are there any online or offline resources that provide a detailed overview of how to produce publication quality tables using R, Sweave, and LaTeX, and that address the issues discussed above?
Just to tie this up with a nice little bow at the time of current writing, the best existant tutorials on publication-quality tables and usage scenarios appear to be an amalgamation of these documents:
A Sweave example (source)
The Joy of Sweave: A Beginner's Guide to Reproducible Research with Sweave (source)
Latex and R via Sweave: An example document how to use Sweave (source)
Sweave = R · LaTeX2 (source)
The xtable gallery (source)
The Sweave Homepage
LaTeX documentation
Going beyond the scope of what currently exists, you may want to ask the author of The Joy of Sweave for a document on publication-quality tables specifically. It seems like he's gone above and beyond this problem in his research. In addition to the questions you've raised, this space specifically could use a style guide that, flatly, does not currently exist.
And, as mentioned in the question errata, this is a perfect example of a question for https://tex.stackexchange.com/. I encourage you to continue to ask specific questions there when you run into any difficulties in your current projects.
The package stargazer can create publication-quality - incl. using templates designed to resemble existing academic journals - from commonly used R statistical functions and packages (lm, glm, plm, svyglm, survival, pscl, AER, and others). Also good for creating summary statistics tables, and can directly output data frame content as well.
There is a tabular function in the tables package which addresses formatting, alignment and label operations. The package has a vignette which is a good starting point.
xtable has worked fine for me so far.
In combination with siunitx, and when necessary, longtable, it can produce pretty effective tables, in my opinion. With packages like booktabs and caption, the aesthetics can be pleasing too.
I am not sure this level of detail was asked for by the OP, but for what it's worth, the basic implementation could be something along these lines: https://tex.stackexchange.com/questions/41067/caption-for-longtable-in-sweave/41183#41183 (my own answer to another question).
I highly recommend ConTeXt which makes use of the TABLE package. There is a Table overview in contextgarden and an exhaustive manual.