jimhester / knitrbootstrap Goto Github PK
View Code? Open in Web Editor NEWA framework to create bootstrap styled HTML reports from knitr Rmarkdown.
License: Other
A framework to create bootstrap styled HTML reports from knitr Rmarkdown.
License: Other
JQuery is pretty heavyweight, do we really need it, especially if we go forward with #32 and output correctly formatted HTML for bootstrap directly.
The links in DESCRIPTION
all point to [https://github.com/hesterj] which 404s on GitHub. It appears the base URL should be [https://github.com/jimhester].
Is there a way that we can control how the TOC are rendered and displayed?
Specifically, I prefer the tocify-style for the TOC and would like to disable the meny functionality (which is cool, but distracting at times).
Hello,
I'm writing a short application note for https://github.com/lcolladotor/derfinderReport and want to cite knitrBootstrap
. I used the information from citation('knitrBootstrap')
but was wondering if that is indeed how you would like knitrBootstrap
to be cited.
Using that information, this would be the citation.
Hester,J. (2014), knitrBootstrap: Knitr Bootstrap framework, R package version
1.0.0, github.com/jimhester/knitrBootstrap.
Thanks
Hi Jim,
I was able to install the updated package via github after installing rmarkdown and a few other dependencies needed to run the vignettes. Unfortunately, now my knit fails to produce the html file. I am using the newest version of RStudio, so I had previously set my defaults via global options:
options(rstudio.markdownToHTML =
function(inputFile, outputFile) {
library(knitrBootstrap)
knit_bootstrap_md(input=inputFile, output=outputFile, code_style="Visual Basic", chooser=c("boot", "code"), show_code=TRUE)
}
)
With the new package, I now get an error:
Error in knit_bootstrap_md(input = inputFile, output = outputFile, code_style = "Visual Basic", :
unused arguments (code_style = "Visual Basic", chooser = c("boot", "code"), show_code = TRUE)
Taking out these arguments allows it to run:
options(rstudio.markdownToHTML =
function(inputFile, outputFile) {
library(knitrBootstrap)
knit_bootstrap_md(input=inputFile, output=outputFile)
}
)
but results in no left margin and no knitrBootstrap additions (similar to a badly formatted typical knitr output).
I then tried the YAML front matter from the README:
output: knitrBootstrap::bootstrap_document:
title: "Test file"
theme: amelia
highlight: sunburst
theme.chooser: TRUE
highlight.chooser: TRUE
But this just puts these words as the first line of my html. I tried with a full range of options(rstudio.markdownToHTML = ...) from the NULL default to those included above.
What am I missing?? I haven't used YAML front matter before, so perhaps I am missing something in the set-up?
I then tried
library(knitrBootstrap)
library(rmarkdown)
render('SpatialProcessingR.Rmd', knitrBootstrap::bootstrap_document)
And after updating my pandoc from 1.12.1 to the 1.12.3 required, I got this error:
Error: Unrecognized output format specified
Thanks again,
Jill
Hello,
I am getting different output when I use knit_bootstrap() and knit_bootstrap_md() with show_code=FALSE.
The way I have things setup, I use knit_boostrap() when working in Textmate2. Basically, I have a shortcut that runs a short bash script that opens R and runs:
library(knitrBootstrap); knit_bootstrap('$FILE', code_style='Brown Paper', chooser=c('boot', 'code'), show_code=FALSE)
As for RStudio, following the setup instructions, this is my .Rprofile https://gist.github.com/lcolladotor/6393166 I use RStudio when I want to submit the html to RPubs. For example, this is the output http://rpubs.com/lcollado/7904
The problem is that show_code=FALSE is not working, and well, you can't toggle code blocks anymore. This is how the output looks like when using knit_boostrap() directly http://biostat.jhsph.edu/~lcollado/misc/outliers-notInteractive.html
Here is the original Rmd file https://gist.github.com/lcolladotor/6370224
In the end, I think that this is related to the fact that knit_boostrap() uses knitr::knit() Or maybe it's also related to knitr::render_html()
Cheers,
Leo
PS, what are the options for the 'graphics' parameter? I can see that it's used in get_style() but I couldn't figure out the options from looking at the code.
I recently came across your knitrBootstrap package, which is really fantastic and the reason why I know switched from Rnw (LaTex) to Rmd mainly.
I sometimes want to include a more polished figure, than the one generated by R. With Rnw I would usually do:
<<someFigure, …more_params…, show="hide">>=
code to generate the figure
@
\begin{figure}
\includegraphics{polished_plot}
…
\end(figure}
Not everyone likes thumbnails, so there should be a way to disable them completely, not just change their size. Also I think I am going to move them back to underneath the blocks, the output seems too fragile as it is.
Images are not being laid out properly at the moment.
http://lcolladotor.github.io/2013/12/10/knitrBootstrap/#.UqdP7mRDt18
Thank you again for such a great package!
Hello,
I am using rCharts to display a dynamic table (DataTable via the dTable function) and knitrBoostrap to get the nice HTML layout. While the rCharts code is working now (see ramnathv/rCharts#227) the HTML is showing as intended.
Basically, the output of knit_boostrap("outliers.Rmd", code_style='Brown Paper', chooser=c('boot', 'code'), show_code=FALSE) is this http://biostat.jhsph.edu/~lcollado/misc/outliers.html The menu is not showing and the R code is showing even though it should be hidden. The code toggling still works except for the code chunks that build the rCharts tables.
I think that this might be related to #15 as the code chunks that call rCharts have the results="asis" option.
The original Rmd file is available here https://gist.github.com/lcolladotor/6393393
Thank you,
Leo
@kohske @jlehtoma @lcolladotor @khughitt @jjallaire,
At some point in the past you expressed interest through questions or bug
reports about knitrBootstrap (https://github.com/jimhester/knitrBootstrap),
to produce Knitr HTML reports utilizing the Bootstrap HTML framework. I have
recently done a major overhaul and rewrite of the package to generate Bootstrap HTML
tags directly using R rather than using javascript to modify the DOM as was done previously.
In addition the package now uses RStudio's new
rmarkdown package to convert the HTML from
markdown and slightly modified the format of the pages in to make them
more consistent and less buggy.
These changes have made the package both easier for me to maintain as well as
easier to enhance. It should also be simpler to use in RStudio and along with
other output formats. I would appreciate both your feedback on the new format
as well as any bugs or feature regressions you find so I can make changes and
fixes before submitting the updates to CRAN.
Thank you for your (past) interest in my package, and I hope these changes improve
your experience!
Jim Hester
I apologize for this slight abuse of the github issue tracker, I did not have an email address to send this message to you!
Thanks for the great package! A humble feature request: numbered sections in rstudio's Rmd -> HTML rendering.
With the minimal .Rmd file below, the div in which the references are placed floats off below the final knitrBookstrap credit at the bottom. (Note that to reproduce the problem, you have to actually have @kellogg_logic_2004 in the .bib file for the reference to be produced.)
---
output:
knitrBootstrap::bootstrap_document
bibliography: "mybib.bib"
---
# a heading
# Bibliography
[@kellogg_logic_2004]
The bottom of the resulting html file looks like this:
<div class="references">
<p>Kellogg, W. K. 2004. “Logic Model Development Guide.”</p>
</div>
</body>
</html>
One thing you may notice if your browser window is relatively small is that there are some TOC entries that can't be seen unless you make the window bigger (the last one is "Canned Comments check"). Is there a way to fix that? Maybe to make the TOC scrollable, or at least indicate that it has further content?
Example:
http://bioconductor.org/developers/BiocCheck.html#Namespace_Import_Suggestion_Checks
Possible fixes:
http://stackoverflow.com/questions/12850531/absolutely-positioned-element-going-off-screen-when-filled
I noticed certain texmath entries in .Rmd docs are being marked up differently in knitrBootstrap than in RStudio's HTML parser (correct term?):
knitrBootstrap: .... (lots of these)
Rstudio's HTML: (.....) (the usual mathjax notation)
I'm getting better results with the second syntax; a table filled with equations renders properly with RStudio's knit button, but not with knitrBootstrap (specified with YAML block). Would it be possible to use the same markup in knitrBootstrap as in RStudio's HTML method for math?
The newer versions of knitr seem to skip adding a code tag to the code blocks, which results in a failure to correctly label and highlight the blocks. You get lots of undefined languages.
Hello,
With the newest version of rmarkdown
(0.1.73), knitrBootstrap
is broken as shown below.
Using a very simple test.Rmd file (see https://gist.github.com/10429813) produces the following error
> library(knitrBootstrap)
> library(rmarkdown)
> render("test.Rmd", bootstrap_document())
processing file: test.Rmd
|...................... | 33%
ordinary text without R code
|........................................... | 67%
label: unnamed-chunk-1
|.................................................................| 100%
ordinary text without R code
output file: test.knit.md
Error in knitr::knit_meta(class = "rmd_warning", clean = TRUE) :
unused argument (class = "rmd_warning")
> sessionInfo()
R version 3.1.0 beta (2014-03-26 r65301)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rmarkdown_0.1.73 knitrBootstrap_1.0.0 colorout_1.0-2
loaded via a namespace (and not attached):
[1] evaluate_0.5.3 formatR_0.10 knitr_1.5.25 markdown_0.6.5 stringr_0.6.2
[6] tools_3.1.0
This is most likely due to the recent changes in the rmarkdown
package, which I can see is under heavy development. It might be best to double check with the authors (@jjallaire) so hopefully new changes in rmarkdown
won't break knitrBootstrap
.
First of all, this is a great package! Thank you. Would be cool if you could add jquerrry DataTables (https://datatables.net/) to improve the handling of large HTML Tables.
This doesn't work (the output has default code style despite code_style
parameter):
knit_bootstrap('./test.Rmd', code_style='Solarized - Dark')
But this does work:
knit_bootstrap('./test.Rmd', code_style='Solarized - Dark', chooser='code')
So apparently the code_style
param only takes effect if the code chooser is present. Seems like a bug to me.
First of all, thank you for your contribution:)
I wonder is there any way to set some of the R Code chunks open and others closed.
Thank you in advance!
Hello,
I'm not sure whether to ask this here or at https://github.com/rstudio/rmarkdown. Anyhow, using rmarkdown
and knitrBootstrap
I generated an HTML file that includes among other things around 110 plots and a datatable output with 2000 rows made with rCharts
.
When generating the report, I basically take the Sys.time()
just before creating the report, and then again at the end of the Rmd file, to then calculate the difference. This is how I know how much time was spent running the R code inside the report. Now, because I was running this in a cluster, I get an email with information as shown below:
Start Time = 04/23/2014 17:05:33
End Time = 04/23/2014 22:02:23
User Time = 01:11:27
System Time = 00:02:30
Wallclock Time = 04:56:50
CPU = 01:13:58
From this, I can see that loading the data needed for the report, running the code in the Rmd file, and then converting the md output to HTML with pandoc took nearly 5 hours. Yet, the time running the R code took ~52 min and was completed at 2014-04-23 18:20:11 EDT. So, around 23 minutes were spent loading the data and 3 hrs 40 min on the pandoc step.
I was surprised by this as I would normally expect running the R code to be the slowest part. Now, the resulting HTML output is ~46 mb big. I know that the recipient hard disk on the cluster network was under heavy I/O load due to someone's else jobs. So maybe that increased the pandoc time, but still, not ~4x vs the R code step.
Any clues? Is there anything I could do to speed things up? Well, maybe generating less plots but that would against the purpose of the report I'm generating.
I'll try re-running it later when the I/O load is lower on the disk, just to rule this out.
Thanks!
The plots were generated using the dev="CairoPNG" knitr option.
There is the R
session info:
## R version 3.1.0 Patched (2014-04-23 r65467)
## Platform: x86_64-unknown-linux-gnu (64-bit)
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] grid parallel methods stats graphics grDevices utils
## [8] datasets base
##
## other attached packages:
## [1] rCharts_0.4.2
## [2] derfinder_0.0.57
## [3] mgcv_1.7-29
## [4] nlme_3.1-117
## [5] RColorBrewer_1.0-5
## [6] xtable_1.7-3
## [7] data.table_1.9.2
## [8] gridExtra_0.9.1
## [9] ggplot2_0.9.3.1
## [10] TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0
## [11] GenomicFeatures_1.16.0
## [12] AnnotationDbi_1.26.0
## [13] Biobase_2.24.0
## [14] GenomicRanges_1.16.2
## [15] GenomeInfoDb_1.0.2
## [16] IRanges_1.22.3
## [17] BiocGenerics_0.10.0
## [18] biovizBase_1.12.0
## [19] derfinderReport_0.0.16
##
## loaded via a namespace (and not attached):
## [1] BatchJobs_1.2 BBmisc_1.5
## [3] bibtex_0.3-6 BiocParallel_0.6.0
## [5] biomaRt_2.20.0 Biostrings_2.32.0
## [7] bitops_1.0-6 brew_1.0-6
## [9] BSgenome_1.32.0 bumphunter_1.4.0
## [11] Cairo_1.5-5 cluster_1.15.2
## [13] codetools_0.2-8 colorspace_1.2-4
## [15] DBI_0.2-7 dichromat_2.0-0
## [17] digest_0.6.4 doRNG_1.6
## [19] evaluate_0.5.3 fail_1.2
## [21] foreach_1.4.2 formatR_0.10
## [23] Formula_1.1-1 GenomicAlignments_1.0.0
## [25] ggbio_1.12.0 gtable_0.1.2
## [27] Hmisc_3.14-4 httr_0.3
## [29] iterators_1.0.7 knitcitations_0.5-0
## [31] knitr_1.5.31 knitrBootstrap_1.0.0
## [33] labeling_0.2 lattice_0.20-29
## [35] latticeExtra_0.6-26 locfit_1.5-9.1
## [37] markdown_0.6.5 MASS_7.3-31
## [39] Matrix_1.1-3 matrixStats_0.8.14
## [41] munsell_0.4.2 pkgmaker_0.20
## [43] plyr_1.8.1 proto_0.3-10
## [45] qvalue_1.38.0 Rcpp_0.11.1
## [47] RCurl_1.95-4.1 registry_0.2
## [49] reshape2_1.2.2 RJSONIO_1.0-3
## [51] rmarkdown_0.1.84 R.methodsS3_1.6.1
## [53] rngtools_1.2.4 Rsamtools_1.16.0
## [55] RSQLite_0.11.4 rtracklayer_1.24.0
## [57] scales_0.2.4 sendmailR_1.1-2
## [59] splines_3.1.0 stats4_3.1.0
## [61] stringr_0.6.2 survival_2.37-7
## [63] tcltk_3.1.0 tools_3.1.0
## [65] VariantAnnotation_1.10.0 whisker_0.3-2
## [67] XML_3.98-1.1 XVector_0.4.0
## [69] yaml_2.1.11 zlibbioc_1.10.0
Pandoc info
$ pandoc --version
pandoc 1.12.3.1
Compiled with texmath 0.6.6, highlighting-kate 0.5.6.
Syntax highlighting is supported for the following languages:
actionscript, ada, apache, asn1, asp, awk, bash, bibtex, boo, c, changelog,
clojure, cmake, coffee, coldfusion, commonlisp, cpp, cs, css, curry, d,
diff, djangotemplate, doxygen, doxygenlua, dtd, eiffel, email, erlang,
fortran, fsharp, gnuassembler, go, haskell, haxe, html, ini, java, javadoc,
javascript, json, jsp, julia, latex, lex, literatecurry, literatehaskell,
lua, makefile, mandoc, markdown, matlab, maxima, metafont, mips, modelines,
modula2, modula3, monobasic, nasm, noweb, objectivec, objectivecpp, ocaml,
octave, pascal, perl, php, pike, postscript, prolog, python, r,
relaxngcompact, restructuredtext, rhtml, roff, ruby, rust, scala, scheme,
sci, sed, sgml, sql, sqlmysql, sqlpostgresql, tcl, texinfo, verilog, vhdl,
xml, xorg, xslt, xul, yacc, yaml
Default user data directory: /home/bst/student/lcollado/.pandoc
Copyright (C) 2006-2013 John MacFarlane
Web: http://johnmacfarlane.net/pandoc
This is free software; see the source for copying conditions. There is no
warranty, not even for merchantability or fitness for a particular purpose.
$ pandoc-citeproc --version
pandoc-citeproc 0.3.0.1
The actual pandoc call
/jhpce/shared/jhpce/core/JHPCE_tools/1.0/bin/pandoc basicExploration.utf8.md --to html --from markdown-hard_line_breaks+superscript+tex_math_dollars+raw_html+markdown_in_html_blocks-implicit_
figures --output basicExploration.html --filter /jhpce/shared/jhpce/core/JHPCE_tools/1.0/bin/pandoc-citeproc -H /scratch/temp/660049.1.shared.q/RtmpgjQsCg/knitr_bootstrap_full.html
Call to derfinderReport::generateReport()
. This is a package I'm making at https://github.com/lcolladotor/derfinderReport
## generateReport(prefix = "run2-v0.0.46", browse = FALSE, makeBestClusters = FALSE,
## nBestClusters = 20, fullCov = fullCov, device = "CairoPNG")
ie. info for messages, danger for errors...
This probably isn't a real issue (just me being ignorant), but for some reason, I can't get proper code highlighting using the RStudio option:
options(rstudio.markdownToHTML =
function(inputFile, outputFile) {
require(knitrBootstrap)
knit_bootstrap_md(input=inputFile, output=outputFile)
}
)
I've also tried changing the default code_style
option:
options(rstudio.markdownToHTML =
function(inputFile, outputFile) {
require(knitrBootstrap)
knit_bootstrap_md(input=inputFile, output=outputFile, code_style='tomorrow')
}
)
Not sure how I can provide a reproducible example, but here is what I'm working on. Also, I'm using RStudio version 0.98.313 and here is my sessionInfo
:
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] knitrBootstrap_0.8.0 markdown_0.6.3 knitr_1.5 dlm_1.1-3 XML2R_0.1
[6] roxygen2_2.2.2 digest_0.6.3 devtools_1.3
loaded via a namespace (and not attached):
[1] brew_1.0-6 evaluate_0.5 formatR_0.9 httr_0.2 memoise_0.1 parallel_3.0.1 plyr_1.8 RCurl_1.95-4.1
[9] stringr_0.6.2 tools_3.0.1 whisker_0.3-2 XML_3.95-0.2
I'm not sure how straight-forward this would be, but would it be possible to add an option to output to PDF? This seems like something Pandoc should be able to handle with a little bit of tweaking.
My ultimate goal is to have a documented knitted once, and converted to both PDF and HTML; this way I can easily archive output at various stages as PDF.
I'm able to use bootstrap knitr in Rstudio after editing my .Rprofile file properly, however I can't seem to be able to set up the document title. How do I do that? I'm able to place headers and everything else just fine. In the .Rprofile, I have have:
options(rstudio.markdownToHTML =
function(inputFile, outputFile) {
library(knitrBootstrap)
knit_bootstrap_md(input=inputFile, output=outputFile, chooser=c("boot", "code"), show_code=FALSE, show_output=FALSE)
}
)
Here's what I have for the Rmarkdown file:
---
output:
knitrBootstrap::bootstrap_document:
title: "Test file"
theme: amelia
highlight: sunburst
theme.chooser: TRUE
highlight.chooser: TRUE
---
A level-one header
=====
$$y=1$$
This is an R Markdown document. Markdown is a simple formatting syntax for authoring web pages (click the **Help** toolbar button for more details on using R Markdown).
When you click the **Knit HTML** button a web page will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
```{r, bootstrap.panel = FALSE }
library(knitr)
render_html()
summary(cars)
```
You can also embed plots, for example:
```{r fig.width=7, fig.height=6}
plot(cars)
```
There is probably already a way to do this but I have not been able to figure one out yet...
Would it be possible to add an option to preserve the intermediate markdown file when generating a HTML?
So using a user define option for code_style does not appear to be working.
For example I use:
knit_bootstrap('test.Rmd', boot_style='Cerulean', code_style='Zenburn', chooser=c('boot','code'))
but this does not affect the syntax highlighting.
Other than that, it's a nice package.
Not sure if this is a bug in my jquery somewhere, or with tocify.
Not present with WebKit.
Hi,
Thank you very much for this package. Is there any way to deactivate meny ? The three dimensional menu is pretty, but a bit cumbersome...
Again, thank you very much.
Best,
David
Hi,
If I apply knitr_bootstrap
on the following file, everything works fine :
# hello markdown
```{r hello-random, echo=TRUE}
plot(rnorm(5))
```
But if I switch to echo=FALSE
, then the image is not displayed anymore in the final html file.
I think the reason is that when echo=FALSE
, there is no <div class="source">
around code chunk anymore, however the javascript which handles thumbnails requires it to insert the images in the DOM :
$('div.rimage').each(function(){
var imgs = $(this).children('img');
var source = $(this).prev('.source');
source.addClass('media-body');
$(this).add(source).wrapAll('<div class="media" />');
//remove div
$(this).remove();
//remove images
imgs.remove();
//add images before source
source.before(imgs);
//add wrapping links to images
imgs.wrap('<a href="#" class="media-object pull-left mfp-image thumbnail ' + thumbsize + '"></a>');
});
Thanks a lot for your very useful package !
The TOC should be on top not the bottom. This is also an issue because the default screen width after knitting in RStudio is just narrow enough to not have the TOC on the side.
I tried to run a basic example and got an error that there are unused arguments
.
The file ex1.Rmd
is simply the basic RMD file that opens in RStudio.
Here is my full code.
> install.packages("knitrBootstrap")
package ‘knitrBootstrap’ successfully unpacked and MD5 sums checked
> setwd("~/Dropbox/Projects/knitr-bootstrap-example")
> list.files()
[1] "ex1.Rmd" "test.Rmd"
> library(knitrBootstrap)
> knit_bootstrap('ex1.Rmd')
Error in knit(input, NULL, text = text, envir = envir, encoding = encoding, : unused argument(s) (quiet = quiet)
Here is my session:
sessionInfo()
R version 2.15.3 (2013-03-01)
Platform: i386-w64-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] knitrBootstrap_0.6.5 markdown_0.6.1 knitr_1.1
loaded via a namespace (and not attached):
[1] digest_0.6.3 evaluate_0.4.3 formatR_0.7 stringr_0.6.2 tools_2.15.3
Many times when I generate *.Rmd
reports, I'd like to run knit_bootstrap
with show_code=FALSE, show_output=FALSE, show_plot=TRUE
since I want the people I'm sharing these with to focus on the results -- the ability to toggle these on/off interactively in the web page is really awesome.
Still, even though I usually (95% of the time) do not want R's output to by shown be default, there are times when I am relying on R's output to be part of the document. A concrete example is when I want to include a tabular result into the web page itself. To do so, I'm using the xtable package to convert data.frame
s to HTML tables, something like:
```{r result-summary, results='asis', echo=FALSE}
df <- data.frame(a=rnorm(5), b=sample(letters, 5))
print(xtable(df), type="html")
```
Is there anyway to get knitr_bootstrap
to be able to have those to show by default even if show_output=FALSE
? Somehow detect output from results='asis'
blocks? I guess this is a bit like Issue #2, although I'm yet to see how I can specify the ID of the output in any meaningful way.
To be frank, your ability to detect an output block in your /* Add div wrapping class to code blocks without them */
javascript section is quite mysterious to me!
Also: This package is insanely great. The ability to set code and output blocks to be globally hidden and toggleable + automatic TOC generation is just awesome ... I rep("love", Inf)
it.
Originally this package was just a replacement header that only modified the knitr HTML output without any R code. However since it now includes some R code it would simplify things to remove as much of the DOM manipulation code as possible and just output the HTML in the correct format from knitr in the first place.
Nothing really works right, at least with an older ie 8, not planning on supporting this, but may do so if I get some time.
Hi!
I write you because I've had problems with the encoding on the website in which I have been working. When I write words in Spanish, that have accent, when I seeing the accent simbole html document is changed by other symbols. I attached an example of what I'm discussing them. I would like you to help me solve this problem.
Thank you for your attention. regards
I was thinking that it would be nice to have knitrBootstrap
listed under the CRAN task view for reproducible research http://cran.r-project.org/web/views/ReproducibleResearch.html.
My guess is that you only have to email the maintainer to get added to the list.
Cheers
I seem to have trouble generating HTML-based table output using xtable. The code looks like the 2d vignette, but the output does not.
Here's the code:
print(xtable(df.impressions),
comment=FALSE,
type="html",
include.rownames=FALSE
)
That output isn't rendered as HTML; it shows up inside an R Output box. The raw HTML for that chunk looks like this:
<pre style="">
<code class="output r">
<TABLE border=1>
(table stuff)
</TABLE>
</code>
</pre>
Hi Jim,
I have posted about the issue I am facing here:
http://stackoverflow.com/q/23370758/1414455
Would appreciate if you could take a look.
T
Hello,
The links at http://jimhester.github.io/knitrBootstrap/#examples to the examples are not loading. For example, http://htmlpreview.github.io/?https://github.com/jimhester/knitrBootstrap/blob/master/inst/doc/math.html
Best,
Leo
The images are not laid out properly on the grid, the bottom images are offset.
Hello,
Thank you again for all your work with knitrBootstrap
. I've been upgrading derfinderReport
(basically, a Rmd file) to your github version of knitrBootstrap
and learning all the new options and the like. I feel like it's basically a complete new version, but like you said in #38, this should make it easier for you to maintain it.
Using it, I have however encountered a couple of hiccups as described below.
First of all, regardless of using the YAML front matter or the options in bootstrap_document
, the specified theme and/or highlight are now shown on load. They appear as selected as seen below:
In this case, I selected the "Brown Paper" highlight option, and you can see that it is selected. If I click on the option again, then it does work. So I'm guessing that a small tweak is missing to make it work from the get-go, instead of relying on the user choosing the option.
As a minor related note, the highlight menu can be too long and not all options will show in the menu as shown below:
While the files I'll link at the end do not show this problem for the theme option, I encountered the same problem described above for the highlight option.
One of the packages that I like to use a lot along with knitrBoostrap
is knitcitations
(I'm using the CRAN release). While the inline code works well, printing the bibliography doesn't because knitrBootstrap
marks the output as "output" when using the code chunk option results='asis'
as shown below:
It won't let the output be interpreted as markdown syntax, like it should. You can get a very similar result even if you use knitcitations::bibliography(style='html')
.
For some reason, I cannot get some of the knitrBootstrap
code chunk options to work. I really like hiding the code by default, and cannot get that work using bootstrap.show.code=FALSE
in the code chunk definition or using opts_chunk$set()
from knitr
.
Note that bootstrap.panel=TRUE
does work.
Actually, the options seem to conflict with each other at times. For example, bootstrap.show.output=TRUE, bootstrap.hide=TRUE
produces:
I would expect the output to be shown in the first chunk (only one with options set) instead of it being hidden.
Then, bootstrap.show.output=TRUE, bootstrap.panel=TRUE, bootstrap.hide=TRUE
produces:
Similar as above. Here bootstrap.panel=TRUE
works as expected.
Finally, bootstrap.show.code=TRUE, bootstrap.hide=TRUE
produces:
In this case, I would except the code to be shown instead of being hidden.
Overall, it seems to be that it might be best to delete the bootstrap.hide
option which seems to create conflicts with bootstrap.show.code
and bootstrap.show.output
.
I have tested this with both R 3.0.3 and R 3.1.0 using the github versions of rmarkdown
and knitrBootstrap
. Files were created like this
$ R --vanilla
> library("rmarkdown")
> library("knitrBootstrap")
> render("maps-yaml.Rmd")
> render("maps.Rmd", bootstrap_document(theme.chooser=TRUE, highlight.chooser=TRUE, highlight="Brown Paper"))
I used a slightly modified version of the maps.Rmd
vignette.
http://biostat.jhsph.edu/~lcollado/misc/knitrBootstrap-2014-03-30-R-3.0/maps.Rmd
http://biostat.jhsph.edu/~lcollado/misc/knitrBootstrap-2014-03-30-R-3.0/maps.html
http://biostat.jhsph.edu/~lcollado/misc/knitrBootstrap-2014-03-30-R-3.0/maps-yaml.Rmd
http://biostat.jhsph.edu/~lcollado/misc/knitrBootstrap-2014-03-30-R-3.0/maps-yaml.html
http://biostat.jhsph.edu/~lcollado/misc/knitrBootstrap-2014-03-30-R-3.1/maps.Rmd
http://biostat.jhsph.edu/~lcollado/misc/knitrBootstrap-2014-03-30-R-3.1/maps.html
http://biostat.jhsph.edu/~lcollado/misc/knitrBootstrap-2014-03-30-R-3.1/maps-yaml.Rmd
http://biostat.jhsph.edu/~lcollado/misc/knitrBootstrap-2014-03-30-R-3.1/maps-yaml.html
Thank you!
PS Opening the files in Firefox instead of Chrome shows some console errors. Nevermind, I had an outdated version of Firefox, it works with version 28.0
Thanks for fantastic package.
Under some environment, knit_bootstrap
doesn't work due to the encoding issue.
This is because markdown::markdownToHTML
couldn't handle encoding.
I have written a patch, and I hope the patch will be merged.
rstudio/markdown#50
After this patch, it is very easy to make knitrBootstrap
to work with non-UTF8 MBCS.
I can write a patch and send PR.
Another problem is read_char
. read_char
may have a trouble under non-UTF8 MB locale (as shown in the help file). So is there any reason you uses read_char
instead of readLines
?
Currently all of the javascript and CSS include URLs use http://
schemes, which means that if you try to serve your knit_bootstrap
-generated content over HTTPS, the page is broken because most browsers block the inclusion of HTTP content by an HTTPS page (or at least show a scary warning).
Most of the include URLs can have the http://
scheme replaced by https://
successfully (yandex, netdna, etc.), with the exception of:
http://gregfranko.com
(tocify)http://dimsemenov.com
(magnific)These two servers do not have HTTPS versions available. Perhaps there are HTTPS mirrors available.
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