I would like to paste the data-frame from the R environment to the latex part (question or solution part) when creating exercises in r-exams. Later the exercises will be imported into Moodle. Is that possible in r-exams? We saw it is possible when the object is matrix object via $\Sexpr{toLatex(matrix_obj)}$. But a similar way does not seem to work with the data-frames. Thank you!
A data.frame would usually be included as a {tabular} in LaTeX and there are various packages for automatic conversion like xtable or using the function kable() in knitr. For PDF output this also works nicely including all vertical and/or horizontal lines included in the table. However, for HTML-based output (as for Moodle) the table as such is converted correctly but without any lines.
An overview of a couple of solutions is available as:
Different copies of question with table for Moodle with R-Exams
Moreover, Kenji Sato has proposed to inject some dedicated CSS code to handle the table formatting in HTML. We are currently working on some automated way of including this in R/exams:
https://www.kenjisato.jp/en/post/2020/07/moodle-bordered-table/
Related
I need to write documentation for a parser that was developed in Kaitai. Given a .ksy file, is there any way to produce "pretty" views of the tree?
There is a two year old fork of ksc that supports GraphViz output but the resulting output is pretty hard to work with.
(https://www.reddit.com/r/dataisbeautiful/comments/4zhpvh/binary_data_formats_network_packets_archives/)
I can easily determine what the nodes are but getting their immediate parent would add very useful context.
Thank you.
-David
Please define what exactly do you expect from a "pretty tree".
GraphViz support is available in master and stable releases for a long time (as -t graphviz), and is very well supported — basically every ksy in official repo is accompanied nowadays with a chart: for example, http://formats.kaitai.io/lzh/index.html
If you want to have a tree of values (as opposed to "tree of data types"), we actually have ksdump, which allows you to dump arbitary data file using arbitrary .ksy in a YAML/JSON/XML tree of values. Will it work for you?
I have a need to go through a set of DICOM files and modify certain tags to be current with the data maintained in the database of an external system. I am looking to use GDCM. I am new to GDCM. A search through stack overflow posts demonstrates that the anonymizer class can be used to change tag values.
Generating a simple CT DICOM image using GDCM
My question is if this is the best use of the GDCM API or if there is a better approach for changing the values of individual tags such as patient name or accession number. I am unfamiliar with all of the API options but have a link to the API documentation. It looks like the DataElement SetValue member could be used, but it doesn't appear that there is a valid constructor for doing this in the Value class. Any assistance would appreciated. This is my current approach:
Anonymizer anon = new Anonymizer();
anon.SetFile(myFile);
anon.Replace(new Tag(0x0010, 0x0010), "BUGS^BUNNY");
Quite late, but maybe it would be still useful. You have not mention if you write in C++ or C#, but I assume the latter, as you do not use pointers. Generally, your approach is correct (unless you use System.IO.File instead of gdcm.File). The value (second parameter of Replace function) has to be a plain string so no special constructor is needed. You should probably start with doxygen documentation of gdcm, and there is especially one complete example. It is in C++, but there should be no problems with translation.
There are two different ways to pad dicom tags:
Anonymizer
gdcm::Anonymizer anon;
anon.SetFile(file);
anon.Replace(gdcm::Tag(0x0002, 0x0013), "Implementation Version Name");
//Implementation Version Name
DatsElement
gdcm::Attribute<0x0018, 0x0088> ss;
ss.SetValue(10.0);
ds.Insert(ss.GetAsDataElement());
Can anyone share his experience on workflow for R peject development under ESS? I tried several times to learn emacs but I have not get it yet. I can understand ESS as an editor, but is there a project view in ESS? what's the efficient ways to set up/view R project directory, coding, and testing, and how's ESS has an edge to facilitate the whole process?
Do you use ESS as a good R editor only or tend to emulate a R IDE environment within ESS?
Thanks for any advices.
It sounds like you're asking two separate questions.
One question concerns workflow and the other concerns using ESS.
As I use StatET and Eclipse, I'll just share my experience regarding the workflow aspect of your question.
As with Vincent I also follow something like the workflow set out by Josh Reich here (also see Hadley's useful comments):
Workflow for statistical analysis and report writing
Although it can vary between projects, I tend to have a couple of main R files
import.R: this imports data files and does any necessary cleaning and manipulation
analyse.R: This generates the output that I need for any final report
main.R: This calls import.R and analyse.R
The aim is for import.R and analyse.R to represent the complete and final workflow for producing the final results of any analyses.
In terms of a directory structure for an analysis project, I'll often also have the following folders
data: for storing any raw data files
meta: for storing meta data, such as variable labels, scoring systems for tests, recoding information, etc.
output: for storing any graphics, tables, or text generated by my analyses that I might want to incorporate into an external program
temp: When exploring the data and brainstorming analyses, I like to type code into files instead of using the console. I tend to label these temp1.R, temp2.R, temp3.R. I store these in a temp folder. That way I have a permanent record that's easily accessible. If the analyses become final they get incorporated into one of the main R files (i.e., import.R or analysis.R)
functions: If I think that a function will be needed across a couple of projects, I often place it one function per file or a set of related functions in a file in a folder called functions. This makes it relatively easy to reuse functions across projects, when the formal requirements of package development are more than needed.
library: If I want to create some general functions that I think will be project specific, I'll place them in this folder
save: A folder to store any saved R objects
StatET and Eclipse make it easy to interact with such a file system.
Of course, given all the R gurus that use ESS and Emacs, I'm sure it also handles interactions with the file system well.
I'm not exactly sure what you expect as an answer on this one. I, for one, have stolen (and adapted) a system that was suggested here a little while ago (by Josh Reich):
Create a folder for every project, and split up your work in a bunch of different .R files:
Load.R for getting your raw data into R;
Prep.R for cleaning the data, recoding variables, etc.;
Func.R for coding any custom functions you will need for evaluation; and
Eval.R for running your final stuff.
If that doesn't fit your style, just change it.
Then, you can either have a master file to call each of the parts one after each other (good for reproducibility), or save at different stages and have the individual scripts load the appropriate data (good if some of the prep work is very computationally/time intensive).
**
On a different note, the trick that is posted at the link really helped me get into ESS. It turns Shift-Enter into a one-stop-ESS-shop: http://www.kieranhealy.org/blog/archives/2009/10/12/make-shift-enter-do-a-lot-in-ess/
Others have given you some good ideas about how to setup your directory/file structure for a project.
You also asked about "project views," in which case you might want to look into the Emacs Code Browser (ECB).
You can find some screen shots of it in action on its site, here:
http://ecb.sourceforge.net/screenshots/index.html
My attorney gave me a 10 page contract that we need to fill in the blanks with the client name, pricing etc and then provide the client with a PDF or equivalent of the contract.
I have looked at PDF::Create but it looks like I would have to create the entire document through code, not just the the placeholders.
CAM::PDF, PDF::API2 can modify existing documents. Your question is not very specific, so no code example.
I would look into using a templating system and LaTeX rather than making the pdf by hand.
I want to highlight some parts of the reports i'm generating for display.
I don't want to change the report definition. I want to highlight the output at runtime.
But the JRViewer i'm using doesn't really have much of an API.
And manipulating the JasperPrint object with setForecolor/setBackcolor before displaying it, didn't seem to change the output.
Any ideas? Or do i have to overload/reimplement the viewer? Wouldn't be much of a problem since it's open source, but i'd like to prevent reinventing the wheel.
Looks like i have to answer my questions myself... again.
I overloaded the JRViewer class (actually copied the code of JRViewer because none of the interesting panels were accessible) and added some highlighting methods to do the following:
Template based JasperPrint data uses - like the name suggests - templates. Meaning the text objects don't have a style of their own, they use their template's style.
That is the reason why setForecolor didn't do anything - the JRTemplatePrintElement implementation is plain empty.
But if i would set the highlight on the text template i would end up with a full column of highlighted texts, since they share the template instance.
Instead i create a new template as a copy of the original with highlighting and use that in the highlighted print elements. Btw, those jasper elements could really use a clone() method.
Feels like a hack, but i don't see a better way.
UPDATE:
However this has a nasty sideeffect for file based (virtualized) reports.
These apparently save any changes you make to the elements while you walk the pages.
If however the viewer in the meantime causes the virtualizer to discard the elements you reference (for example by flipping pages), your further changes won't be saved...
So that made me reconsider and now i'm just drawing my highlighting on top of the Graphics object painted by Jasper's PageRenderer.
Much simpler and cleaner. Only highlighting the background won't work this way.