I often use Sweave to produce LaTeX documents where certain chunks are produced dynamically by executing R code. This works well - but is it also possible to have code chunks that are executed in different ways, e.g. by executing the code in the shell, or by running Perl, and so on? It would be helpful to be able to mix things up, so I could do things like run some shell commands to fetch some data, run some perl commands to pre-process it, and then run R commands to analyze it.
Of course I could use all R chunks and use system() as a poor-man's substitute, but that doesn't make for very pleasant reading in the document.
The new new thing (for multi-language, multi-format) docs may be dexy.it which for example these guys at opengamma.org use as the backend.
Ana, who is behind dexy, is also giving a lot of talks about it so also look at the dexy blog.
It's not directly related to Sweave, but org-babel, which is part of Emacs org-mode, allows to mix code chunks of different languages in one file, pass data from one chunk to another, execute them, and generate LaTeX or HTML export from the output.
You can find more informations about org-mode here :
http://www.orgmode.org/
And to see how org-babel works :
http://orgmode.org/worg/org-contrib/babel/
There is certainly no easy way to do this other than through either foreign language interfaces from R (maybe through inline if it's supported), or system(). For what it's worth, I would just use system(); that should be easy enough.
You can see this previous question about having a Sweave equivalent for Python, where one of the respondents actually creates a separate interface. This can give you a sense what what it would take to embed other languages which may not already be supported. At a minimum, you have to do major hacking on the Sweave driver.
Do you know emacs" org-mode and, more specifically, Babel? If you already know Emacs or are willing to switch to Emacs, then org-mode and Babel are the answer to your question(s).
For instance, I am currently working on a document which contains some shell-scripts, does computations with R and creates flow charts with dot (graphviz). Org-mode can export a variety of formats, e.g. LaTeX (that's what I use).
There is the StatWeave project which uses java rather than R to do the weaving, but will run multiple programs instead of just R. I don't know how hard it would be to get it to do Perl or other programs like that, but the homepage indicates that it already works with R, SAS, Stata, and others:
http://www.cs.uiowa.edu/~rlenth/StatWeave/
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I've read some of the recent language vs. language questions with interest... Perl vs. Python, Python vs. Java, Can one language be better than another?
One thing I've noticed is that a lot of us have very superficial reasons for disliking languages. We notice these things at first glance and they turn us off. We shun what are probably perfectly good languages as a result of features that we'd probably learn to love or ignore in 2 seconds if we bothered.
Well, I'm as guilty as the next guy, if not more. Here goes:
Ruby: All the Ruby example code I see uses the puts command, and that's a sort of childish Yiddish anatomical term. So as a result, I can't take Ruby code seriously even though I should.
Python: The first time I saw it, I smirked at the whole significant whitespace thing. I avoided it for the next several years. Now I hardly use anything else.
Java: I don't like identifiersThatLookLikeThis. I'm not sure why exactly.
Lisp: I have trouble with all the parentheses. Things of different importance and purpose (function declarations, variable assignments, etc.) are not syntactically differentiated and I'm too lazy to learn what's what.
Fortran: uppercase everything hurts my eyes. I know modern code doesn't have to be written like that, but most example code is...
Visual Basic: it bugs me that Dim is used to declare variables, since I remember the good ol' days of GW-BASIC when it was only used to dimension arrays.
What languages did look right to me at first glance? Perl, C, QBasic, JavaScript, assembly language, BASH shell, FORTH.
Okay, now that I've aired my dirty laundry... I want to hear yours. What are your language hangups? What superficial features bother you? How have you gotten over them?
I hate Hate HATE "End Function" and "End IF" and "If... Then" parts of VB. I would much rather see a curly bracket instead.
PHP's function name inconsistencies.
// common parameters back-to-front
in_array(needle, haystack);
strpos(haystack, needle);
// _ to separate words, or not?
filesize();
file_exists;
// super globals prefix?
$GLOBALS;
$_POST;
I never really liked the keywords spelled backwards in some scripting shells
if-then-fi is bad enough, but case-in-esac is just getting silly
I just thought of another... I hate the mostly-meaningless URLs used in XML to define namespaces, e.g. xmlns="http://purl.org/rss/1.0/"
Pascal's Begin and End. Too verbose, not subject to bracket matching, and worse, there isn't a Begin for every End, eg.
Type foo = Record
// ...
end;
Although I'm mainly a PHP developer, I dislike languages that don't let me do enough things inline. E.g.:
$x = returnsArray();
$x[1];
instead of
returnsArray()[1];
or
function sort($a, $b) {
return $a < $b;
}
usort($array, 'sort');
instead of
usort($array, function($a, $b) { return $a < $b; });
I like object-oriented style. So it bugs me in Python to see len(str) to get the length of a string, or splitting strings like split(str, "|") in another language. That is fine in C; it doesn't have objects. But Python, D, etc. do have objects and use obj.method() other places. (I still think Python is a great language.)
Inconsistency is another big one for me. I do not like inconsistent naming in the same library: length(), size(), getLength(), getlength(), toUTFindex() (why not toUtfIndex?), Constant, CONSTANT, etc.
The long names in .NET bother me sometimes. Can't they shorten DataGridViewCellContextMenuStripNeededEventArgs somehow? What about ListViewVirtualItemsSelectionRangeChangedEventArgs?
And I hate deep directory trees. If a library/project has a 5 level deep directory tree, I'm going to have trouble with it.
C and C++'s syntax is a bit quirky. They reuse operators for different things. You're probably so used to it that you don't think about it (nor do I), but consider how many meanings parentheses have:
int main() // function declaration / definition
printf("hello") // function call
(int)x // type cast
2*(7+8) // override precedence
int (*)(int) // function pointer
int x(3) // initializer
if (condition) // special part of syntax of if, while, for, switch
And if in C++ you saw
foo<bar>(baz(),baaz)
you couldn't know the meaning without the definition of foo and bar.
the < and > might be a template instantiation, or might be less-than and greater-than (unusual but legal)
the () might be a function call, or might be just surrounding the comma operator (ie. perform baz() for size-effects, then return baaz).
The silly thing is that other languages have copied some of these characteristics!
Java, and its checked exceptions. I left Java for a while, dwelling in the .NET world, then recently came back.
It feels like, sometimes, my throws clause is more voluminous than my method content.
There's nothing in the world I hate more than php.
Variables with $, that's one extra odd character for every variable.
Members are accessed with -> for no apparent reason, one extra character for every member access.
A freakshow of language really.
No namespaces.
Strings are concatenated with ..
A freakshow of language.
All the []s and #s in Objective C. Their use is so different from the underlying C's native syntax that the first time I saw them it gave the impression that all the object-orientation had been clumsily bolted on as an afterthought.
I abhor the boiler plate verbosity of Java.
writing getters and setters for properties
checked exception handling and all the verbiage that implies
long lists of imports
Those, in connection with the Java convention of using veryLongVariableNames, sometimes have me thinking I'm back in the 80's, writing IDENTIFICATION DIVISION. at the top of my programs.
Hint: If you can automate the generation of part of your code in your IDE, that's a good hint that you're producing boilerplate code. With automated tools, it's not a problem to write, but it's a hindrance every time someone has to read that code - which is more often.
While I think it goes a bit overboard on type bureaucracy, Scala has successfully addressed some of these concerns.
Coding Style inconsistencies in team projects.
I'm working on a large team project where some contributors have used 4 spaces instead of the tab character.
Working with their code can be very annoying - I like to keep my code clean and with a consistent style.
It's bad enough when you use different standards for different languages, but in a web project with HTML, CSS, Javascript, PHP and MySQL, that's 5 languages, 5 different styles, and multiplied by the number of people working on the project.
I'd love to re-format my co-workers code when I need to fix something, but then the repository would think I changed every line of their code.
It irritates me sometimes how people expect there to be one language for all jobs. Depending on the task you are doing, each language has its advantages and disadvantages. I like the C-based syntax languages because it's what I'm most used to and I like the flexibility they tend to bestow on the developer. Of course, with great power comes great responsibility, and having the power to write 150 line LINQ statements doesn't mean you should.
I love the inline XML in the latest version of VB.NET although I don't like working with VB mainly because I find the IDE less helpful than the IDE for C#.
If Microsoft had to invent yet another C++-like language in C# why didn't they correct Java's mistake and implement support for RAII?
Case sensitivity.
What kinda hangover do you need to think that differentiating two identifiers solely by caSE is a great idea?
I hate semi-colons. I find they add a lot of noise and you rarely need to put two statements on a line. I prefer the style of Python and other languages... end of line is end of a statement.
Any language that can't fully decide if Arrays/Loop/string character indexes are zero based or one based.
I personally prefer zero based, but any language that mixes the two, or lets you "configure" which is used can drive you bonkers. (Apache Velocity - I'm looking in your direction!)
snip from the VTL reference (default is 1, but you can set it to 0):
# Default starting value of the loop
# counter variable reference.
directive.foreach.counter.initial.value = 1
(try merging 2 projects that used different counter schemes - ugh!)
In no particular order...
OCaml
Tuples definitions use * to separate items rather than ,. So, ("Juliet", 23, true) has the type (string * int * bool).
For being such an awesome language, the documentation has this haunting comment on threads: "The threads library is implemented by time-sharing on a single processor. It will not take advantage of multi-processor machines. Using this library will therefore never make programs run faster." JoCaml doesn't fix this problem.
^^^ I've heard the Jane Street guys were working to add concurrent GC and multi-core threads to OCaml, but I don't know how successful they've been. I can't imagine a language without multi-core threads and GC surviving very long.
No easy way to explore modules in the toplevel. Sure, you can write module q = List;; and the toplevel will happily print out the module definition, but that just seems hacky.
C#
Lousy type inference. Beyond the most trivial expressions, I have to give types to generic functions.
All the LINQ code I ever read uses method syntax, x.Where(item => ...).OrderBy(item => ...). No one ever uses expression syntax, from item in x where ... orderby ... select. Between you and me, I think expression syntax is silly, if for no other reason than that it looks "foreign" against the backdrop of all other C# and VB.NET code.
LINQ
Every other language uses the industry standard names are Map, Fold/Reduce/Inject, and Filter. LINQ has to be different and uses Select, Aggregate, and Where.
Functional Programming
Monads are mystifying. Having seen the Parser monad, Maybe monad, State, and List monads, I can understand perfectly how the code works; however, as a general design pattern, I can't seem to look at problems and say "hey, I bet a monad would fit perfect here".
Ruby
GRRRRAAAAAAAH!!!!! I mean... seriously.
VB
Module Hangups
Dim _juliet as String = "Too Wordy!"
Public Property Juliet() as String
Get
Return _juliet
End Get
Set (ByVal value as String)
_juliet = value
End Set
End Property
End Module
And setter declarations are the bane of my existence. Alright, so I change the data type of my property -- now I need to change the data type in my setter too? Why doesn't VB borrow from C# and simply incorporate an implicit variable called value?
.NET Framework
I personally like Java casing convention: classes are PascalCase, methods and properties are camelCase.
In C/C++, it annoys me how there are different ways of writing the same code.
e.g.
if (condition)
{
callSomeConditionalMethod();
}
callSomeOtherMethod();
vs.
if (condition)
callSomeConditionalMethod();
callSomeOtherMethod();
equate to the same thing, but different people have different styles. I wish the original standard was more strict about making a decision about this, so we wouldn't have this ambiguity. It leads to arguments and disagreements in code reviews!
I found Perl's use of "defined" and "undefined" values to be so useful that I have trouble using scripting languages without it.
Perl:
($lastname, $firstname, $rest) = split(' ', $fullname);
This statement performs well no matter how many words are in $fullname. Try it in Python, and it explodes if $fullname doesn't contain exactly three words.
SQL, they say you should not use cursors and when you do, you really understand why...
its so heavy going!
DECLARE mycurse CURSOR LOCAL FAST_FORWARD READ_ONLY
FOR
SELECT field1, field2, fieldN FROM atable
OPEN mycurse
FETCH NEXT FROM mycurse INTO #Var1, #Var2, #VarN
WHILE ##fetch_status = 0
BEGIN
-- do something really clever...
FETCH NEXT FROM mycurse INTO #Var1, #Var2, #VarN
END
CLOSE mycurse
DEALLOCATE mycurse
Although I program primarily in python, It irks me endlessly that lambda body's must be expressions.
I'm still wrapping my brain around JavaScript, and as a whole, Its mostly acceptable. Why is it so hard to create a namespace. In TCL they're just ugly, but in JavaScript, it's actually a rigmarole AND completely unreadable.
In SQL how come everything is just one, huge freekin SELECT statement.
In Ruby, I very strongly dislike how methods do not require self. to be called on current instance, but properties do (otherwise they will clash with locals); i.e.:
def foo()
123
end
def foo=(x)
end
def bar()
x = foo() # okay, same as self.foo()
x = foo # not okay, reads unassigned local variable foo
foo = 123 # not okay, assigns local variable foo
end
To my mind, it's very inconsistent. I'd rather prefer to either always require self. in all cases, or to have a sigil for locals.
Java's packages. I find them complex, more so because I am not a corporation.
I vastly prefer namespaces. I'll get over it, of course - I'm playing with the Android SDK, and Eclipse removes a lot of the pain. I've never had a machine that could run it interactively before, and now I do I'm very impressed.
Prolog's if-then-else syntax.
x -> y ; z
The problem is that ";" is the "or" operator, so the above looks like "x implies y or z".
Java
Generics (Java version of templates) are limited. I can not call methods of the class and I can not create instances of the class. Generics are used by containers, but I can use containers of instances of Object.
No multiple inheritance. If a multiple inheritance use does not lead to diamond problem, it should be allowed. It should allow to write a default implementation of interface methods, a example of problem: the interface MouseListener has 5 methods, one for each event. If I want to handle just one of them, I have to implement the 4 other methods as an empty method.
It does not allow to choose to manually manage memory of some objects.
Java API uses complex combination of classes to do simple tasks. Example, if I want to read from a file, I have to use many classes (FileReader, FileInputStream).
Python
Indentation is part of syntax, I prefer to use the word "end" to indicate end of block and the word "pass" would not be needed.
In classes, the word "self" should not be needed as argument of functions.
C++
Headers are the worst problem. I have to list the functions in a header file and implement them in a cpp file. It can not hide dependencies of a class. If a class A uses the class B privately as a field, if I include the header of A, the header of B will be included too.
Strings and arrays came from C, they do not provide a length field. It is difficult to control if std::string and std::vector will use stack or heap. I have to use pointers with std::string and std::vector if I want to use assignment, pass as argument to a function or return it, because its "=" operator will copy entire structure.
I can not control the constructor and destructor. It is difficult to create an array of objects without a default constructor or choose what constructor to use with if and switch statements.
In most languages, file access. VB.NET is the only language so far where file access makes any sense to me. I do not understand why if I want to check if a file exists, I should use File.exists("") or something similar instead of creating a file object (actually FileInfo in VB.NET) and asking if it exists. And then if I want to open it, I ask it to open: (assuming a FileInfo object called fi) fi.OpenRead, for example. Returns a stream. Nice. Exactly what I wanted. If I want to move a file, fi.MoveTo. I can also do fi.CopyTo. What is this nonsense about not making files full-fledged objects in most languages? Also, if I want to iterate through the files in a directory, I can just create the directory object and call .GetFiles. Or I can do .GetDirectories, and I get a whole new set of DirectoryInfo objects to play with.
Admittedly, Java has some of this file stuff, but this nonsense of having to have a whole object to tell it how to list files is just silly.
Also, I hate ::, ->, => and all other multi-character operators except for <= and >= (and maybe -- and ++).
[Disclaimer: i only have a passing familiarity with VB, so take my comments with a grain of salt]
I Hate How Every Keyword In VB Is Capitalized Like This. I saw a blog post the other week (month?) about someone who tried writing VB code without any capital letters (they did something to a compiler that would let them compile VB code like that), and the language looked much nicer!
My big hangup is MATLAB's syntax. I use it, and there are things I like about it, but it has so many annoying quirks. Let's see.
Matrices are indexed with parentheses. So if you see something like Image(350,260), you have no clue from that whether we're getting an element from the Image matrix, or if we're calling some function called Image and passing arguments to it.
Scope is insane. I seem to recall that for loop index variables stay in scope after the loop ends.
If you forget to stick a semicolon after an assignment, the value will be dumped to standard output.
You may have one function per file. This proves to be very annoying for organizing one's work.
I'm sure I could come up with more if I thought about it.