How can you efficiently check values of large vectors in R? - r

One thing I want to do all the time in my R code is to test whether certain conditions hold for a vector, such as whether it contains any or all values equal to some specified value. The Rish way to do this is to create a boolean vector and use any or all, for example:
any(is.na(my_big_vector))
all(my_big_vector == my_big_vector[[1]])
...
It seems really inefficient to me to allocate a big vector and fill it with values, just to throw it away (especially if any() or all() call can be short-circuited after testing only a couple of the values. Is there a better way to do this, or should I just hand in my desire to write code that is both efficient and succinct when working in R?

"Cheap, fast, reliable: pick any two" is a dry way of saying that you sometimes need to order your priorities when building or designing systems.
It is rather similar here: the cost of the concise expression is the fact that memory gets allocated behind the scenes. If that really is a problem, then you can always write a (compiled ?) routines to runs (quickly) along the vectors and uses only pair of values at a time.
You can trade off memory usage versus performance versus expressiveness, but is difficult to hit all three at the same time.

which(is.na(my_big_vector))
which(my_big_vector == 5)
which(my_big_vector < 3)
And if you want to count them...
length(which(is.na(my_big_vector)))

I think it is not a good idea -- R is a very high-level language, so what you should do is to follow standards. This way R developers know what to optimize. You should also remember that while R is functional and lazy language, it is even possible that statement like
any(is.na(a))
can be recognized and executed as something like
.Internal(is_any_na,a)

Related

Struggling with building an intuition for recursion

Though I have studied and able am able to understand some programs in recursion, I am still not able to intuitively obtain a solution using recursion as I do easily using Iteration. Is there any course or track available in order to build an intuition for recursion? How can one master the concept of recursion?
if you want to gain a thorough understanding of how recursion works, I highly recommend that you start with understanding mathematical induction, as the two are very closely related, if not arguably identical.
Recursion is a way of breaking down seemingly complicated problems into smaller bits. Consider the trivial example of the factorial function.
def factorial(n):
if n < 2:
return 1
return n * factorial(n - 1)
To calculate factorial(100), for example, all you need is to calculate factorial(99) and multiply 100. This follows from the familiar definition of the factorial.
Here are some tips for coming up with a recursive solution:
Assume you know the result returned by the immediately preceding recursive call (e.g. in calculating factorial(100), assume you already know the value of factorial(99). How do you go from there?)
Consider the base case (i.e. when should the recursion come to a halt?)
The first bullet point might seem rather abstract, but all it means is this: a large portion of the work has already been done. How do you go from there to complete the task? In the case of the factorial, factorial(99) constituted this large portion of work. In many cases, you will find that identifying this portion of work simply amounts to examining the argument to the function (e.g. n in factorial), and assuming that you already have the answer to func(n - 1).
Here's another example for concreteness. Let's say we want to reverse a string without using in-built functions. In using recursion, we might assume that string[:-1], or the substring until the very last character, has already been reversed. Then, all that is needed is to put the last remaining character in the front. Using this inspiration, we might come up with the following recursive solution:
def my_reverse(string):
if not string: # base case: empty string
return string # return empty string, nothing to reverse
return string[-1] + my_reverse(string[:-1])
With all of this said, recursion is built on mathematical induction, and these two are inseparable ideas. In fact, one can easily prove that recursive algorithms work using induction. I highly recommend that you checkout this lecture.

How to speed up writing to a matrix in a reference class in R

Here is a piece of R code that writes to each element of a matrix in a reference class. It runs incredibly slowly, and I’m wondering if I’ve missed a simple trick that will speed this up.
nx = 2000
ny = 10
ref_matrix <- setRefClass(
"ref_matrix",fields = list(data = "matrix"),
)
out <- ref_matrix(data = matrix(0.0,nx,ny))
#tracemem(out$data)
for (iy in 1:ny) {
for (ix in 1:nx) {
out$data[ix,iy] <- ix + iy
}
}
It seems that each write to an element of the matrix triggers a check that involves a copy of the entire matrix. (Uncommenting the tracemen() call shows this.) Now, I’ve found a discussion that seems to confirm this:
https://r-devel.r-project.narkive.com/8KtYICjV/rd-copy-on-assignment-to-large-field-of-reference-class
and this also seems to be covered by Speeding up field access in R reference classes
but in both of these this behaviour can be bypassed by not declaring a class for the field, and this works for the example in the first link which uses a 1D vector, b, which can just be set as b <<- 1:10000. But I’ve not found an equivalent way of creating a 2D array without using a explicit “matrix” instance.
Am I just missing something simple, or is this actually not possible?
Let me add a couple of things. First, I’m very new to R, so could easily have missed something. Second, I’m really just curious about the way reference classes work in this case and whether there’s a simple way to use them efficiently; I’m not looking for a really fast way to set the elements of a matrix - I can do that by not having the matrix in a reference class at all, and if I really care about speed I can write a C routine to do it and call it from R.
Here’s some background that might explain why I’m interested in this, which you’re welcome to ignore.
I got here by wanting to see how different languages, and even different compiler options and different ways of coding the same operation, compared for efficiency when accessing 2D rectangular arrays. I’ve been playing with a test program that creates two 2D arrays of the same size, and calls a subroutine that sets the first to the elements of the second plus their index values. (Almost any operation would do, but this one isn’t completely trivial to optimise.) I have this in a number of languages now, C, C++, Julia, Tcl, Fortran, Swift, etc., even hand-coded assembler (spoiler alert: assembler isn’t worth the effort any more) and thought I’d try R. The obvious implementation in R passes the two arrays to a subroutine that does the work, but because R doesn’t normally pass by reference, that routine has to make a copy of the modified array and return that as the function value. I thought using a reference class would avoid the relatively minor overhead of that copy, so I tried that and was surprised to discover that, far from speeding things up, it slowed them down enormously.
Use outer:
out$data <- outer(1:ny, 1:nx, `+`)
Also, don't use reference classes (or R6 classes) unless you actually need reference semantics. KISS and all that.

Solve Physics exercise by brute force approach

Being unable to reproduce a given result. (either because it's wrong or because I was doing something wrong) I was asking myself if it would be easy to just write a small program which takes all the constants and given number and permutes it with a possible operators (* / - + exp(..)) etc) until the result is found.
Permutations of n distinct objects with repetition allowed is n^r. At least as long as r is small I think you should be able to do this. I wonder if anybody did something similar here..
Yes, it has been done here: Code Golf: All +-*/ Combinations for 3 integers
However, because a formula gives the desired result doesn't guarantee that it's the correct formula. Also, you don't learn anything by just guessing what to do to get to the desired result.
If you're trying to fit some data with a function whose form is uncertain, you can try using Eureqa.

Multidimensional vectors in Scheme?

I earlier asked a question about arrays in scheme (turns out they're called vectors but are basically otherwise the same as you'd expect).
Is there an easy way to do multidimensional arrays vectors in PLT Scheme though? For my purposes I'd like to have a procedure called make-multid-vector or something.
By the way if this doesn't already exist, I don't need a full code example of how to implement it. If I have to roll this myself I'd appreciate some general direction though. The way I'd probably do it is to just iterate through each element of the currently highest dimension of the vector to add another dimension, but I can see that being a bit ugly using scheme's recursive setup.
Also, this seems like something I should have been able to find myself so please know that I did actually google it and nothing came up.
The two common approaches are the same as in many languages, either use a vector of vectors, or (more efficiently) use a single vector of X*Y and compute the location of each reference. But there is a library that does that -- look in the docs for srfi/25, which you can get with (require srfi/25).

Efficiency of stack-based expression evaluation for math parsing

I have to write, for academic purposes, an application that plots user-input expressions like: f(x) = 1 - exp(3^(5*ln(cosx)) + x)
The approach I've chosen to write the parser is to convert the expression in RPN with the Shunting-Yard algorithm, treating primitive functions like "cos" as unary operators. This means the function written above would be converted in a series of tokens like:
1, x, cos, ln, 5, *,3, ^, exp, -
The problem is that to plot the function I have to evaluate it LOTS of times, so applying the stack evaluation algorithm for each input value would be very inefficient.
How can I solve this? Do I have to forget the RPN idea?
How much is "LOTS of times"? A million?
What kind of functions could be input? Can we assume they are continuous?
Did you try measuring how well your code performs?
(Sorry, started off with questions!)
You could try one of the two approaches (or both) described briefly below (there are probably many more):
1) Parse Trees.
You could create a Parse Tree. Then do what most compilers do to optimize expressions, constant folding, common subexpression elimination (which you could achieve by linking together the common expression subtrees and caching the result), etc.
Then you could use lazy evaluation techniques to avoid whole subtrees. For instance if you have a tree
*
/ \
A B
where A evaluates to 0, you could completely avoid evaluating B as you know the result is 0. With RPN you would lose out on the lazy evaluation.
2) Interpolation
Assuming your function is continuous, you could approximate your function to a high degree of accuracy using Polynomial Interpolation. This way you can do the complicated calculation of the function a few times (based on the degree of polynomial you choose), and then do fast polynomial calculations for the rest of the time.
To create the initial set of data, you could just use approach 1 or just stick to using your RPN, as you would only be generating a few values.
So if you use Interpolation, you could keep your RPN...
Hope that helps!
Why reinvent the wheel? Use a fast scripting language instead.
Integrating something like lua into your code will take very little time and be very fast.
You'll usually be able byte compile your expression, and that should result in code that runs very fast, certainly fast enough for simple 1D graphs.
I recommend lua as its fast, and integrates with C/C++ easier than any other scripting language. Another good options would be python, but while its better known I found it trickier to integrate.
Why not keep around a parse tree (I use "tree" loosely, in your case it's a sequence of operations), and mark input variables accordingly? (e.g. for inputs x, y, z, etc. annotate "x" with 0 to signify the first input variable, "y" with 1 to signify the 2nd input variable, etc.)
That way you can parse the expression once, keep the parse tree, take in an array of inputs, and apply the parse tree to evaluate.
If you're worrying about the performance aspects of the evaluation step (vs. the parsing step), I don't think you'd do much better unless you get into vectorizing (applying your parse tree on a vector of inputs at once) or hard-coding the operations into a fixed function.
What I do is use the shunting algorithm to produce the RPN. I then "compile" the RPN into a tokenised form that can be executed (interpretively) repeatedly without re-parsing the expression.
Michael Anderson suggested Lua. If you want to try Lua for just this task, see my ae library.
Inefficient in what sense? There's machine time and programmer time. Is there a standard for how fast it needs to run with a particular level of complexity? Is it more important to finish the assignment and move on to the next one (perfectionists sometimes never finish)?
All those steps have to happen for each input value. Yes, you could have a heuristic that scans the list of operations and cleans it up a bit. Yes, you could compile some of it down to assembly instead of calling +, * etc. as high level functions. You can compare vectorization (doing all the +'s then all the *'s etc, with a vector of values) to doing the whole procedure for one value at a time. But do you need to?
I mean, what do you think happens if you plot a function in gnuplot or Mathematica?
Your simple interpretation of RPN should work just fine, especially since it contains
math library functions like cos, exp, and ^(pow, involving logs)
symbol table lookup
Hopefully, your symbol table (with variables like x in it) will be short and simple.
The library functions will most likely be your biggest time-takers, so unless your interpreter is poorly written, it will not be a problem.
If, however, you really gotta go for speed, you could translate the expression into C code, compile and link it into a dll on-the-fly and load it (takes about a second). That, plus memoized versions of the math functions, could give you the best performance.
P.S. For parsing, your syntax is pretty vanilla, so a simple recursive-descent parser (about a page of code, O(n) same as shunting-yard) should work just fine. In fact, you might just be able to compute the result as you parse (if math functions are taking most of the time), and not bother with parse trees, RPN, any of that stuff.
I think this RPN based library can serve the purpose: http://expressionoasis.vedantatree.com/
I used it with one of my calculator project and it works well. It is small and simple, but extensible.
One optimization would be to replace the stack with an array of values and implement the evaluator as a three address mechine where each operation loads from two (or one) location and saves to a third. This can make for very tight code:
struct Op {
enum {
add, sub, mul, div,
cos, sin, tan,
//....
} op;
int a, b, d;
}
void go(Op* ops, int n, float* v) {
for(int i = 0; i < n; i++) {
switch(ops[i].op) {
case add: v[op[i].d] = v[op[i].a] + v[op[i].b]; break;
case sub: v[op[i].d] = v[op[i].a] - v[op[i].b]; break;
case mul: v[op[i].d] = v[op[i].a] * v[op[i].b]; break;
case div: v[op[i].d] = v[op[i].a] / v[op[i].b]; break;
//...
}
}
}
The conversion from RPN to 3-address should be easy as 3-address is a generalization.

Resources