Can anyone help me with taking Wreath Products of Groups in Sagemath?
I haven't been able to find a online reference and it doesn't appear to be built in as far as I can tell.
As far as I know, you would have to use GAP to compute them within Sage (and then can manipulate them from within Sage as well). See e.g. this discussion from 2012. This question has information about it, here is the documentation, and here it is within Sage:
F = AbelianGroup(3,[2]*3)
G = PermutationGroup([[(1,2,3),(4,5)],[(3,4)]])
Gp = gap.StandardWreathProduct(gap(F),gap(G))
print Gp
However, if you try to get this back into Sage, you will get a NotImplementedError because Sage doesn't understand what GAP returns in this wacky case (which I hope even is legitimate). Presumably if a recognized group is returned then one could eventually get it back to Sage for further processing. In this case, you might be better off doing some GAP computations and then putting them back in Sage after doing all your group stuff (which isn't always the case).
Related
Sage seems to want to evaluate derivatives as far as possible using the chain rule. A simple example is:
var('theta')
f = function('f')(theta)
g = function('g')(theta)
h = f*g
diff(h,theta)
which would display
g(theta)*diff(f(theta), theta) + f(theta)*diff(g(theta), theta)
My question is, is there a way to control just how far Sage will take derivatives? In the example above for instance, how would I get Sage to display instead:
diff(f(theta)*g(theta))
I'm working through some pretty intensive derivations in fluid mechanics, and being able to not evaluate derivatives all the way like discussed above would really help with this. Thanks in advance. Would appreciate any help on this.
This would be called "holding" the derivative.
Adding this possibility to Sage has already been considered.
Progress on this is tracked at:
Sage Trac ticket 24861
and the ticket even links to a branch with code implementing this.
Although progress on this is stalled, and the branch has not been merged,
you could use the code from the branch.
This seems like a simple problem:
let slice = " some wacky text. ";
let trimmed = slice.trim();
// how do I get the index of the start and end within the original slice?
Attempt 1
Look for an alternative API. trim wraps trim_matches which deals with indices internally anyway: so lets copy this code! But this uses std::str::pattern::Pattern which is unstable, thus can't be used outside std in stable Rust.
Attempt 2
Just use trim and calculate the slice indices from the pointers. There's a nice as_ptr_range method, but its also unstable; luckily as the PR says there's an easy work-around.
let slice_ptr = slice.as_ptr();
let trimmed_ptr = trimmed.as_ptr();
// don't bother about the end (we can use trimmed.len())
Now that we've got some pointers, we need their difference. sub is not the right method for this. offset_from is, but it's unstable (as noted in the design, it's only valid use is to compare two pointers into the same slice, which is exactly what we want to do, unfortunately it's yet another thing delayed by the details).
Now, there are hackier ways of solving this problem. We could transmute the pointers to usize (we know the element size is 1 byte, so no need to multiply). But this is most likely the Undefined Behaviour type of unsafe, so lets not go there.
Attempt 3
Edit: the source problem is easy to solve directly, so probably the answer in this case is roll-my-own. Possibly I should just close this.
Right upfront: this is an issue I encountered when submitting an R package to CRAN. So I
dont have control of the stack size (as the issue occured on one of CRANs platforms)
I cant provide a reproducible example (as I dont know the exact configurations on CRAN)
Problem
When trying to submit the cSEM.DGP package to CRAN the automatic pretest (for Debian x86_64-pc-linux-gnu; not for Windows!) failed with the NOTE: C stack usage 7975520 is too close to the limit.
I know this is caused by a function with three arguments whose body is about 800 rows long. The function body consists of additions and multiplications of these arguments. It is the function varzeta6() which you find here (from row 647 onwards).
How can I adress this?
Things I cant do:
provide a reproducible example (at least I would not know how)
change the stack size
Things I am thinking of:
try to break the function into smaller pieces. But I dont know how to best do that.
somehow precompile? the function (to be honest, I am just guessing) so CRAN doesnt complain?
Let me know your ideas!
Details / Background
The reason why varzeta6() (and varzeta4() / varzeta5() and even more so varzeta7()) are so long and R-inefficient is that they are essentially copy-pasted from mathematica (after simplifying the mathematica code as good as possible and adapting it to be valid R code). Hence, the code is by no means R-optimized (which #MauritsEvers righly pointed out).
Why do we need mathematica? Because what we need is the general form for the model-implied construct correlation matrix of a recursive strucutral equation model with up to 8 constructs as a function of the parameters of the model equations. In addition there are constraints.
To get a feel for the problem, lets take a system of two equations that can be solved recursivly:
Y2 = beta1*Y1 + zeta1
Y3 = beta2*Y1 + beta3*Y2 + zeta2
What we are interested in is the covariances: E(Y1*Y2), E(Y1*Y3), and E(Y2*Y3) as a function of beta1, beta2, beta3 under the constraint that
E(Y1) = E(Y2) = E(Y3) = 0,
E(Y1^2) = E(Y2^2) = E(Y3^3) = 1
E(Yi*zeta_j) = 0 (with i = 1, 2, 3 and j = 1, 2)
For such a simple model, this is rather trivial:
E(Y1*Y2) = E(Y1*(beta1*Y1 + zeta1) = beta1*E(Y1^2) + E(Y1*zeta1) = beta1
E(Y1*Y3) = E(Y1*(beta2*Y1 + beta3*(beta1*Y1 + zeta1) + zeta2) = beta2 + beta3*beta1
E(Y2*Y3) = ...
But you see how quickly this gets messy when you add Y4, Y5, until Y8.
In general the model-implied construct correlation matrix can be written as (the expression actually looks more complicated because we also allow for up to 5 exgenous constructs as well. This is why varzeta1() already looks complicated. But ignore this for now.):
V(Y) = (I - B)^-1 V(zeta)(I - B)'^-1
where I is the identity matrix and B a lower triangular matrix of model parameters (the betas). V(zeta) is a diagonal matrix. The functions varzeta1(), varzeta2(), ..., varzeta7() compute the main diagonal elements. Since we constrain Var(Yi) to always be 1, the variances of the zetas follow. Take for example the equation Var(Y2) = beta1^2*Var(Y1) + Var(zeta1) --> Var(zeta1) = 1 - beta1^2. This looks simple here, but is becomes extremly complicated when we take the variance of, say, the 6th equation in such a chain of recursive equations because Var(zeta6) depends on all previous covariances betwenn Y1, ..., Y5 which are themselves dependend on their respective previous covariances.
Ok I dont know if that makes things any clearer. Here are the main point:
The code for varzeta1(), ..., varzeta7() is copy pasted from mathematica and hence not R-optimized.
Mathematica is required because, as far as I know, R cannot handle symbolic calculations.
I could R-optimze "by hand" (which is extremly tedious)
I think the structure of the varzetaX() must be taken as given. The question therefore is: can I somehow use this function anyway?
Once conceivable approach is to try to convince the CRAN maintainers that there's no easy way for you to fix the problem. This is a NOTE, not a WARNING; The CRAN repository policy says
In principle, packages must pass R CMD check without warnings or significant notes to be admitted to the main CRAN package area. If there are warnings or notes you cannot eliminate (for example because you believe them to be spurious) send an explanatory note as part of your covering email, or as a comment on the submission form
So, you could take a chance that your well-reasoned explanation (in the comments field on the submission form) will convince the CRAN maintainers. In the long run it would be best to find a way to simplify the computations, but it might not be necessary to do it before submission to CRAN.
This is a bit too long as a comment, but hopefully this will give you some ideas for optimising the code for the varzeta* functions; or at the very least, it might give you some food for thought.
There are a few things that confuse me:
All varzeta* functions have arguments beta, gamma and phi, which seem to be matrices. However, in varzeta1 you don't use beta, yet beta is the first function argument.
I struggle to link the details you give at the bottom of your post with the code for the varzeta* functions. You don't explain where the gamma and phi matrices come from, nor what they denote. Furthermore, seeing that beta are the model's parameter etimates, I don't understand why beta should be a matrix.
As I mentioned in my earlier comment, I would be very surprised if these expressions cannot be simplified. R can do a lot of matrix operations quite comfortably, there shouldn't really be a need to pre-calculate individual terms.
For example, you can use crossprod and tcrossprod to calculate cross products, and %*% implements matrix multiplication.
Secondly, a lot of mathematical operations in R are vectorised. I already mentioned that you can simplify
1 - gamma[1,1]^2 - gamma[1,2]^2 - gamma[1,3]^2 - gamma[1,4]^2 - gamma[1,5]^2
as
1 - sum(gamma[1, ]^2)
since the ^ operator is vectorised.
Perhaps more fundamentally, this seems somewhat of an XY problem to me where it might help to take a step back. Not knowing the full details of what you're trying to model (as I said, I can't link the details you give to the cSEM.DGP code), I would start by exploring how to solve the recursive SEM in R. I don't really see the need for Mathematica here. As I said earlier, matrix operations are very standard in R; analytically solving a set of recursive equations is also possible in R. Since you seem to come from the Mathematica realm, it might be good to discuss this with a local R coding expert.
If you must use those scary varzeta* functions (and I really doubt that), an option may be to rewrite them in C++ and then compile them with Rcpp to turn them into R functions. Perhaps that will avoid the C stack usage limit?
I have question that comes from a algorithms book I'm reading and I am stumped on how to solve it (it's been a long time since I've done log or exponent math). The problem is as follows:
Suppose we are comparing implementations of insertion sort and merge sort on the same
machine. For inputs of size n, insertion sort runs in 8n^2 steps, while merge sort runs in 64n log n steps. For which values of n does insertion sort beat merge sort?
Log is base 2. I've started out trying to solve for equality, but get stuck around n = 8 log n.
I would like the answer to discuss how to solve this mathematically (brute force with excel not admissible sorry ;) ). Any links to the description of log math would be very helpful in my understanding your answer as well.
Thank you in advance!
http://www.wolframalpha.com/input/?i=solve%288+log%282%2Cn%29%3Dn%2Cn%29
(edited since old link stopped working)
Your best bet is to use Newton;s method.
http://en.wikipedia.org/wiki/Newton%27s_method
One technique to solving this would be to simply grab a graphing calculator and graph both functions (see the Wolfram link in another answer). Find the intersection that interests you (in case there are multiple intersections, as there are in your example).
In any case, there isn't a simple expression to solve n = 8 log₂ n (as far as I know). It may be simpler to rephrase the question as: "Find a zero of f(n) = n - 8 log₂ n". First, find a region containing the intersection you're interested in, and keep shrinking that region. For instance, suppose you know your target n is greater than 42, but less than 44. f(42) is less than 0, and f(44) is greater than 0. Try f(43). It's less than 0, so try 43.5. It's still less than 0, so try 43.75. It's greater than 0, so try 43.625. It's greater than 0, so keep going down, and so on. This technique is called binary search.
Sorry, that's just a variation of "brute force with excel" :-)
Edit:
For the fun of it, I made a spreadsheet that solves this problem with binary search: binary‑search.xls . The binary search logic is in the second data column, and I just auto-extended that.
I've written an experimental function evaluator that allows me to bind simple functions together such that when the variables change, all functions that rely on those variables (and the functions that rely on those functions, etc.) are updated simultaneously. The way I do this is instead of evaluating the function immediately as it's entered in, I store the function. Only when an output value is requested to I evaluate the function, and I evaluate it each and every time an output value is requested.
For example:
pi = 3.14159
rad = 5
area = pi * rad * rad
perim = 2 * pi * rad
I define 'pi' and 'rad' as variables (well, functions that return a constant), and 'area' and 'perim' as functions. Any time either 'pi' or 'rad' change, I expect the results of 'area' and 'perim' to change in kind. Likewise, if there were any functions depending on 'area' or 'perim', the results of those would change as well.
This is all working as expected. The problem here is when the user introduces recursion - either accidental or intentional. There is no logic in my grammar - it's simply an evaluator - so I can't provide the user with a way to 'break out' of recursion. I'd like to prevent it from happening at all, which means I need a way to detect it and declare the offending input as invalid.
For example:
a = b
b = c
c = a
Right now evaluating the last line results in a StackOverflowException (while the first two lines evaluate to '0' - an undeclared variable/function is equal to 0). What I would like to do is detect the circular logic situation and forbid the user from inputing such a statement. I want to do this regardless of how deep the circular logic is hidden, but I have no idea how to go about doing so.
Behind the scenes, by the way, input strings are converted to tokens via a simple scanner, then to an abstract syntax tree via a hand-written recursive descent parser, then the AST is evaluated. The language is C#, but I'm not looking for a code solution - logic alone will be fine.
Note: this is a personal project I'm using to learn about how parsers and compilers work, so it's not mission critical - however the knowledge I take away from this I do plan to put to work in real life at some point. Any help you guys can provide would be appreciated greatly. =)
Edit: In case anyone's curious, this post on my blog describes why I'm trying to learn this, and what I'm getting out of it.
I've had a similar problem to this in the past.
My solution was to push variable names onto a stack as I recursed through the expressions to check syntax, and pop them as I exited a recursion level.
Before I pushed each variable name onto the stack, I would check if it was already there.
If it was, then this was a circular reference.
I was even able to display the names of the variables in the circular reference chain (as they would be on the stack and could be popped off in sequence until I reached the offending name).
EDIT: Of course, this was for single formulae... For your problem, a cyclic graph of variable assignments would be the better way to go.
A solution (probably not the best) is to create a dependency graph.
Each time a function is added or changed, the dependency graph is checked for cylces.
This can be cut short. Each time a function is added, or changed, flag it. If the evaluation results in a call to the function that is flagged, you have a cycle.
Example:
a = b
flag a
eval b (not found)
unflag a
b = c
flag b
eval c (not found)
unflag b
c = a
flag c
eval a
eval b
eval c (flagged) -> Cycle, discard change to c!
unflag c
In reply to the comment on answer two:
(Sorry, just messed up my openid creation so I'll have to get the old stuff linked later...)
If you switch "flag" for "push" and "unflag" for "pop", it's pretty much the same thing :)
The only advantage of using the stack is the ease of which you can provide detailed information on the cycle, no matter what the depth. (Useful for error messages :) )
Andrew