I am trying to solve a numerical equation in R but would want a method which perform similar to vpasolve in Matlab. I have a non linear equation (involving lot of log functions) which when solve in R with uniroot gives me complete different answer compared to what vpasolve gives in matlab.
First, a word of caution: it's often much more productive to learn that there's a better way to do something than the way you are used to doing.
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I went back to MATLAB and realized that the "vpa" collection is using extended precision. Is that absolutely necessary for your purposes? If not, then my suggestions below may suffice.
If you do require extended precision, then perhaps Rmpfr::unirootR function will suffice. I would like to point out that, since all these solvers are generating an approximate solution (as opposed to analytic), the use of extended precision operations seems a bit pointless.
Next, you need to determine whether MATLAB::vpasolve or uniroot is getting you the correct answer. Or maybe you simply are converging to a root that's not the one you want, in which case you need to read up on setting limits on the starting conditions or the search region.
Finally, in addition to uniroot, I recommend you learn to use the R packages BBsolve , nleqslv, rootsolve, and ktsolve (disclaimer: I am the owner and maintainer of ktsolve). These packages are pretty flexible and may lead you to better solutions to your original problem.
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As far as I understand R's nonlinear equation solver nleqslv(x, fn) finds only one solution of the nonlinear equation.
However (as Bhas commented) searchZeros function (the same package) can find my solutions depending on the starting points.
Question: are there some function in R which can help choosing the set of initial points for searchZeros ,which will help me to find all the solutions ?
I am interested in the case of function with several variables.
I undestand that solution to be found pretty much depends on the initial approximation. So the brute force way is to check some reasonable grid of intial approximations. However there might be some more intelligent way to get all the solutions ?
This is quite a general question, but I have not been able to find a solution so far.
I am trying to solve a problem of combinatorial optimization in which I have several objective functions to optimize, as well as several constraints to impose. I am thus trying to find some software (an R package preferably) that can solve this problem.
I have explored several options, but none of them seems to be useful for my purpose: lpSolveAPI is aimed for linear programming only, which is not the case; mco can minimize a multidimensional objective function, but does not seem to be able to manage binary (i.e. decision) variables, needed for combinatorial problems; adagio and CEGO can deal with combinatorial optimization problems, but as far as I can see they can only optimize a single unidimensional function.
Is there any other package I am not aware of that can handle this type of problem? Or any of the aforementioned may be useful, though I may be missing the way to the functionality I need?
Thank you so much in advance with this. It is being really a nightmare trying to find this out.
I need to solve (many times, for lots of data, alongside a bunch of other things) what I think boils down to a second order cone program. It can be succinctly expressed in CVX something like this:
cvx_begin
variable X(2000);
expression MX(2000);
MX = M * X;
minimize( norm(A * X - b) + gamma * norm(MX, 1) )
subject to
X >= 0
MX((1:500) * 4 - 3) == MX((1:500) * 4 - 2)
MX((1:500) * 4 - 1) == MX((1:500) * 4)
cvx_end
The data lengths and equality constraint patterns shown are just arbitrary values from some test data, but the general form will be much the same, with two objective terms -- one minimizing error, the other encouraging sparsity -- and a large number of equality constraints on the elements of a transformed version of the optimization variable (itself constrained to be non-negative).
This seems to work pretty nicely, much better than my previous approach, which fudges the constraints something rotten. The trouble is that everything else around this is happening in R, and it would be quite a nuisance to have to port it over to Matlab. So is doing this in R viable, and if so how?
This really boils down to two separate questions:
1) Are there any good R resources for this? As far as I can tell from the CRAN task page, the SOCP package options are CLSCOP and DWD, which includes an SOCP solver as an adjunct to its classifier. Both have similar but fairly opaque interfaces and are a bit thin on documentation and examples, which brings us to:
2) What's the best way of representing the above problem in the constraint block format used by these packages? The CVX syntax above hides a lot of tedious mucking about with extra variables and such, and I can just see myself spending weeks trying to get this right, so any tips or pointers to nudge me in the right direction would be very welcome...
You might find the R package CVXfromR useful. This lets you pass an optimization problem to CVX from R and returns the solution to R.
OK, so the short answer to this question is: there's really no very satisfactory way to handle this in R. I have ended up doing the relevant parts in Matlab with some awkward fudging between the two systems, and will probably migrate everything to Matlab eventually. (My current approach predates the answer posted by user2439686. In practice my problem would be equally awkward using CVXfromR, but it does look like a useful package in general, so I'm going to accept that answer.)
R resources for this are pretty thin on the ground, but the blog post by Vincent Zoonekynd that he mentioned in the comments is definitely worth reading.
The SOCP solver contained within the R package DWD is ported from the Matlab solver SDPT3 (minus the SDP parts), so the programmatic interface is basically the same. However, at least in my tests, it runs a lot slower and pretty much falls over on problems with a few thousand vars+constraints, whereas SDPT3 solves them in a few seconds. (I haven't done a completely fair comparison on this, because CVX does some nifty transformations on the problem to make it more efficient, while in R I'm using a pretty naive definition, but still.)
Another possible alternative, especially if you're eligible for an academic license, is to use the commercial Mosek solver, which has an R interface package Rmosek. I have yet to try this, but may give it a go at some point.
(As an aside, the other solver bundled with CVX, SeDuMi, fails completely on the same problem; the CVX authors aren't kidding when they suggest trying multiple solvers. Also, in a significant subset of cases, SDTP3 has to switch from Cholesky to LU decomposition, which makes the processing orders of magnitude slower, with only very marginal improvement in the objective compared to the pre-LU steps. I've found it worth reducing the requested precision to avoid this, but YMMV.)
There is a new alternative: CVXR, which comes from the same people.
There is a website, a paper and a github project.
Disciplined Convex Programming seems to be growing in popularity observing cvxpy (Python) and Convex.jl (Julia), again, backed by the same people.
Basically I have created two MATLAB functions which involve some basic signal processing and I need to describe how these functions work in a written report. It specifically requires me to describe the algorithms using mathematical notation.
Maths really isn't my strong point at all, in fact I'm quite surprised I've even been able to develop the functions in the first place. I'm quite worried about the situation at the moment, it's the last section of writing I need to complete but it is crucially important.
What I want to know is whether I'm going to have to grab a book and teach myself mathematical notation in a very short space of time or is there possibly an easier/quicker way to learn? (Yes I know reading a book should be simple enough, but maths + short time frame = major headache + stress)
I've searched through some threads on here already but I really don't know where to start!
Although your question is rather vague, and I have no idea what sorts of algorithms you have coded that you are trying to describe in equation form, here are a few pointers that may help:
Check the MATLAB documentation: If you are using built-in MATLAB functions, they will sometimes give an equation in the documentation that describes what they are doing internally. Some examples are the functions CONV, CORRCOEF, and FFT. If the function is rather complicated, it may not have an equation but instead have links to some papers describing the algorithm, which may themselves have equations for the algorithm. An example is the function HILBERT (which you can also find equations for on Wikipedia).
Find some lists of common mathematical symbols: Some standard symbols used to represent common mathematical operations can be found here.
Look at some sample pseudocode to see how it's done: For algorithms you yourself have coded up, you'll have to write them out in equation or pseudocode form. A paper that I've used often in my work is Templates for the Solution of Linear Systems, and it has some examples of pseudocode that may be helpful to you. I would suggest first looking at the list of symbols used in that paper (on page iv) to see some typical notations used to represent various mathematical operations. You can then look at some of the examples of pseudocode throughout the rest of the document, such as in the box on page 8.
I suggest that you learn a little bit of LaTeX and investigate Matlab's publish feature. You only need to learn enough LaTeX to write mathematical expressions. Then you have to write Matlab comments in your source file in LaTeX, but only for the bits you want to look like high-quality maths. Finally, open the Matlab editor on your .m file, and select File | Publish.
See Very Quick Intro to LaTeX and check your Matlab documentation for publish.
In addition to the answers already here, I would strongly advise using words in addition to forumlae in your report to describe the maths that you are presenting.
If I were marking a student's report and they explained the concepts of what they were doing correctly, but had poor or incorrect mathematical notation to back it up: this would lose them some marks, but would hopefully not impede my understanding of the hard work they've put in.
If they had poor/wrong maths, with no explanation of what they meant to say, this could jeapordise my understanding of their entire project and cost them a passing grade.
The reason you haven't found any useful threads is because most of the time, people are trying to turn maths into algorithms, not vice versa!
Starting from an arbitrary algorithm, sometimes pseudo-code, along with suitable comments, is the clearest (and possibly only) representation.
I would like to know if there is a package in R handling non linear integer optimization.
"Basically", I would like to solve the following problem:
max f(x) s.t x in (0,10) and x is integer.
I know that some branching algorithms are able to handle the linear version of this problem, but here my function f() might be more complicated. (I can't even make sure it would be quadratic of the form f(x)=xQx).
I guess there is always the brute force solution to test all the possibilities as long as they are bounded, but I was wondering if there wasn't anything smarter.
I have a few options for you, but none of them is the silver bullet, although it looks like your silver bullet is in the works under the rino project: http://r-forge.r-project.org/projects/rino/.
Since your function is complicated, you may want to use a genetic algorithm (i.e., gradient-based optimizers may not be reliable). genoud in the rgenoud library may do the trick (link text). If you set data.type.int=TRUE it should do the trick. I have not used this library, but have some experience with GAs in matlab and the time to convergence is sensitive to the settings, so you'll be well served to read the man page a few times through.
Or, if your function in strictly concave (unlikely, since you say it may be complicated) you can solve with a gradient solver (e.g., optim) then check the neighborhood around the optimum (can't be more than 2^n points to check).
Sorry, I can't be of more help.
If it is hardly nonlinear there is no better method than brute force (you will never know if the minimum is local or if some flat-looking fragment doesn't have any narrow and deep valleys), except of course symbolic computation (which probably won't work because the function is too complicated) or soft computing, I mean things like genetic algorithms, Monte-Carlo, swarms, etc. (here you don't have a guarantee that it will find the very global minimum and because you have integer x it can be slower than brute force).
http://cran.r-project.org/web/views/Optimization.html lists the packages Rdonlp2 and Rsolnp which may be suitable.
Discrete filled function method is one of the recent methods that can find global solution of nonlinear integer programming with about 100 constraints and variables.