So I am stuck on this problem for a long time.
I was think I should first create the two functions, like this:
n = runif(10000)
int sum = 0
estimator1_fun = function(n){
for(i in 1:10000){
sum = sum + ((n/i)*runif(1))
)
return (sum)
}
and do the same for the other function, and use the mse formula? Am I even approaching this correctly? I tried formatting it, but found that using an image would be better.
Assuming U(0,Theta_0) is the uniform distribution from 0 to Theta_0, and that Theta_0 is a fixed constant, I would proceed as follows:
1. Define Theta_0. Give it a fixed value.
2. Write the function that gives a random number from that distribution
- The distribution function is runif(0,Theta_0).
- Arguments could be Theta_0 and N.
3. Sample it a few thousand (or whatever) times into a vector X.
4. Calculate the two estimates.
5. Repeat steps 3 & 4 for more samples
6. Plot the two estimates against the number of samples and
see if it is approaching Theta_0
I have a problem using fisher’s exact test in R with a simulated p-value, but I don’t know if it’s a caused by “the technique” ( R ) or if it is (statistically) intended to work that way.
One of the datasets I want to work with:
matrix(c(103,0,2,1,0,0,1,0,3,0,0,3,0,0,0,0,0,0,19,3,57,11,2,87,1,2,0,869,4,2,8,1,4,3,18,16,5,60,60,42,1,1,1,1,21,704,40,759,404,151,1491,9,40,144),ncol=2,nrow=27)
The resulting p-value is always the same, no matter how often I repeat the test:
p = 1 / (B+1)
(B = number of replicates used in the Monte Carlo test)
When I shorten the matrix it works if the number of rows is lower than 19. Nevertheless it is not a matter of number of cells in the matrix. After transforming it into a matrix with 3 columns it still does not work, although it does when using the same numbers in just two columns.
Varying simulated p-values:
>a <- matrix(c(103,0,2,1,0,0,1,0,3,0,0,3,0,0,0,0,0,0,869,4,2,8,1,4,3,18,16,5,60,60,42,1,1,1,1,21),ncol=2,nrow=18)
>b <- matrix(c(103,0,2,1,0,0,1,0,3,0,0,3,0,0,0,0,0,0,19,869,4,2,8,1,4,3,18,16,5,60,60,42,1,1,1,1,21,704),ncol=2,nrow=19)
>c <- matrix(c(103,0,2,1,0,0,1,0,3,0,0,3,0,0,0,0,0,0,869,4,2,8,1,4,3,18,16,5,60,60,42,1,1,1,1,21),ncol=3,nrow=12)
>fisher.test(a,simulate.p.value=TRUE)$p.value
Number of cells in a and b are the same, but the simulation only works with matrix a.
Does anyone know if it is a statistical issue or a R issue and, if so, how it could be solved?
Thanks for your suggestions
I think that you are just seeing a very significant result. The p-value is being computed as the number of simulated (and the original) matrices that are as extreme or more extreme than the original. If none of the randomly generated matrices are as or more extreme then the p-value will just be 1 (the original matrix is as extreme as itself) divided by the total number of matrices which is $B+1$ (the B simulated and the 1 original matrix). If you run the function with enough samples (high enough B) then you will start to see some of the random matrices as or more extreme and therefor varying p-values, but the time to do so is probably not reasonable.
p1 <- c(.25,.025,.025,.1,.2,.4)
T <- sample(1:6,size=N,replace=TRUE, prob=someprobabilityvector)
Y <- rbinom(N,1,p1[c(T)])
HI folks, I am new to R and programming in general and need some help with understanding sth basic. could someone explain to me one what is happening in vector Y above. I figure out what p1[c(T)] does above. But have no idea what vector Y is doing. All help is appreciated in advance.
The first line of your code creates a vector of six probabilities:
p1 <- c(.25,.025,.025,.1,.2,.4)
In the second line, you randomly choose N values from the numbers one to six (with replacement). The probability for each value is specified in someprobabilityvector. Hence, the function will return a vector of length N including values between 1 and 6
T <- sample(1:6,size=N,replace=TRUE, prob=someprobabilityvector)
In the third line, N random numbers from a binomial distribution with one trial and probablities specified in p1[c(T)] are generated. c(T) is the same as T: the vector including values from 1 to 6. The vector is used for indexing the vector p1. Hence, p1[c(T)] will return a vector including N values from vector p1.
Y <- rbinom(N,1,p1[c(T)])
Since the specified binomial distribution has one trial only, the vector Y will contain zeroes and ones.
I am new to R and cointegration so please have patience with me as I try to explain what it is that I am trying to do. I am trying to find cointegrated variables among 1500-2000 voltage variables in the west power system in Canada/US. THe frequency is hourly (common in power) and cointegrated combinations can be as few as N variables and a maximum of M variables.
I tried to use ca.jo but here are issues that I ran into:
1) ca.jo (Johansen) has a limit to the number of variables it can work with
2) ca.jo appears to force the first variable in the y(t) vector to be the dependent variable (see below).
Eigenvectors, normalised to first column: (These are the cointegration relations)
V1.l2 V2.l2 V3.l2
V1.l2 1.0000000 1.0000000 1.0000000
V2.l2 -0.2597057 -2.3888060 -0.4181294
V3.l2 -0.6443270 -0.6901678 0.5429844
As you can see ca.jo tries to find linear combinations of the 3 variables but by forcing the coefficient on the first variable (in this case V1) to be 1 (i.e. the dependent variable). My understanding was that ca.jo would try to find all combinations such that every variable is selected as a dependent variable. You can see the same treatment in the examples given in the documentation for ca.jo.
3) ca.jo does not appear to find linear combinations of fewer than the number of variables in the y(t) vector. So if there were 5 variables and 3 of them are cointegrated (i.e. V1 ~ V2 + V3) then ca.jo fails to find this combination. Perhaps I am not using ca.jo correctly but my expectation was that a cointegrated combination where V1 ~ V2 + V3 is the same as V1 ~ V2 + V3 + 0 x V4 + 0 x V5. In other words the coefficient of the variable that are NOT cointegrated should be zero and ca.jo should find this type of combination.
I would greatly appreciate some further insight as I am fairly new to R and cointegration and have spent the past 2 months teaching myself.
Thank you.
I have also posted on nabble:
http://r.789695.n4.nabble.com/ca-jo-cointegration-multivariate-case-tc3469210.html
I'm not an expert, but since no one is responding, I'm going to try to take a stab at this one.. EDIT: I noticed that I just answered to a 4 year old question. Hopefully it might still be useful to others in the future.
Your general understanding is correct. I'm not going to go in great detail about the whole procedure but will try to give some general insight. The first thing that the Johansen procedure does is create a VECM out of the VAR model that best corresponds to the data (This is why you need the lag length for the VAR as input to the procedure as well). The procedure will then investigate the non-lagged component matrix of the VECM by looking at its rank: If the variables are not cointegrated then the rank of the matrix will not be significantly different from 0. A more intuitive way of understanding the johansen VECM equations is to notice the comparibility with the ADF procedure for each distinct row of the model.
Furthermore, The rank of the matrix is equal to the number of its eigenvalues (characteristic roots) that are different from zero. Each eigenvalue is associated with a different cointegrating vector, which
is equal to its corresponding eigenvector. Hence, An eigenvalue significantly different
from zero indicates a significant cointegrating vector. Significance of the vectors can be tested with two distinct statistics: The max statistic or the trace statistic. The trace test tests the null hypothesis of less than or equal to r cointegrating vectors against the alternative of more than r cointegrating vectors. In contrast, The maximum eigenvalue test tests the null hypothesis of r cointegrating vectors against the alternative of r + 1 cointegrating vectors.
Now for an example,
# We fit data to a VAR to obtain the optimal VAR length. Use SC information criterion to find optimal model.
varest <- VAR(yourData,p=1,type="const",lag.max=24, ic="SC")
# obtain lag length of VAR that best fits the data
lagLength <- max(2,varest$p)
# Perform Johansen procedure for cointegration
# Allow intercepts in the cointegrating vector: data without zero mean
# Use trace statistic (null hypothesis: number of cointegrating vectors <= r)
res <- ca.jo(yourData,type="trace",ecdet="const",K=lagLength,spec="longrun")
testStatistics <- res#teststat
criticalValues <- res#criticalValues
# chi^2. If testStatic for r<= 0 is greater than the corresponding criticalValue, then r<=0 is rejected and we have at least one cointegrating vector
# We use 90% confidence level to make our decision
if(testStatistics[length(testStatistics)] >= criticalValues[dim(criticalValues)[1],1])
{
# Return eigenvector that has maximum eigenvalue. Note: we throw away the constant!!
return(res#V[1:ncol(yourData),which.max(res#lambda)])
}
This piece of code checks if there is at least one cointegrating vector (r<=0) and then returns the vector with the highest cointegrating properties or in other words, the vector with the highest eigenvalue (lamda).
Regarding your question: the procedure does not "force" anything. It checks all combinations, that is why you have your 3 different vectors. It is my understanding that the method just scales/normalizes the vector to the first variable.
Regarding your other question: The procedure will calculate the vectors for which the residual has the strongest mean reverting / stationarity properties. If one or more of your variables does not contribute further to these properties then the component for this variable in the vector will indeed be 0. However, if the component value is not 0 then it means that "stronger" cointegration was found by including the extra variable in the model.
Furthermore, you can test test significance of your components. Johansen allows a researcher to test a hypothesis about one or more
coefficients in the cointegrating relationship by viewing the hypothesis as
a restriction on the non-lagged component matrix in the VECM. If there exist r cointegrating vectors, only these linear combinations or linear transformations of them, or combinations of the cointegrating vectors, will be stationary. However, I'm not aware on how to perform these extra checks in R.
Probably, the best way for you to proceed is to first test the combinations that contain a smaller number of variables. You then have the option to not add extra variables to these cointegrating subsets if you don't want to. But as already mentioned, adding other variables can potentially increase the cointegrating properties / stationarity of your residuals. It will depend on your requirements whether or not this is the behaviour you want.
I've been searching for an answer to this and I think I found one so I'm sharing with you hoping it's the right solution.
By using the johansen test you test for the ranks (number of cointegration vectors), and it also returns the eigenvectors, and the alphas and betas do build said vectors.
In theory if you reject r=0 and accept r=1 (value of r=0 > critical value and r=1 < critical value) you would search for the highest eigenvalue and from that build your vector. On this case, if the highest eigenvalue was the first, it would be V1*1+V2*(-0.26)+V3*(-0.64).
This would generate the cointegration residuals for these variables.
Again, I'm not 100%, but preety sure the above is how it works.
Nonetheless, you can always use the cajools function from the urca package to create a VECM automatically. You only need to feed it a cajo object and define the number of ranks (https://cran.r-project.org/web/packages/urca/urca.pdf).
If someone could confirm / correct this, it would be appreciated.
Consider a vector V riddled with noisy elements. What would be the fastest (or any) way to find a reasonable maximum element?
For e.g.,
V = [1 2 3 4 100 1000]
rmax = 4;
I was thinking of sorting the elements and finding the second differential {i.e. diff(diff(unique(V)))}.
EDIT: Sorry about the delay.
I can't post any representative data since it contains 6.15e5 elements. But here's a plot of the sorted elements.
By just looking at the plot, a piecewise linear function may work.
Anyway, regarding my previous conjecture about using differentials, here's a plot of diff(sort(V));
I hope it's clearer now.
EDIT: Just to be clear, the desired "maximum" value would be the value right before the step in the plot of the sorted elements.
NEW ANSWER:
Based on your plot of the sorted amplitudes, your diff(sort(V)) algorithm would probably work well. You would simply have to pick a threshold for what constitutes "too large" a difference between the sorted values. The first point in your diff(sort(V)) vector that exceeds that threshold is then used to get the threshold to use for V. For example:
diffThreshold = 2e5;
sortedVector = sort(V);
index = find(diff(sortedVector) > diffThreshold,1,'first');
signalThreshold = sortedVector(index);
Another alternative, if you're interested in toying with it, is to bin your data using HISTC. You would end up with groups of highly-populated bins at both low and high amplitudes, with sparsely-populated bins in between. It would then be a matter of deciding which bins you count as part of the low-amplitude group (such as the first group of bins that contain at least X counts). For example:
binEdges = min(V):1e7:max(V); % Create vector of bin edges
n = histc(V,binEdges); % Bin amplitude data
binThreshold = 100; % Pick threshold for number of elements in bin
index = find(n < binThreshold,1,'first'); % Find first bin whose count is low
signalThreshold = binEdges(index);
OLD ANSWER (for posterity):
Finding a "reasonable maximum element" is wholly dependent upon your definition of reasonable. There are many ways you could define a point as an outlier, such as simply picking a set of thresholds and ignoring everything outside of what you define as "reasonable". Assuming your data has a normal-ish distribution, you could probably use a simple data-driven thresholding approach for removing outliers from a vector V using the functions MEAN and STD:
nDevs = 2; % The number of standard deviations to use as a threshold
index = abs(V-mean(V)) <= nDevs*std(V); % Index of "reasonable" values
maxValue = max(V(index)); % Maximum of "reasonable" values
I would not sort then difference. If you have some reason to expect continuity or bounded change (the vector is of consecutive sensor readings), then sorting will destroy the time information (or whatever the vector index represents). Filtering by detecting large spikes isn't a bad idea, but you would want to compare the spike to a larger neighborhood (2nd difference effectively has you looking within a window of +-2).
You need to describe formally the expected information in the vector, and the type of noise.
You need to know the frequency and distribution of errors and non-errors. In the simplest model, the elements in your vector are independent and identically distributed, and errors are all or none (you randomly choose to store the true value, or an error). You should be able to figure out for each element the chance that it's accurate, vs. the chance that it's noise. This could be very easy (error data values are always in a certain range which doesn't overlap with non-error values), or very hard.
To simplify: don't make any assumptions about what kind of data an error produces (the worst case is: you can't rule out any of the error data points as ridiculous, but they're all at or above the maximum among non-error measurements). Then, if the probability of error is p, and your vector has n elements, then the chance that the kth highest element in the vector is less or equal to the true maximum is given by the cumulative binomial distribution - http://en.wikipedia.org/wiki/Binomial_distribution
First, pick your favorite method for identifying outliers...
If you expect the numbers to come from a normal distribution, you can use a say 2xsd (standard deviation) above the mean to determine your max.
Do you have access to bounds of your noise-free elements. For example, do you know that your noise-free elements are between -10 and 10 ?
In that case, you could remove noise, and then find the max
max( v( find(v<=10 & v>=-10) ) )