What is difference between non-stationary and random data. To my understanding, non-stationary data is the one whose mean, variance and co-variance change over time. The same must be true for random data which does not have any fixed mean or variance.
A non-stationary process has a distribution law that varies over time. The fact mean, variance and autocorrelation change over time is a sufficient but not necessary condition.
A random process is just a process whose values cannot be known at the beginning of the process. You can have non-stationary process as well as stationary process.
Related
I have a few questions regarding using a random effect in a GAM. First, how do you interpret and communicate the output graph?
I have fire modeled as a random effect in this GAM because it is largely a random occurrence at my different field sites and I only noted it as a binary. It wouldn't work as a normal variable since it has too few levels and there is also relatively few sites with fire. However, it greatly improved model variance capture when included so I don't want to simply exclude it. I don't know how to interpret the output and I am also not entirely confident that there wouldn't be another way to include it in the model other than as a random effect. Any help would be greatly appreciated!
The effect has been modelled as a random slope if you didn't code it as a factor in the data. The value on the y axis is the estimated slope; it will be a little smaller in absolute value than if you use Fire as a linear fixed effect in the model formula because it is being penalised (shrunk) towards zero.
This likely should have been fitted as a binary fixed effect; code Fire as a factor with two levels (Yes/No, or Burned / Unburned say). Just because a variable represents something that is random over the data doesn't mean it is a suitable random effect; fire here has some average effect and the fixed effect describes that well. There's nothing stopping you from using Fire coded as a factor as a random effect via the smooth, but with only two levels it's not going the two intercepts aren't going to be estimate that precisely.
Now, if you had repeated observations on n sites and you thought the Fire effect varied across the n sites then you could do s(Site, Fire, bs = 're') where both Site and Fire are factors and you'll get different Fire effects for each Site. Then the plot you show would have many points on it as it is a QQ-plot of the estimated values for the effect of Fire in each Site, hence 1 point per Site. Given the way this model is estimated, these are somewhat assumed to be distributed Gaussian with some variance that is inversely proportional to the smoothness parameter selected by gam() when fitting this random effect smoother. That's why the default plot is as it is; it's a QQ-plot comparing the observed distribution of estimate values of the random effects against the theoretical expectation.
I want to design a score or signature function based on a time series signal. Usually, the signal has ups and downs.
For a given time window, I desire to design the score function based on the number of times it fluctuates, the duration of the fluctuations, and the magnitude of the fluctuations. I am wondering what kind of math I can use to design the function. I am not sure if the statistical features (mean, median, and so on) would be enough to design unique function such that two time windows would be distinguishable.
Thanks!
Summary statistics will not give you what you want... but it can still be useful.
Things you can try:
Zero crossings on the signal will give you number of fluctuations. You'll have to use some central tendency value to move the signal about the 0 line in order to do this. Alternatively you can use FFT on the original to find the harmonic frequency as part of the score.
Could define the duration of fluctuations as the difference between zero crossings divided by two (since one fluctuation will reach the 0-line twice).
Magnitude can be done by finding the local minima and maxima - check out some packages with peak finding functions. You might want to use the mean or median to rule out local minima and maxima that fall on the wrong side of the line. Alternatively, finding the zero crossings on the derivative signal and then mapping them back to the original will give you all the local minima and maxima as well.
I have network of approx 8K segments each of 20m. A random poisson process creates a realization on this network. Next I want to add another poisson process but the points from second process should not fall on segments that are already containing points from first process.
Q1> Largely, I am curios to know if points per segments can be defined. My understanding is this is not possible because of the properties of poisson process. But may be there is a optional argument to limit points per segment? I know it is possible to limit number of points on the whole linnet object, but I am wondering if this is possible per segment of linnet.
Q2> I thought of excluding the segments with points from the first process. My understanding is that I cannot exclude segments from a linnet because the the network gets disconnected / disjoint and this is not preferred in spatstat.
Please correct me on these two issues.
Currently I plan to use random poisson but later when some surveys are finished, I will use covariates to model intensity of points.
Thank you.
What do you mean by avoiding locations picked by the first process? If you are just talking about the exact locations it is already very unlikely that a previously picked point will be chosen unless you have massive amounts of data. These are random double precision numbers so there is room for a lot of distinct points along the linear network.
I had a question about solving a weighted interval scheduling problem given a fixed number of classrooms. So, initially, we are given a set of intervals, each with a starting time and finishing time, and each with a weight. So, the aim of the problem is to find a scheduling in two classrooms that maximizes the weight. Is there an efficient way to do this by dynamic programming?
My approach was trivial, since I built an algorithm that simply maximizes the intervals for each classroom. Is there a better way to do this?
My idea is not fully dynamic programming. But I think it will help.
Sort all classes by their starting time.
Now for a class i find next class j which start time is greater or equal then this end time. (Using binary search you can find this because we have an sorted array which is sorted by starting time)
Assume max_so_far is an array and max_so_far[z] contain the max_weight class from z to last
For all i find the max of summation of weight of class[i] and weight max_so_far[j]
Please find the code here
Time complexity of this code is O(nLog(n)).
I feel very confused with the following syntax in jags, for example,
n.iter=100,000
thin=100
n.adapt=100
update(model,1000,progress.bar = "none")
Currently I think
n.adapt=100 means you set the first 100 draws as burn-in,
n.iter=100,000 means the MCMC chain has 100,000 iterations including the burn-in,
I have checked the explanation for this question a lot of time but still not sure whether my interpretation about n.iter and n.adapt is correct and how to understand update() and thinning.
Could anyone explain to me?
This answer is based on the package rjags, which takes an n.adapt argument. First I will discuss the meanings of adaptation, burn-in, and thinning, and then I will discuss the syntax (I sense that you are well aware of the meaning of burn-in and thinning, but not of adaptation; a full explanation may make this answer more useful to future readers).
Burn-in
As you probably understand from introductions to MCMC sampling, some number of iterations from the MCMC chain must be discarded as burn-in. This is because prior to fitting the model, you don't know whether you have initialized the MCMC chain within the characteristic set, the region of reasonable posterior probability. Chains initialized outside this region take a finite (sometimes large) number of iterations to find the region and begin exploring it. MCMC samples from this period of exploration are not random draws from the posterior distribution. Therefore, it is standard to discard the first portion of each MCMC chain as "burn-in". There are several post-hoc techniques to determine how much of the chain must be discarded.
Thinning
A separate problem arises because in all but the simplest models, MCMC sampling algorithms produce chains in which successive draws are substantially autocorrelated. Thus, summarizing the posterior based on all iterations of the MCMC chain (post burn-in) may be inadvisable, as the effective posterior sample size can be much smaller than the analyst realizes (note that STAN's implementation of Hamiltonian Monte-Carlo sampling dramatically reduces this problem in some situations). Therefore, it is standard to make inference on "thinned" chains where only a fraction of the MCMC iterations are used in inference (e.g. only every fifth, tenth, or hundredth iteration, depending on the severity of the autocorrelation).
Adaptation
The MCMC samplers that JAGS uses to sample the posterior are governed by tunable parameters that affect their precise behavior. Proper tuning of these parameters can produce gains in the speed or de-correlation of the sampling. JAGS contains machinery to tune these parameters automatically, and does so as it draws posterior samples. This process is called adaptation, but it is non-Markovian; the resulting samples do not constitute a Markov chain. Therefore, burn-in must be performed separately after adaptation. It is incorrect to substitute the adaptation period for the burn-in. However, sometimes only relatively short burn-in is necessary post-adaptation.
Syntax
Let's look at a highly specific example (the code in the OP doesn't actually show where parameters like n.adapt or thin get used). We'll ask rjags to fit the model in such a way that each step will be clear.
n.chains = 3
n.adapt = 1000
n.burn = 10000
n.iter = 20000
thin = 50
my.model <- jags.model(mymodel.txt, data=X, inits=Y, n.adapt=n.adapt) # X is a list pointing JAGS to where the data are, Y is a vector or function giving initial values
update(my.model, n.burn)
my.samples <- coda.samples(my.model, params, n.iter=n.iter, thin=thin) # params is a list of parameters for which to set trace monitors (i.e. we want posterior inference on these parameters)
jags.model() builds the directed acyclic graph and then performs the adaptation phase for a number of iterations given by n.adapt.
update() performs the burn-in on each chain by running the MCMC for n.burn iterations without saving any of the posterior samples (skip this step if you want to examine the full chains and discard a burn-in period post-hoc).
coda.samples() (from the coda package) runs the each MCMC chain for the number of iterations specified by n.iter, but it does not save every iteration. Instead, it saves only ever nth iteration, where n is given by thin. Again, if you want to determine your thinning interval post-hoc, there is no need to thin at this stage. One advantage of thinning at this stage is that the coda syntax makes it simple to do so; you don't have to understand the structure of the MCMC object returned by coda.samples() and thin it yourself. The bigger advantage to thinning at this stage is realized if n.iter is very large. For example, if autocorrelation is really bad, you might run 2 million iterations and save only every thousandth (thin=1000). If you didn't thin at this stage, you (and your RAM) would need to manipulate an object with three chains of two million numbers each. But by thinning as you go, the final object only has 2 thousand numbers in each chain.