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Tags
list
3387
2
null
3386
10
null
The UCLA website has a bunch of great tutorials for every procedure broken down by the software type that you're familiar with. Check out [Annotated SPSS Output: Logistic Regression](http://www.ats.ucla.edu/stat/spss/output/logistic.htm) -- the SES variable they mention is categorical (and not binary). SPSS will auto...
null
CC BY-SA 2.5
null
2010-10-07T15:18:08.673
2010-10-07T15:18:08.673
null
null
1499
null
3388
2
null
3386
8
null
Logistic regression is a pretty flexible method. It can readily use as independent variables categorical variables. Most software that use Logistic regression should let you use categorical variables. As an example, let's say one of your categorical variable is temperature defined into three categories: cold/mild/h...
null
CC BY-SA 2.5
null
2010-10-07T15:56:05.430
2010-10-07T15:56:05.430
null
null
1329
null
3389
2
null
3377
3
null
There is also a parametric approach. Ignoring the vector nature of your data, and looking only at the marginals, it suffices to solve the problem: find an online algorithm to compute the mean absolute deviation of scalar $X$. If (and this is the big 'if' here) you thought that $X$ followed some probability distribution...
null
CC BY-SA 2.5
null
2010-10-07T16:27:19.653
2010-10-07T16:27:19.653
null
null
795
null
3390
1
4057
null
11
2726
The [Cornish-Fisher Expansion](http://www.riskglossary.com/link/cornish_fisher.htm) provides a way to estimate the quantiles of a distribution based on moments. (In this sense, I see it as a complement to the [Edgeworth Expansion](http://en.wikipedia.org/wiki/Edgeworth_expansion#Edgeworth_series), which gives an estima...
Why Use the Cornish-Fisher Expansion Instead of Sample Quantile?
CC BY-SA 2.5
null
2010-10-07T17:00:40.833
2017-09-28T18:28:02.507
2017-09-28T18:28:02.507
60613
795
[ "distributions", "quantiles", "finance" ]
3391
2
null
3331
7
null
You could look at the work of [Eamonn Keogh](http://www.cs.ucr.edu/~eamonn/) (UC Riverside) on time series clustering. His website has a lot of resources. I think he provides Matlab code samples, so you'd have to translate this to R.
null
CC BY-SA 2.5
null
2010-10-07T17:42:05.903
2010-10-07T17:45:59.027
2010-10-07T17:45:59.027
930
1436
null
3392
1
3398
null
53
3656
It seems that lots of people (including me) like to do exploratory data analysis in Excel. Some limitations, such as the number of rows allowed in a spreadsheet, are a pain but in most cases don't make it impossible to use Excel to play around with data. [A paper by McCullough and Heiser](http://www.pages.drexel.edu/~b...
Excel as a statistics workbench
CC BY-SA 2.5
null
2010-10-07T17:44:32.840
2022-12-02T14:26:39.963
null
null
666
[ "software", "computational-statistics", "excel" ]
3393
2
null
3294
12
null
There is also a really good book by Oliver Cappe et. al: [Inference in Hidden Markov Models](http://rads.stackoverflow.com/amzn/click/0387402640). However, it is fairly theoretical and very light on the applications. There is another book with examples in R, but I couldn't stand it - [Hidden Markov Models for Time Ser...
null
CC BY-SA 2.5
null
2010-10-07T17:59:07.497
2010-10-07T17:59:07.497
null
null
1499
null
3394
2
null
3392
7
null
Incidently, a question around the use of Google spreadsheets raised contrasting (hence, interesting) opinions about that, [Do some of you use Google Docs spreadsheet to conduct and share your statistical work with others?](https://stats.stackexchange.com/questions/3244/do-some-of-you-use-google-docs-spreadsheet-to-cond...
null
CC BY-SA 4.0
null
2010-10-07T18:15:35.337
2022-12-02T14:26:39.963
2022-12-02T14:26:39.963
362671
930
null
3395
1
3396
null
4
339
I am currently working on a model which takes two parameters and produces a measurement statistic. Think of it as Z = f(X,Y). Z is a matrix of my statistics and I am creating a surface plot of it in matlab. Basically, I am looking for a mathematical/analytical way of determining if the surface is smooth, or if it is j...
Smoothness of a surface
CC BY-SA 2.5
null
2010-10-07T19:21:25.180
2010-10-08T02:43:53.970
2010-10-07T19:23:34.423
930
null
[ "clustering", "smoothing", "matlab", "spatial", "autocorrelation" ]
3396
2
null
3395
4
null
One model for this situation is to view $Z$ as a realization of a stationary 2D stochastic process. The limiting behavior at zero (distance) of its empirical [variogram](http://en.wikipedia.org/wiki/Variogram) or correlogram provides information about its smoothness: if the limiting correlation is less than one, the p...
null
CC BY-SA 2.5
null
2010-10-07T19:52:10.740
2010-10-08T02:43:53.970
2010-10-08T02:43:53.970
8
919
null
3397
2
null
3392
11
null
Well, the question whether the paper is correct or biased should be easy: you could just replicate some of their analyses and see whether you get the same answers. McCullough has been taking different versions of MS Excel apart for some years now, and apparently MS haven't seen fit to fix errors he pointed out years ag...
null
CC BY-SA 2.5
null
2010-10-07T19:57:40.057
2010-10-07T19:57:40.057
null
null
1352
null
3398
2
null
3392
47
null
Use the right tool for the right job and exploit the strengths of the tools you are familiar with. In Excel's case there are some salient issues: - Please don't use a spreadsheet to manage data, even if your data will fit into one. You're just asking for trouble, terrible trouble. There is virtually no protection aga...
null
CC BY-SA 3.0
null
2010-10-07T20:15:27.567
2012-04-03T11:18:05.973
2012-04-03T11:18:05.973
9007
919
null
3399
2
null
3392
7
null
The papers and other participants point out to technical weaknesses. Whuber does a good job of outlining at least some of its strengths. I personally do extensive statistical work in Excel (hypothesis testing, linear and multiple regressions) and love it. I use Excel 2003 with a capacity of 256 columns and 65,000 ro...
null
CC BY-SA 3.0
null
2010-10-07T21:36:51.820
2016-05-26T15:52:14.530
2016-05-26T15:52:14.530
1329
1329
null
3400
1
3411
null
27
6961
Question: From the standpoint of statistician (or a practitioner), can one infer causality using [propensity scores](http://en.wikipedia.org/wiki/Propensity_score) with an observational study (not an experiment)? Please, do not want to start a flame war or a fanatical debate. Background: Within our stat PhD program, we...
From a statistical perspective, can one infer causality using propensity scores with an observational study?
CC BY-SA 2.5
null
2010-10-07T23:27:47.727
2016-12-01T09:49:04.243
null
null
1499
[ "causality", "propensity-scores" ]
3402
1
3403
null
9
699
I'm a newbie at stats, so if I make any mistaken assumptions here please tell me. There's a population `N` of people. (For example `N` can be 1,000,000.) Some of the people are redheads. I take a sample `n` of people (say 10,) and find that `j` of them are redheads. What can I say about the general proportion of redhea...
What's the accuracy of data obtained through a random sample?
CC BY-SA 2.5
null
2010-10-08T00:51:55.783
2010-10-08T23:30:44.833
2010-10-08T02:39:46.587
8
5793
[ "standard-deviation", "sample-size", "binomial-distribution", "standard-error" ]
3403
2
null
3402
8
null
You can think of this as a binomial trial -- your trials are sampling "redhead" or "not readhead". In which case, you can build a confidence interval for your sample proportion ($j/n$) as documented on Wikipedia: - Binomial proportion confidence interval A 95% confidence interval basically says that, using the same...
null
CC BY-SA 2.5
null
2010-10-08T01:01:57.537
2010-10-08T01:12:34.190
2010-10-08T01:12:34.190
251
251
null
3404
2
null
3400
8
null
Only a prospective randomized trial can determine causality. In observational studies, there will always be the chance of an unmeasured or unknown covariate which makes ascribing causality impossible. However, observational trials can provide evidence of a strong association between x and y, and are therefore useful fo...
null
CC BY-SA 2.5
null
2010-10-08T01:39:26.280
2010-10-08T01:39:26.280
null
null
561
null
3405
2
null
3392
20
null
An interesting paper about using Excel in a Bioinformatics setting is: > Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics, BMC Bioinformatics, 2004 (link). This short paper describes the problem of automatic type conversions in Excel (in particular [date...
null
CC BY-SA 2.5
null
2010-10-08T02:35:37.343
2010-10-08T13:01:56.017
2010-10-08T13:01:56.017
919
8
null
3407
1
3410
null
15
4555
I am building an android application that records accelerometer data during sleep, so as to analyze sleep trends and optionally wake the user near a desired time during light sleep. I have already built the component that collects and stores data, as well as the alarm. I still need to tackle the beast of displaying and...
Smoothing time series data
CC BY-SA 4.0
null
2010-10-08T07:59:32.177
2019-01-11T19:04:52.047
2019-01-11T19:04:52.047
79696
1520
[ "time-series", "smoothing", "signal-processing", "java" ]
3408
2
null
3407
10
null
There are many nonparametric smoothing algorithms including splines and loess. But they will smooth out the sudden changes too. So will low-pass filters. I think you might need a wavelet-based smoother which allows the sudden jumps but still smooths the noise. Check out [Percival and Walden (2000)](http://rads.stackove...
null
CC BY-SA 2.5
null
2010-10-08T09:35:30.260
2010-10-08T09:35:30.260
null
null
159
null
3409
2
null
3407
3
null
This is somewhat tangential to what you're asking, but it may be worth taking a look at the Kalman filter.
null
CC BY-SA 2.5
null
2010-10-08T09:54:24.820
2010-10-08T09:54:24.820
null
null
439
null
3410
2
null
3407
16
null
First up, the requirements for compression and analysis/presentation are not necessarily the same -- indeed, for analysis you might want to keep all the raw data and have the ability to slice and dice it in various ways. And what works best for you will depend very much on what you want to get out of it. But there are ...
null
CC BY-SA 2.5
null
2010-10-08T09:57:22.490
2010-10-08T10:11:31.953
2010-10-08T10:11:31.953
174
174
null
3411
2
null
3400
17
null
At the beginning of an article aiming at promoting the use of PSs in epidemiology, Oakes and Church (1) cited Hernán and Robins's claims about confounding effect in epidemiology (2): > Can you guarantee that the results from your observational study are unaffected by unmeasured confounding? The only answer an ep...
null
CC BY-SA 3.0
null
2010-10-08T11:30:29.323
2013-10-30T21:28:34.690
2013-10-30T21:28:34.690
930
930
null
3412
1
3415
null
17
3674
I have an experiment that I'll try to abstract here. Imagine I toss three white stones in front of you and ask you to make a judgment about their position. I record a variety of properties of the stones and your response. I do this over a number of subjects. I generate two models. One is that the nearest stone to...
Comparing mixed effect models with the same number of degrees of freedom
CC BY-SA 2.5
null
2010-10-08T12:34:11.673
2022-09-18T20:11:05.137
2011-03-13T16:27:57.167
601
601
[ "r", "mixed-model", "model-selection" ]
3413
1
3414
null
4
3327
I am looking for the Hurst exponent calculation methodology. Please suggest online materials / methodology papers.
Hurst exponent calculation methodology
CC BY-SA 2.5
null
2010-10-08T13:24:33.177
2015-11-18T14:26:04.613
2015-11-18T14:26:04.613
22468
1250
[ "references", "fractal" ]
3414
2
null
3413
8
null
The calculation is covered on [the related wikipedia page](http://en.wikipedia.org/wiki/Hurst_exponent). R has several implementations for this: - The fArma package provides 10 different functions to estimate the Hurst exponent (see LrdModelling). - The Rwave package has the hurst.est() function. - The fractal packa...
null
CC BY-SA 2.5
null
2010-10-08T13:33:08.560
2010-10-08T15:05:16.480
2010-10-08T15:05:16.480
5
5
null
3415
2
null
3412
9
null
Still, you can compute confidence intervals for your fixed effects, and report AIC or BIC (see e.g. [Cnann et al.](http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.133.2052&rep=rep1&type=pdf), Stat Med 1997 16: 2349). Now, you may be interested in taking a look at [Assessing model mimicry using the parametric ...
null
CC BY-SA 2.5
null
2010-10-08T13:41:22.563
2010-10-08T13:49:37.653
2010-10-08T13:49:37.653
930
930
null
3416
2
null
3412
3
null
I do not know R well enough to parse your code but here is one idea: Estimate a model where you have both center and near as covariates (call this mBoth). Then mCenter and mNear are nested in mBoth and you could use mBoth as a benchmark to compare the relative performance of mCenter and mNear.
null
CC BY-SA 2.5
null
2010-10-08T13:53:52.570
2010-10-08T13:53:52.570
null
null
null
null
3417
2
null
3287
5
null
I'm an ecologist, so I apologise in advance is this sounds a bit strange :-) I like to think of these plots in terms of weighted averages. The region points are at the weighted averages of the smoking status classes and vice versa. The problem with the above figure is the axis scaling and the fact that you can't displa...
null
CC BY-SA 2.5
null
2010-10-08T16:16:58.473
2010-10-08T16:22:10.900
2010-10-08T16:22:10.900
1390
1390
null
3419
1
3673
null
7
452
There are umpteen million research papers regarding relationships between various patient attributes (e.g. how does gene x affect condition y?). What I am interested in though is a distance metric between patients in toto. Sort of like if I were constructing a dating site, I'd want to know how similar two people are. (...
Patient distance metrics
CC BY-SA 2.5
null
2010-10-08T17:52:20.097
2017-11-16T13:21:24.017
2010-10-15T16:18:12.350
900
900
[ "clustering", "biostatistics" ]
3420
2
null
3296
1
null
Addressing the issue mentioned under Update 2. You are dealing with outliers. Those outliers have a significant impact on your Logistic Regression coefficients. By removing them, you found that your models performed better on the validation set. Does it mean that the outliers are "bad"? No. It means that they a...
null
CC BY-SA 2.5
null
2010-10-08T19:38:39.063
2010-10-08T19:38:39.063
null
null
1329
null
3421
2
null
3419
3
null
The whole field of [Cluster Analysis](http://www.amazon.com/s/ref=nb_sb_noss?url=search-alias%3Dstripbooks&field-keywords=Cluster+analysis&x=0&y=0) is relevant to your concept of multi-variable statistical distance. The linked book on the subject is very short and pretty good.
null
CC BY-SA 2.5
null
2010-10-08T20:05:14.780
2010-10-08T20:05:14.780
null
null
1329
null
3422
2
null
3412
12
null
Following ronaf's suggestion leads to a more recent paper by Vuong for a Likelihood Ratio Test on nonnested models. It's based on the KLIC (Kullback-Leibler Information Criterion) which is similar to the AIC in that it minimizes the KL distance. But it sets up a probabilistic specification for the hypothesis so the u...
null
CC BY-SA 4.0
null
2010-10-08T20:58:17.027
2022-06-19T15:54:27.863
2022-06-19T15:54:27.863
361019
251
null
3423
1
null
null
8
412
I'm working on a web app, and I'm creating some data viz tools for it. For one particular series, I've got an extremely wide variance in data values (0 to millions). We're using a column chart to view the data now, which of course results in some columns that are a pixel high or smaller. We already have some ways to sl...
Recommendations for visualization type when data has an extremely wide variance
CC BY-SA 2.5
null
2010-10-08T21:01:20.033
2010-10-09T15:40:21.837
2010-10-09T15:40:21.837
null
1531
[ "data-visualization" ]
3424
2
null
3423
9
null
A standard approach to dealing with data that has a wide variance is to use a [log scale](http://en.wikipedia.org/wiki/Logarithmic_scale) (or some other kind of scaling approach) regardless of the visualization itself. This could be applied in any graphical package (including a JS library like [Protovis](http://vis.st...
null
CC BY-SA 2.5
null
2010-10-08T21:20:22.510
2010-10-08T21:36:33.643
2010-10-08T21:36:33.643
5
5
null
3425
1
3433
null
44
61699
I am not sure how this should be termed, so please correct me if you know a better term. I've got two lists. One of 55 items (e.g: a vector of strings), the other of 92. The item names are similar but not identical. I wish to find the best candidates in the 92 list to the items in the 55 list (I will then go through ...
How to quasi match two vectors of strings (in R)?
CC BY-SA 4.0
null
2010-10-08T21:31:00.867
2020-10-16T16:12:09.383
2018-12-15T23:43:20.467
11887
253
[ "r", "text-mining" ]
3426
2
null
2948
2
null
I've an java implementation for non-overlapping, weighted/unweighted network that could probably handle 3 million nodes (I've tested it for a million node dataset). However, it works like k-means, and needs the number of partitions to be detected as an input (k in kmeans). You can find more info [here](http://www.googl...
null
CC BY-SA 3.0
null
2010-10-08T21:42:44.397
2017-03-01T19:47:15.617
2017-03-01T19:47:15.617
-1
null
null
3427
2
null
3425
15
null
There are many ways to measure distances between two strings. Two important (standard) approaches widely implemented in R are the Levenshtein and the Hamming distance. The former is avalaible in package 'MiscPsycho' and the latter in 'e1071'. Using these, i would simply compute a 92 by 55 matrix of pairwise distances, ...
null
CC BY-SA 2.5
null
2010-10-08T21:45:29.480
2010-10-09T20:14:40.313
2010-10-09T20:14:40.313
603
603
null
3428
2
null
3412
4
null
there is a paper by [d.r.cox](https://projecteuclid.org/ebooks/berkeley-symposium-on-mathematical-statistics-and-probability/Proceedings%20of%20the%20Fourth%20Berkeley%20Symposium%20on%20Mathematical%20Statistics%20and%20Probability,%20Volume%201:%20Contributions%20to%20the%20Theory%20of%20Statistics/chapter/Tests%20of...
null
CC BY-SA 4.0
null
2010-10-08T22:27:14.820
2022-09-18T20:11:05.137
2022-09-18T20:11:05.137
79696
1112
null
3429
2
null
346
12
null
I re-direct you to my answer to a similar [question](https://stats.stackexchange.com/questions/3372/is-it-possible-to-accumulate-a-set-of-statistics-that-describes-a-large-number-of/3376#3376). In a nutshell, it's a read once, 'on the fly' algorithm with $O(n)$ worst case complexity to compute the (exact) median.
null
CC BY-SA 2.5
null
2010-10-08T22:49:46.743
2010-10-08T22:49:46.743
2017-04-13T12:44:55.360
-1
603
null
3430
2
null
3402
0
null
if your sample size $n$ is not such a tiny fraction of the population size $N$ as in your example, and if you sample without replacement [Sw/oR], a better expression for the [estimated] SE is $$\hat{SE} = \sqrt{\frac{N - n}{N}\frac{\hat p \hat q}{n}},$$ where $\hat p$ is the estimated proportion $j/n$ and $\hat q = 1- ...
null
CC BY-SA 2.5
null
2010-10-08T23:11:33.593
2010-10-08T23:30:44.833
2010-10-08T23:30:44.833
1112
1112
null
3431
2
null
3413
3
null
[Octave](http://www.gnu.org/software/octave/) has a built-in Hurst Exponent function.
null
CC BY-SA 2.5
null
2010-10-08T23:53:06.367
2010-10-08T23:53:06.367
null
null
226
null
3432
2
null
3425
7
null
To supplement Kwak's useful answer, allow me to add some simple principles and ideas. A good way to determine the metric is by considering how the strings might vary from their target. "Edit distance" is useful when the variation is a combination of typographic errors like transposing neighbors or mis-typing a single...
null
CC BY-SA 2.5
null
2010-10-09T00:12:17.553
2010-10-09T00:12:17.553
null
null
919
null
3433
2
null
3425
22
null
I've had similar problems. (seen here: [https://stackoverflow.com/questions/2231993/merging-two-data-frames-using-fuzzy-approximate-string-matching-in-r](https://stackoverflow.com/questions/2231993/merging-two-data-frames-using-fuzzy-approximate-string-matching-in-r)) Most of the recommendations that I received fell ar...
null
CC BY-SA 2.5
null
2010-10-09T02:41:55.300
2010-10-09T20:00:20.550
2017-05-23T12:39:26.167
-1
776
null
3434
2
null
3377
4
null
I've used the following approach in the past to calculate absolution deviation moderately efficiently (note, this a programmers approach, not a statisticians, so indubitably there may be clever tricks like [shabbychef's](https://stats.stackexchange.com/questions/3377/online-algorithm-for-mean-absolute-deviation-and-lar...
null
CC BY-SA 2.5
null
2010-10-09T03:27:11.417
2010-11-09T05:33:11.947
2017-04-13T12:44:36.923
-1
179
null
3435
2
null
3425
3
null
I would also suggest you check out [N-grams](http://en.wikipedia.org/wiki/N-gram) and the [Damerau–Levenshtein](http://en.wikipedia.org/wiki/Damerau%E2%80%93Levenshtein_distance) distance besides the other suggestions of Kwak. This [paper](http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.15.178&rep=rep1&type=p...
null
CC BY-SA 2.5
null
2010-10-09T03:32:47.390
2010-10-09T03:32:47.390
null
null
1036
null
3436
2
null
3381
3
null
I would see each histogram as a different model (parametrized by the width). Fitting a smoothing spline or some other kind of smoother for each of the models is simple. You can then do model selection (such as cross-validation) to choose the histogram width that gives the best results, or do model stacking to fit least...
null
CC BY-SA 2.5
null
2010-10-09T09:16:11.677
2010-10-09T09:16:11.677
null
null
1526
null
3437
2
null
3419
3
null
The simple idea is to make PCA and base distance of few first components (yet I don't like this technique because of assumptions it makes). The complex idea is to use machine learning; the resulting distances will expose the classifier structure, so will be about as good as the classification accuracy. The simplest app...
null
CC BY-SA 2.5
null
2010-10-09T11:59:06.653
2010-10-09T11:59:06.653
null
null
null
null
3438
1
3440
null
14
55594
See this Wikipedia page: [Binomial proportion confidence interval](http://en.wikipedia.org/wiki/Binomial_proportion_confidence_interval#Agresti-Coull_Interval). To get the Agresti-Coull Interval, one needs to calculate a percentile of the normal distribution, called $z$. How do I calculate the percentile? Is there a re...
Calculating percentile of normal distribution
CC BY-SA 4.0
null
2010-10-09T13:34:40.713
2020-08-23T04:02:16.183
2020-08-23T04:02:16.183
236645
5793
[ "python", "normal-distribution" ]
3439
2
null
3438
4
null
Well, you didn't ask about R, but in R you do it using ?qnorm (It's actually the quantile, not the percentile, or so I believe) ``` > qnorm(.5) [1] 0 > qnorm(.95) [1] 1.644854 ```
null
CC BY-SA 2.5
null
2010-10-09T13:40:55.500
2010-10-09T13:40:55.500
null
null
253
null
3440
2
null
3438
3
null
For Mathematica `$VersionNumber > 5` you can use ``` Quantile[NormalDistribution[μ, σ], 100 q] ``` for the `q`-th percentile. Otherwise, you have to load the appropriate Statistics package first.
null
CC BY-SA 3.0
null
2010-10-09T14:08:55.643
2017-01-17T09:38:14.200
2017-01-17T09:38:14.200
830
830
null
3441
2
null
3438
4
null
In Python, you can use the [stats](http://www.scipy.org/SciPyPackages/Stats) module from the [scipy](http://www.scipy.org/) package (look for `cdf()`, as in the following [example](http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.norm.html)). (It seems the [transcendantal](http://bonsai.hgc.jp/~mdehoon/s...
null
CC BY-SA 2.5
null
2010-10-09T14:20:58.783
2010-10-09T14:20:58.783
null
null
930
null
3442
2
null
97
28
null
For basic summaries, I agree that reporting frequency tables and some indication about central tendency is fine. For inference, a recent article published in PARE discussed t- vs. MWW-test, [Five-Point Likert Items: t test versus Mann-Whitney-Wilcoxon](http://pareonline.net/pdf/v15n11.pdf). For more elaborated treatmen...
null
CC BY-SA 3.0
null
2010-10-09T15:03:51.913
2014-01-21T21:33:29.013
2014-01-21T21:33:29.013
2921
930
null
3443
2
null
3400
11
null
Propensity scores are typically used in the matching literature. Propensity scores use pre-treatment covariates to estimate the probability of receiving treatment. Essentially, a regression (either just regular OLS or logit, probit, etc) is used to calculate the propensity score with treatment as your outcome and pre-t...
null
CC BY-SA 2.5
null
2010-10-09T16:02:58.157
2010-10-09T18:23:45.387
2010-10-09T18:23:45.387
930
401
null
3444
2
null
3438
21
null
John Cook's page, [Distributions in Scipy](http://www.johndcook.com/distributions_scipy.html), is a good reference for this type of stuff: ``` In [15]: import scipy.stats In [16]: scipy.stats.norm.ppf(0.975) Out[16]: 1.959963984540054 ```
null
CC BY-SA 2.5
null
2010-10-09T16:09:00.780
2010-10-09T16:09:00.780
null
null
251
null
3445
1
null
null
3
10854
I have the following data, which is the output from the [MS Hudson](http://bioinformatics.oxfordjournals.org/content/18/2/337.full.pdf+html) software. ``` segsites: 6 positions: 0.1256 0.3122 0.3218 0.4970 0.5951 0.7943 001010 110101 010100 001010 010100 ``` I want to make an R function to calculate the R-Squa...
How to calculate the pairwise LD for the given data?
CC BY-SA 3.0
null
2010-10-09T16:28:24.350
2017-02-02T21:14:02.180
2013-04-14T10:54:52.443
null
null
[ "r", "correlation", "genetics" ]
3446
1
3454
null
9
2543
I've been looking at some of the packages from the High perf task [view](http://cran.r-project.org/web/views/HighPerformanceComputing.html) dealing with GPU computations, and given that most GPU seem to be an order of magnitude stronger at performing single precision arithmetics than DP [ones](http://en.wikipedia.org/w...
Significance of single precision floating point
CC BY-SA 4.0
null
2010-10-09T17:47:05.413
2020-11-15T18:55:57.833
2020-11-15T18:55:57.833
265676
603
[ "r", "python", "gpu" ]
3447
2
null
3445
4
null
I know the `LDheatmap` function/package can calculate the pairwise LDs, see `ldhm$LDmatrix` in the example below. I'm not familiar with the software you mention or how to get data into the required format for `LDheatmap`. ``` > library(LDheatmap) > data(CEUData) > ldhm <- LDheatmap(CEUSNP, genetic.distances=CEUDist...
null
CC BY-SA 2.5
null
2010-10-09T18:14:22.367
2010-10-09T18:14:22.367
null
null
251
null
3448
2
null
3445
3
null
There are various R/Bioconductor packages that allow you to compute pairwise correlation for SNPs in linkage disequilibrium, see the CRAN Task View [Statistical Genetics](http://cran.r-project.org/web/views/Genetics.html). As I worked directly with whole genome scan, I've been mainly using `snpMatrix`, but [LDheatmap](...
null
CC BY-SA 2.5
null
2010-10-09T18:14:36.530
2010-10-10T14:05:27.840
2010-10-10T14:05:27.840
930
930
null
3449
2
null
134
14
null
#Edit: As @Hunaphu's points out (and @whuber below in his answer) the original answer I gave to the OP (below) is wrong. It is indeed quicker to first sort the initial batch and then keep updating the median up or down (depending on whether a new data points falls to the left or to the right of the current median). --...
null
CC BY-SA 4.0
null
2010-10-09T19:02:09.717
2021-08-19T04:28:21.460
2021-08-19T04:28:21.460
603
603
null
3450
2
null
3400
7
null
The question seems to involve two things that really ought to be considered separately. First is whether one can infer causality from an observational study, and on that you might contrast the views of, say, Pearl (2009), who argues yes so long as you can model the process properly, versus the view @propofol, who will ...
null
CC BY-SA 2.5
null
2010-10-09T19:17:12.947
2010-10-09T19:17:12.947
null
null
96
null
3451
2
null
2849
4
null
I guess the current (econometrics) industry standard for this setting is fixed effects regression. Take a look at the section on panel data in [this paper](http://www-personal.umich.edu/~nicholsa/ciwod.pdf) by Austin Nichols for a concise discussion. For these kinds of analyses you want larger N, typically, though. ...
null
CC BY-SA 2.5
null
2010-10-09T19:40:28.550
2010-10-09T19:40:28.550
null
null
96
null
3452
2
null
3446
6
null
- Because before GPUs there was no practical sense of using single reals; you never have too much accuracy and memory is usually not a problem. And supporting only doubles made R design simpler. (Although R supports reading/writing single reals.) - Yes, because Python is aimed to be more compatible with compiled lang...
null
CC BY-SA 2.5
null
2010-10-09T20:12:24.353
2010-10-09T20:12:24.353
null
null
null
null
3453
2
null
3446
4
null
I presume that by GPU programming, you mean programming nvidia cards? In which case the underlying code calls from R and python are to C/[CUDA](http://en.wikipedia.org/wiki/CUDA). --- The simple reason that only single precision is offered is because that is what most GPU cards support. However, the new nvidia [Fe...
null
CC BY-SA 2.5
null
2010-10-09T20:40:43.653
2010-10-09T20:47:49.703
2010-10-09T20:47:49.703
8
8
null
3454
2
null
3446
5
null
From the [GPUtools help file](http://cran.r-project.org/web/packages/gputools/gputools.pdf), it seems that `useSingle=TRUE` is the default for the functions.
null
CC BY-SA 2.5
null
2010-10-09T22:56:45.643
2010-10-09T22:56:45.643
null
null
251
null
3455
2
null
3446
1
null
The vast majority of GPUs in circulation only support single precision floating point. As far as the title question, you need to look at the data you'll be handling to determine if single precision is enough for you. Often, you'll find that singles are perfectly acceptable for >90% of the data you handle, but will fai...
null
CC BY-SA 2.5
null
2010-10-10T05:22:38.977
2010-10-10T05:22:38.977
null
null
1539
null
3456
2
null
3419
3
null
There is a subfield called Distance Metric Learning. One such method is Information Theoretic Metric Learning (ITML).
null
CC BY-SA 2.5
null
2010-10-10T06:12:37.237
2010-10-10T06:12:37.237
null
null
1540
null
3457
2
null
138
4
null
One more: R bloggers has many posts with tutorials materials: [http://www.r-bloggers.com/?s=tutorial](http://www.r-bloggers.com/?s=tutorial)
null
CC BY-SA 2.5
null
2010-10-10T06:27:50.547
2010-10-10T06:27:50.547
null
null
253
null
3458
1
3459
null
25
12284
I am looking for an alternative to Classification Trees which might yield better predictive power. The data I am dealing with has factors for both the explanatory and the explained variables. I remember coming across random forests and neural networks in this context, although never tried them before, are there another...
Alternatives to classification trees, with better predictive (e.g: CV) performance?
CC BY-SA 2.5
null
2010-10-10T09:27:49.817
2013-10-09T17:51:28.310
2010-10-10T13:24:22.520
null
253
[ "r", "machine-learning", "classification", "cart" ]
3459
2
null
3458
31
null
I think it would be worth giving a try to Random Forests ([randomForest](http://cran.r-project.org/web/packages/randomForest/index.html)); some references were provided in response to related questions: [Feature selection for “final” model when performing cross-validation in machine learning](https://stats.stackexchang...
null
CC BY-SA 3.0
null
2010-10-10T09:50:16.577
2012-05-01T10:48:25.300
2017-04-13T12:44:29.923
-1
930
null
3460
1
3464
null
45
1916
For some of us, refereeing papers is part of the job. When refereeing statistical methodology papers, I think advice from other subject areas is fairly useful, i.e. [computer science](https://cstheory.stackexchange.com/questions/1893/how-do-i-referee-a-paper) and [Maths](https://mathoverflow.net/questions/36596/referee...
Reviewing statistics in papers
CC BY-SA 2.5
null
2010-10-10T09:55:00.890
2010-10-12T09:49:10.387
2017-04-13T12:58:32.177
-1
8
[ "references", "referee" ]
3461
2
null
3458
8
null
For multi-class classification, support vector machines are also a good choice. I typically use the the R kernlab package for this. See the following JSS paper for a good discussion: [http://www.jstatsoft.org/v15/i09/](http://www.jstatsoft.org/v15/i09/)
null
CC BY-SA 2.5
null
2010-10-10T10:19:27.863
2010-10-10T10:19:27.863
null
null
5
null
3462
2
null
3296
3
null
I think you are suffering from the presence of outliers in your design matrix. The remedy is to detect them using a multivariate robust estimator of location/scale (just as you can use the median to detect outliers in an univariate setting but you can't use the mean because the mean itself is sensitive to the presence...
null
CC BY-SA 2.5
null
2010-10-10T11:10:14.780
2010-10-12T15:02:24.580
2010-10-12T15:02:24.580
603
603
null
3463
1
null
null
15
9228
I have two time series S, and T. they have the same frequency and the same length. I would like to calculate (using R), the correlation between this pair (i.e. S and T), and also be able to calculate the significance of the correlation), so I can determine whether the correlation is due to chance or not. I would like t...
Computing correlation (and the significance of said correlation) between a pair of time series
CC BY-SA 2.5
null
2010-10-10T11:11:52.523
2010-10-13T06:37:12.110
null
null
1216
[ "r", "time-series", "correlation" ]
3464
2
null
3460
23
null
I am not sure about which area of science you are referring to (I'm sure the answer would be really different if dealing with biology vs physics for instance...) Anyway, as a biologist, I will answer from a "biological" point of view: > How much effort should we put in to understand the application area? I tend at l...
null
CC BY-SA 2.5
null
2010-10-10T11:27:35.330
2010-10-10T11:33:27.747
2010-10-10T11:33:27.747
582
582
null
3465
2
null
3458
3
null
As already mentioned Random Forests are a natural "upgrade" and, these days, SVM are generally the recommended technique to use. I want to add that more often than not switching to SVM yields very disappointing results. Thing is, whilst techniques like random trees are almost trivial to use, SVM are a bit trickier. ...
null
CC BY-SA 2.5
null
2010-10-10T12:08:40.070
2010-10-10T17:31:45.723
2010-10-10T17:31:45.723
300
300
null
3466
1
3467
null
63
69981
Imagine the following common design: - 100 participants are randomly allocated to either a treatment or a control group - the dependent variable is numeric and measured pre- and post- treatment Three obvious options for analysing such data are: - Test the group by time interaction effect in mixed ANOVA - Do an AN...
Best practice when analysing pre-post treatment-control designs
CC BY-SA 2.5
null
2010-10-10T13:04:18.347
2022-08-21T17:03:50.260
2022-08-21T17:03:50.260
121522
183
[ "ancova", "clinical-trials", "pre-post-comparison", "faq" ]
3467
2
null
3466
43
null
There is a huge literature around this topic (change/gain scores), and I think the best references come from the biomedical domain, e.g. > Senn, S (2007). Statistical issues in drug development. Wiley (chap. 7 pp. 96-112) In biomedical research, interesting work has also been done in the study of [cross-over trials]...
null
CC BY-SA 4.0
null
2010-10-10T13:59:47.777
2020-09-14T18:03:39.107
2020-09-14T18:03:39.107
930
930
null
3471
1
3493
null
0
159
Is it possible to load an S-PLUS Linux workspace in Windows? If I try it I get this error: "Problem in exists(name, where = db): This directory has both Unix style __nonfile and Windows style __nonfi" The __nonfi file is created when I first try to load that Linux workspace in Windows. Is there any way to convert it to...
Load Linux workspace in S-PLUS for Windows
CC BY-SA 2.5
null
2010-10-10T20:35:54.560
2010-10-11T20:27:59.543
null
null
749
[ "splus" ]
3472
2
null
3307
4
null
I doubt you're going to find a single answer to this, given the space of fractal dimensions. Most papers (in physics, geology) looking at correlation simply stick to a Pearson correlation with fractal math reserved for identifying dimension/self-similarity, etc. But you might be interested in the following papers w...
null
CC BY-SA 2.5
null
2010-10-10T21:16:38.417
2010-10-10T21:16:38.417
null
null
251
null
3474
1
3481
null
9
2462
As the title says, I'm looking for the marginal densities of $$f (x,y) = c \sqrt{1 - x^2 - y^2}, x^2 + y^2 \leq 1.$$ So far I have found $c$ to be $\frac{3}{2 \pi}$. I figured that out through converting $f(x,y)$ into polar coordinates and integrating over $drd\theta$, which is why I'm stuck on the marginal densities ...
Finding marginal densities of $f (x,y) = c \sqrt{1 - x^2 - y^2}, x^2 + y^2 \leq 1$
CC BY-SA 3.0
null
2010-10-11T03:48:14.103
2014-03-13T21:55:48.787
2014-03-13T21:55:48.787
919
1545
[ "self-study", "marginal-distribution", "multivariable" ]
3475
2
null
2467
7
null
Caution: I'm assuming that when you said "classification", you are rather referring to cluster analysis (as understood in French), that is an unsupervised method for allocating individuals in homogeneous groups without any prior information/label. It's not obvious to me how class membership might come into play in your...
null
CC BY-SA 3.0
null
2010-10-11T06:30:02.287
2012-02-03T12:00:08.003
2012-02-03T12:00:08.003
930
930
null
3476
1
3477
null
20
180938
Python [matplotlib](http://matplotlib.sourceforge.net/) has a [boxplot command](http://matplotlib.sourceforge.net/api/pyplot_api.html#matplotlib.pyplot.boxplot). Normally, all the parts of the graph are numerically ticked. How can I change the ticks to names instead of positions? For illustration, I mean the Mon Tue We...
How to name the ticks in a python matplotlib boxplot
CC BY-SA 2.5
null
2010-10-11T06:39:50.770
2016-01-27T20:05:46.097
null
null
190
[ "python", "matplotlib" ]
3477
2
null
3476
30
null
Use the second argument of `xticks` to set the labels: ``` import numpy as np import matplotlib.pyplot as plt data = [[np.random.rand(100)] for i in range(3)] plt.boxplot(data) plt.xticks([1, 2, 3], ['mon', 'tue', 'wed']) ``` edited to remove `pylab` bc [pylab is a convenience module that bulk imports matplotlib.pypl...
null
CC BY-SA 3.0
null
2010-10-11T07:12:12.017
2016-01-27T20:05:46.097
2016-01-27T20:05:46.097
94986
251
null
3478
2
null
3460
12
null
My POV would be reviewing a paper in psychology or forecasting on its statistical merits. I'll mostly second Nico's very good remarks. > How much effort should we put in to understand the application area? Quite a lot, actually. I wouldn't trust myself to comment on more than the most basic statistical problems wi...
null
CC BY-SA 2.5
null
2010-10-11T08:09:36.607
2010-10-12T09:49:10.387
2010-10-12T09:49:10.387
1352
1352
null
3479
1
3482
null
11
5005
What is the rationale, if any, to use Discriminant Analysis (DA) on the results of a clustering algorithm like k-means, as I see it from time to time in the literature (essentially on clinical subtyping of mental disorders)? It is generally not recommended to test for group differences on the variables that were used d...
Cluster Analysis followed by Discriminant Analysis
CC BY-SA 2.5
null
2010-10-11T08:37:31.890
2010-10-11T15:10:57.870
null
null
930
[ "clustering", "discriminant-analysis" ]
3480
2
null
3471
2
null
I don't know for certain, but that won't stop me from wildly speculating: The __nonfi file lists what's in the workspace. You can open it with a text editor and look at the contents. It might be possible to either manipulate the unix version (e.g. using dos2unix) or else copy the contents over into your new file. Tha...
null
CC BY-SA 2.5
null
2010-10-11T13:11:51.507
2010-10-11T13:11:51.507
null
null
5
null
3481
2
null
3474
15
null
Geometry helps here. The graph of $f$ is a spherical dome of unit radius. (It follows immediately that its volume is half that of a unit sphere, $(4 \pi /3)/2$, whence $c=3/(2 \pi)$.) The marginal densities are given by areas of vertical cross-sections through this sphere. Obviously each cross-section is a semicirc...
null
CC BY-SA 2.5
null
2010-10-11T14:55:07.220
2010-10-11T14:55:07.220
null
null
919
null
3482
2
null
3479
5
null
I don't know of any papers on this. I've used this approach, for descriptive purposes. DFA provides a nice way to summarize group differences and dimensionality with respect to the original variables. One might more easily just profile the groups on the original variables, however, this loses the inherently multivar...
null
CC BY-SA 2.5
null
2010-10-11T15:10:57.870
2010-10-11T15:10:57.870
null
null
485
null
3483
2
null
3460
17
null
This addresses the new question #6: "What's the maximum number of papers you would review in a year?" I'm responding as a member of several editorial boards. The perennial problem is finding enough reviewers. Depending on the journal, every submitted paper needs one to three peer reviewers, usually three. If the jo...
null
CC BY-SA 2.5
null
2010-10-11T15:35:26.567
2010-10-11T15:56:43.347
2010-10-11T15:56:43.347
919
919
null
3484
1
3487
null
8
7209
I have been looking at analyst job postings and one of the most common requirement is experience of SAS. - Unless your organisation currently uses SAS, how can you train as a SAS user? - What programming language would be equivalent to SAS that employers might be happy to accept?
Obtaining SAS experience
CC BY-SA 2.5
null
2010-10-11T15:42:06.377
2017-02-22T22:44:58.320
null
null
1077
[ "sas", "careers" ]
3485
2
null
3199
4
null
Good question. A trivial way to find "cluster of high values in the upper left" (as opposed to correlations) is to split the image into tiles and look at tile means. For example, ``` means of 100 x 100 tiles: [[ 82 78 80 94 99 100] [ 80 53 66 62 80 100] [ 82 61 65 64 72 98] [ 87 83 99 81 80 100] [...
null
CC BY-SA 2.5
null
2010-10-11T15:46:43.540
2010-10-11T15:46:43.540
null
null
557
null
3487
2
null
3484
5
null
I would recommend going through a self-study course such as the [UCLA website](http://www.ats.ucla.edu/stat/sas/) and specifically the [SAS Starter Kit](http://www.ats.ucla.edu/stat/sas/sk/default.htm). If you learn better within an interactive environment, I would suggest checking out online course offerings such as ...
null
CC BY-SA 2.5
null
2010-10-11T17:08:44.130
2010-10-11T17:37:01.560
2010-10-11T17:37:01.560
1499
1499
null
3488
2
null
3463
6
null
You can use the ccf function to get the cross-correlation, but this will only give you a plot. If the estimated cross correlations fall outside the dash red line, then you can conclude that there is a statistically significant cross-correlation. But I do not know of a package with a formally encapsulated test. Examp...
null
CC BY-SA 2.5
null
2010-10-11T17:17:26.393
2010-10-11T17:17:26.393
2017-04-13T12:44:40.807
-1
1499
null
3489
1
3508
null
6
10089
I have a biometric system that outputs a distribution of scores that resembles a Gaussian distribution (similar to the example graph in the following link: [LINK](http://support.bioid.com/sdk/docs/About_EER.htm)). My point of confusion is how I calculate the False Acceptance Rate. How does threshold factor into the who...
Calculating False Acceptance Rate for a Gaussian Distribution of scores
CC BY-SA 2.5
null
2010-10-11T17:21:37.217
2010-10-20T21:12:08.117
2010-10-20T21:12:08.117
8
1224
[ "bioinformatics" ]
3490
2
null
3484
5
null
As far as SAS goes, getting [certified is resume gold](http://support.sas.com/certify/). The SAS Institute offers [classes and exams](http://support.sas.com/certify/creds/prep.html) to receive the certification. There are also books you can use if you are self-motivated. Getting SAS is quite difficult if your company d...
null
CC BY-SA 2.5
null
2010-10-11T17:27:37.583
2010-10-11T17:27:37.583
null
null
1118
null
3491
2
null
3489
5
null
I'm not certain. I'm curious as to the other responses you get. However, I think you'll need to clarify a bit: Does your Gaussian distribution represent the scores for a population of individuals which should be rejected by your biometric system? If so, then I think you simply need to compute a cumulative probability...
null
CC BY-SA 2.5
null
2010-10-11T17:33:16.783
2010-10-11T17:33:16.783
null
null
1499
null
3492
2
null
3484
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The programming language most similar to SAS is... SAS. Which you can interpret using [WPS, which will run SAS code and evidently costs substantially less than a SAS license](http://en.wikipedia.org/wiki/World_Programming_System) and has [a 30 day free trial](http://www.teamwpc.co.uk/tryorbuy). I haven't used it myse...
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2010-10-11T18:07:43.963
2010-10-11T18:07:43.963
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Tibco support gave me a solution: - Create a new Windows workspace - Attach the Linux workspace attach("C:\\Linux\\Workspace\\Path") - Copy the contents of the Linux workspace to the Windows workspace objs <- objects(2) for (i in objs) assign(i, value=get(i, where=2), where=1) objs <- objects(2, meta=1) for (i in ob...
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2010-10-11T20:27:59.543
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The following provides an inaccurate approximation, although the inaccuracy will depend on the distribution of the input data. It is an online algorithm, but only approximates the absolute deviance. It is based on a [well known algorithm](http://www.johndcook.com/blog/2008/09/26/comparing-three-methods-of-computing-s...
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CC BY-SA 2.5
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2010-10-11T23:15:33.223
2010-11-09T05:36:27.843
2010-11-09T05:36:27.843
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