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Questions tagged [software]

Make sure your question is related to STATISTICS, MACHINE LEARNING, or DATA ANALYSIS and is not solely about programming, support, or bugs. Include additional tags referring to the statistical issues involved.

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9
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3answers
2k views

How do you go from paper to code?

My background is in Computational Biology, although I am a Biologist by training. I just recently started my PhD, and while I have a strong interest/curiosity in Computational Biostatistics/...
0
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0answers
14 views

Code availability for Bayesian inference based resolution of Simpson’s Paradox

I went though this blog. It describes how to compute the effect of an intervention involving a situation like Simpson’s Paradox. They are basically trying to answer a what-if question and they show ...
0
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0answers
21 views

How to determine number of boost for calculating Krippendorff’s Alpha?

I'm using the SPSS macro for computing Krippendorff’s Alpha, developed by Andrew F. Hayes & Klaus Krippendorff. One argument needed is the units of bootstrapping, and I did not find formula for ...
2
votes
0answers
81 views

How to calculate two-way mixed ICC?

I want to calculate ICC for two-way mixed model, single rater, and either for consistency and absolute agreement. I found two packages for calculating ICC (intra-class correlation coefficient), that ...
5
votes
1answer
81 views

Estimate parameter in $x(t) = A \cdot \sin{\left(\omega \cdot t + \varphi \right)} + A_0$ through least squares method

I have a bunch of data $(x_i, \, t_i)$ that is expected to distribute like $x(t) = A \cdot \sin{\left(\omega \cdot t + \varphi \right)} + A_0$. Now I have to estimate the four parameters $(A, \, \...
0
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0answers
12 views

SAS: joint model with proc glimmix

I am attempting to perform a joint generalized linear mixed model with one binary variable and one continuous variable with proc glimmix. The preferred random effects structure for my binary variable ...
5
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0answers
79 views

Official name of a common type of Bayesian simulation study

There is a kind of simulation study that is commonly used to validate an implementation of a Bayesian model: For independent replication $i = 1, ..., n$: Draw a set of "true" parameters ...
0
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0answers
21 views

Do people use "textbook backpropagation" when training neural network?

I know two references on the inner details of backpropagation, Chapter 13, an Introduction to Optimization, 4th edition, Edwin Chong and Stanislaw Zak, 2013 Chapter 7, Learning from Data by Abu ...
8
votes
2answers
840 views

Generating random samples obeying the exponential distribution with a given min and max

Random samples obeying the exponential distribution can be generated by the inverse sampling technique by using the quantile function of the exponential distribution: $$ x = F^{-1}(u) = - \frac{1}{\...
2
votes
1answer
46 views

Linear regression with only unique value pairs?

Does it every make sense to discard duplicate value pairs and only perform the linear regression on unique value pairs? I've never heard of using such a method, so I wanted to see if I'm missing ...
3
votes
1answer
31 views

Can you perform dose-response meta-analysis with only two studies?

Currently, I am conducting a meta-analysis on the association between BMI and prognosis. I discovered that the studies used various cut-offs. However, only two studies are eligible for dose-response ...
1
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0answers
144 views

Bayesian Regression with ARIMA errors

Is there a framework (e.g. R package) which allows for Bayesian estimation of dynamic regression models with AR(I)MA errors (similar to the frequentist implementation in the ...
1
vote
0answers
20 views

Conditional probabilities from two data sets using software

I am working on a project where I have two pieces of information for each individual $i$, $x_i$ and $y_i$. There are $n$ individuals in total. I want to find the probability that $y_i \geq y_j$ given $...
2
votes
0answers
446 views

R alternative to scikit-learn [closed]

As a statics researcher, I've been using R since university and I know it quite well, I also know that it's immediate, but it quickly gets chaotic, and this also happens because of the variety and ...
0
votes
0answers
13 views

Why would we use different output and recurrent activations in an LSTM? [duplicate]

I am developing a LSTM network with Tensorflow. The Tensorflow LSTM documentation shows that there are different activations for the output of the timestep (tanh) and for the data flowing back in to ...
0
votes
1answer
18 views

Frequency of a value in R [closed]

If there is a data set in R and I want know how many of one value is in it, is there a command for this? thanks
1
vote
1answer
22 views

Software for multiple logistic regression analysis

Which free and easy to use statistical software can I use to perform a multiple logistic regression analysis?
0
votes
0answers
60 views

Courses or sources to learn ANOVA

What sources would you recommend to learn ANOVA (with and without software)? What are the prerequisites? If you could recommend me a complete course, online or books (I'd prefer videos but books/...
2
votes
1answer
58 views

Has the Apophenia C library been used for publications?

Are there analysis works that were conducted using the Apophenia library and were published? This is a C library for statistical analysis. I wanted to know about use cases.
1
vote
1answer
186 views

Getting different Percentile results when using two different software

I'm calculating 90th percentile values in two different places using two different pieces of software, and I'm getting different results. These results need to be comparable. I understand there are ...
1
vote
1answer
55 views

software for one class classification with a Bayesian Network

I'm looking for a software package that would allow to do a one class classification with a Bayesian Network (anomaly detection). I was planning to use bnlearn but so far I'm unable to find out if ...
2
votes
1answer
448 views

What SPSS test should I use for blood pressure pre- and post-intervention for comparison?

I have 10 participants who consumed an intervention for 3 weeks. I would like to look at any significance between pre-intervention and post-intervention readings. What SPSS test should I use? I ...
2
votes
0answers
159 views

SAS and R gives different standard error when fitting Tweedie model

I would like to fit a Tweedie GLM to the data. However, even though PROC GENMOD from SAS and glm() from R gives the same coefficient estimates, they give quite different standard error. What it the ...
7
votes
1answer
603 views

Why is the intercept typed in as a 1 in stats packages (R, python)

When using statistics software, When defining your linear models, why is the intercept typed in as a 1, rather than "const" or "intercept" or something. What significance does 1 have? Is there some ...
1
vote
1answer
59 views

Statistical Analysis Software [closed]

I am a psychology student at UCF. I intend to pursue a master's degree in industrial and organizational psychology. We use SPSS in the psychology department. How prevalent is SPSS used in offices? ...
0
votes
0answers
61 views

combine samples of supersets to get a reservoir sample of the subset

Here's some background before my question (Bear with me! :D) I am working on a data pipeline that deals with a massive input log dataset; instead of saving the full input log, current version of this ...
8
votes
1answer
726 views

Alternatives to Journal of Statistical Software?

I have developed an R package for a general class of regression models with applications in survival analysis. I have prepared a paper describing the package and the methods, and the applications. One ...
2
votes
0answers
121 views

Implementation of time-varying coefficients model for Cox regression

I would like to implement the time-varying coefficients model (cf. Fan and Zhang, 1999) for a Cox proportional hazards model, as proposed by Cai and Sun (2003), and studied by Tian, Zucker and Wei (...
0
votes
0answers
121 views

Implementation of regularized competing risk models with random effects

Are there any existing software implementations of regularized competing risk cox models with that also allow for random effects (i.e., competing risk frailty models)? That is, models that allow for ...
0
votes
0answers
19 views

Data Correlation for computing software metrics

I have the below sets of data per application, you can call them as software metrics. These metrics vary depending on the size of an application. ...
2
votes
0answers
27 views

Design of Experiments through Algebraic Statistics [closed]

I would like to ask you about how to compute a circuit basis of a design matrix in software R. Let me explain you. I have found a software, named Macaulay2, that calculates some algebraic tools, and ...
0
votes
2answers
130 views

Automating a search for correlation

Note: I am not a statistician, though I do have a mathematics background. I know what I would like to do, but I don't have deep subject knowledge. If you use any special jargon, please try to use ...
1
vote
1answer
882 views

How to normalize text when computing the word error rate of a speech recognition system?

I am looking for a library, script or program that can normalize the transcribed and gold texts when computing the word error rate (WER) of an automated speech recognition system. For example, if: ...
1
vote
0answers
27 views

How to design a complex machine learning system where individual classifiers can be retrained without modifying rest of the system?

I am designing a machine learning system which consists a bunch of classifiers (each output a confidence score between 0 to 1). Some classifiers consume output from other classifiers as features. Now ...
0
votes
0answers
68 views

How many different statistics packages use GPL (Graphical Programming Language)?

QUESTION: How many different statistics packages use GPL? BACKGROUND: Most of what I am finding regarding GPL (Graphical Programming Language) is in relation to SPSS. While the literature I've seen ...
11
votes
1answer
987 views

What is probabilistic programming?

For the past year, I've been hearing a lot about Probabilistic Programming (PP) frameworks like PyMC3 and Stan, and how great PP is. And today, someone shared this link with me: Pyro: a Deep ...
0
votes
0answers
50 views

How do I analyze "unit test" results as part of a software project?

Many software projects have "unit tests", which vary in definition and implementation, but are generally agreed to specific tests of a small "unit" of software. For example, an "addition" function <...
1
vote
0answers
2k views

CRF (TensorFlow) log-likelihood becomes positive

I am currently doing a multiclass classification task on sequence data and am using tf.contrib.crf.crf_log_likelihood to compute sentence level log-likelihood values. In particular it implements a ...
3
votes
2answers
322 views

How to fit to sum of observations?

From a practical point of view, how does one go about fitting a model to training data that consists of sums of a dependent variable over multiple conditions? For example, fitting a model to predict ...
3
votes
0answers
232 views

Program to evaluate the output of a speech recognition system

I am looking for a library, script or program that can evaluate the output of a speech recognition system. The output of the speech recognition system is a simple text file, and I have the gold output ...
4
votes
1answer
833 views

Combine crude events and Hazard Ratio in Meta-analysis

I'm running a meta-analysis on several studies; most of them have crude event numbers that I can put in my software, but other ones have hazard ratios with 95% C.I. reported and no crude number ...
1
vote
1answer
465 views

Latent Dirichlet Allocation (LDA) package that allows specifying asymmetric prior? [closed]

Are there any packages there any LDA packages out there that allow you to specify the full asymmetric prior? I know Mallet uses asymmetric priors, but I don't believe it allows you to specify them.
6
votes
2answers
549 views

Python package that allows to train a CRF on two datasets

I am looking for a Python package that allows to train a conditional random field (CRF) on two datasets. For example: I have two datasets, dataset A and dataset B. I want to train a conditional ...
1
vote
1answer
2k views

Calculation of IV Standard Errors using R

One thing that I cannot find very clear, perhaps because I am still new in using R, is the derivation of the standard errors in instrumental variable packages using R (e.g., ivreg, sem, plm). I am ...
1
vote
2answers
370 views

software for genome wide associations studies (GWAS) [closed]

I have just started learning about genome wide associations studies (GWAS) as I will have to run some of them in the near future, and I am pretty confused about which are the best computational tools ...
1
vote
0answers
50 views

Software for cluster analysis of dichotomous data

can anybody recommend software for cluster analysis of dichotomous data (using appropriate coefficients, e.g. from Finch, 2005 1)? I have access to Statistica but it seems to me that it is not ...
1
vote
0answers
41 views

Re-running randomly seeded analyses produces unreplicable results, so why don't packages use a deterministic seed by default?

Analyses based on iterative model fitting or simulations are typically seeded with an unpredictable random value based on a PRNG function plus the program / computer state. This causes analyses to ...
2
votes
1answer
303 views

Is Maximum Likelihood implemented differently in different supervised classification systems?

Some functions are identical between systems, for example nearest neighbour analysis. It would be unusual to have nearest neighbour implemented differently as appears in academic papers. Is it the ...
1
vote
1answer
175 views

Are there alternatives to MCR-ALS for determining pure response profiles of a mixture?

MCR-ALS says it is a tool for "the recovery of the pure response profiles of the chemical constituents or species of an unresolved mixture when no prior information is available about the nature and ...
1
vote
1answer
3k views

Choosing statistical software based on the size of dataset

The statistical software that I am familiar with, like Stata, is no longer capable for processing 3GB dataset with more than 1 million records, or bigger. Now I am working with JMP pro and a little ...

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