# 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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It is well known that Probit regression can be formulated as transformed linear model in the following sense: Suppose that $Z = X\beta + \epsilon$ for some normally distributed $\epsilon$ and let $Y = ... • 198 0 votes 0 answers 7 views ### Fast package for quadratic form using an inverse of a kernel The following situation comes up a lot when working with Gaussian processes. Let's say we have a vector$h \in \mathbb{R}^n$. We are in the setting where$n$is small enough to a fit a float array of ... 23 votes 5 answers 2k views ### How should we do boxplots with small samples? This question is inspired by this posting, plus a comment by @StephanKolassa and an answer by @dipetkov who point out that the boxplots presented in that question are misleading. As is pointed out, ... • 16.7k 1 vote 0 answers 16 views ### Examples of statistical research affected by errors in package/library code I can't figure out if this belongs in Cross Validated, Stack Overflow, or Academia, but I think this may be a good place to start: Can anyone suggest examples of published prospective/retrospective/... 2 votes 1 answer 63 views ### Establish numerical equivalence of statistical model across software we are trying to establish numerical equivalence (within reasonable precision) for selected statistical models across programming languages such as SAS, R & Python or even different packages ... • 21 0 votes 2 answers 61 views ### Is there a statistical software package for the generalized conditional/multinomial logit model? I have a discrete choice model of moving from one state to the other, so alternatives=states. I have case-specific variables such as income, race, and gender. In addition, I have moving distance ... 1 vote 1 answer 44 views ### Statistical comparison of grand/pooled means (nested, mixed-model, t tests) My problem: I am comparing the means of means of means in my data set. However, my stats software (GraphPad Prism) doesn't know that these said individual values (the means of means of means) are ... 0 votes 0 answers 79 views ### Exporting data from .am format, AM statistical software Apologies for topic that may be a bit off-topic, but it seemed a bit better fit than Stack Overflow, as this is not a programming issue per se. I am trying to analyze some data published by the US ... • 441 0 votes 0 answers 42 views ### How can I perform a hypothesis test for this harmonic mean? Abstract I have a software process that I try to measure with a calculation I call the EHD. The EHD value is computed this way: I perform searches for a "best fit" number in a search space, ... 1 vote 1 answer 26 views ### Should data be anonymized irrespective of the domain? [closed] I am using a dataset from Marketing and sales department. The dataset contains customer name (company name), company address, pincode, no of orders placed, revenue generated from that customer etc. My ... • 2,104 0 votes 0 answers 38 views ### probabilistic regression in existing packages I know that typical machine-learning packages (such as scikit-learn or TensorFlow) contain plenty of functions for probabilistic classification: given a training set of pairs$(x_i,y_i)$, where$y_i$... • 1 1 vote 1 answer 26 views ### What are alternatives of Visual Statistics in R? [closed] There is software, "Visual Statistics", which helps to visualize some concepts in Statistics. For example, if I want to teach confidence interval at confidence level %95, I would say if I ... • 513 9 votes 3 answers 2k views ### How do you go from paper to code? My background is in Computational Biology, although I am a Biologist by training. I just recently started my PhD, and while I have a strong interest/curiosity in Computational Biostatistics/... • 657 0 votes 0 answers 51 views ### How to determine number of boost for calculating Krippendorff’s Alpha? I'm using the SPSS macro for computing Krippendorff’s Alpha, developed by Andrew F. Hayes & Klaus Krippendorff. One argument needed is the units of bootstrapping, and I did not find formula for ... • 39 2 votes 1 answer 508 views ### How to calculate two-way mixed ICC? I want to calculate ICC for two-way mixed model, single rater, and either for consistency and absolute agreement. I found two packages for calculating ICC (intra-class correlation coefficient), that ... • 39 5 votes 1 answer 104 views ### Estimate parameter in$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, \, \... 180 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 ...
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### 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}{\...
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### 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 ...
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### 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 vote
220 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 ...
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### 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 \$...
652 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 ...
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### 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 ...
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### 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
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### Software for multiple logistic regression analysis

Which free and easy to use statistical software can I use to perform a multiple logistic regression analysis?
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### 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/...
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### 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
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### 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
64 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 ...
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### 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 ...
214 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 ...
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### 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 ...
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### 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? ...
129 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 ...
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### 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 ...
127 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 (...
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141 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 ...
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### 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. ...
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### 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 ...
160 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
1k 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: ...
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1 vote
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### 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 ...
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### 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 ...
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1k 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 ...
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### 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
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 ...
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### 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 ...
234 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 ...
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