Use this tag for any *on-topic* question that (a) involves `R` either as a critical part of the question or expected answer (b) is not *just* about how to use `R`.

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10
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0answers
549 views

MLEs from glmer {lme4} in R

Numerically deriving the MLEs of GLMM is difficult and, in practice, I know, we should not use the brute force optimization (e.g., using optim in a simple way). But ...
9
votes
0answers
3k views

What does the anova() command do with a lmer model object?

Hopefully this is a question that someone here can answer for me on the nature of decomposing sums of squares from a mixed-effects model fit with lmer (from the ...
9
votes
0answers
2k views

How to analyze longitudinal count data: accounting for temporal autocorrelation in GLMM?

Hello statistical gurus and R programming wizards, I am interested in modeling animal captures as a function of environmental conditions and day of the year. As part of another study, I have counts ...
8
votes
0answers
3k views

Unable to fit negative binomial regression in R (attempting to replicate published results)

Attempting to replicate the results from the recently published article, Aghion, Philippe, John Van Reenen, and Luigi Zingales. 2013. "Innovation and Institutional Ownership." American Economic ...
7
votes
0answers
570 views

Contrast matrix definition

What exactly is contrast matrix and how exactly is contrast matrix specified? I.e. what are columns, what are rows, what are the constraints on that matrix and what does number in column ...
7
votes
0answers
269 views

p-value adjustment for Local Moran's I statistic (LISA)

I'm working with some exploratory spatial analysis in R using spdep package. I came across an option to adjust p-values of local indicators of spatial association (LISA) calculated using ...
7
votes
0answers
401 views

Can these data be aggregated into a proportion for a binomial glm?

We asked 60 people to list as many restaurant franchises in Atlanta as they could. The overall list included over 70 restaurants, but we eliminated those that were mentioned by fewer than 10% of the ...
6
votes
0answers
101 views

What is the name of the density estimation method where all possible pairs are used to create a Normal mixture distribution?

I just thought of a neat (not necessarily good) way of creating one dimensional density estimates and my question is: Does this density estimation method have a name? If not, is it a special case of ...
6
votes
0answers
784 views

glmer in R: Significance estimates are not robust to order of data frame

I'm using a mixed effects model with logistic link function (using lme4 version 1.1-7 in R). However, I noticed that the estimates of significance for fixed effects change depending on the order of ...
6
votes
0answers
1k views

What's wrong with t-SNE vs PCA for dimensional reduction using R?

I have a matrix of 336x256 floating point numbers (336 bacterial genomes (columns) x 256 normalized tetranucleotide frequencies (rows), e.g. every column adds up to 1). I get nice results when I run ...
6
votes
0answers
117 views

Why are confidence intervals for predicted values so large?

The data for this question can be downloaded with this code: ...
6
votes
0answers
386 views

Lasso on Negative Binomial Regression Model

Is there anyway that I can perform LASSO with Negative Binomial Regression on R? I am performing a negative binomial regression on my dataset because the data are too dispersed to impose poisson ...
6
votes
0answers
148 views

Standard errors from flexsurvreg

I'm using the flexsurv package (in R) to fit an exponential distribution to the veteran ...
6
votes
0answers
67 views

Territories from observations

I have a number of animal observations, and want to deduce the number of territories (i.e. the number of individual animals) from this. More formally, the problem can be stated as follows: Each ...
6
votes
0answers
752 views

How to interpret coefficients of a multivariate mixed model in lme4 without overall intercept?

I'm trying to fit a multivariate (i.e., multiple response) mixed model in R. Aside from the ASReml-r and ...
6
votes
0answers
1k views

How to compute confidence interval in ANOVA with repeated measures?

I made a model using repeated measures univariate ANOVA in R. ...
6
votes
0answers
283 views

Average Structural Function Calculation

EDIT: I have solved this problem myself. The problem with the simulation below is that the omitted variable should not be included in the 'true model'. I have written a blog post with a more detailed ...
6
votes
0answers
501 views

Modeling a spline over time — design matrix and survey of approaches

A response variable y is a nonlinear function of a number of predictor variables X (in my real data the response is binomially distributed, but here I'm using a normally-distributed value for ...
6
votes
0answers
577 views

Testing for a significant difference between ML estimates: Likelihood ratio or Wald test?

I am trying to test whether or not there is a significant difference between maximum likelihood estimates of two genetic parameters (selection and dominance) across two environments with genotype data ...
6
votes
0answers
295 views

Tree size in gradient tree boosting

Gradient tree boosting as proposed by Friedman uses decision trees with J terminal nodes (=leaves) as base learners. There are a number of ways to grow a tree with ...
6
votes
0answers
474 views

Fitting a special mixed model in R - alternatives to optim()

I would like to do something in R that SAS can do using SAS's proc mixed (there is some way to do in STATA es well), namely fitting the so called Bivariate model from Reitsma et al (2005). This model ...
6
votes
0answers
103 views

Is there an equivalent of ARMA for rank correlation?

I am looking at extremely non linear data for which the ARMA/ARIMA models do not work well. Though, I see some autocorrelation, and I suspect to have better results for non linear autocorrelation. 1/ ...
5
votes
0answers
43 views

Quantile regression for Sales forecast in R

Issue: Cannot forecast sales accurately using quantile regression in R. I am using rq function from "quantreg" package which is giving me warning "Result might have Non unique solutions" Aim: I am ...
5
votes
0answers
40 views

How to calculate log-normal distribution parameters with partial data?

Imagine we have a partial data and we know that this partial data represent only the left 5% of the log-normal distribution, which the overall data follow. How can we calculate the mean-log and sd-log ...
5
votes
0answers
37 views

Kaplan Meier estimate for data with unequal numbers in treatments

Is it possible to estimate Kaplan-Meier medians, CIs and difference with unequal sample size in treatments or do I have to do coxph? For example, in my dataset, ...
5
votes
0answers
173 views

What's wrong with this visualization of eigenvalues/vectors/PCA?

I have a dataset of 17 people, ranking 77 statements. I want to extract principal components on a rotated correlation matrix of correlations between people (as variables) across statements (as ...
5
votes
0answers
472 views

Accounting for heteroskedasticity in lme linear mixed model?

I have a data set where I measured the number of molecules (M) present in cells as a function of drug (with or without) and days of treatment (5 timepoints). I repeated the experiment 3 times, with ...
5
votes
0answers
230 views

How to deal with underdispersion with binomial data

I'm working with a pretty large dataset (n = 4,500) where 10% of my points (pixels in a GIS landscape) are 1s and the rest are 0s. The full model for my data looks something like this: ...
5
votes
0answers
219 views

Generalized linear model with lasso regularization for continuous non-negative response

I have a big data problem with a large number of predictors and a non-negative response (time until inspection). For a full model I would use a glm with Gamma distributed response (link="log"). ...
5
votes
0answers
248 views

How to create a multivariate Brownian Bridge

It is known, that a standard multivariate Brownian bridge $ y(\mathbf u) $ is a centered Gaussian process with covariance function $$ \mathbb E(y(\mathbf u) y(\mathbf v)) = \prod_{j=1}^d (u_j \wedge ...
5
votes
0answers
312 views

Comparing ISOMAP residual variance to PCA explained variance

I am using R princomp function (from stats package) to run a PCA on a data set and I want to compare its output to that of the ...
5
votes
0answers
97 views

Variational inference engines

After doing some research on the topic, I have noticed a surprising deficit of inference packages and libraries that rely on message-passing or optimization methods for Python and R. To the best of ...
5
votes
0answers
760 views

Meaning of a convergence warning in glmer

I am using the glmer function from the lme4 package in R, and I'm using the bobyqa optimizer ...
5
votes
0answers
905 views

Fitting multilevel models to complex survey data in R

I'm looking for advice on how to analyze complex survey data with multilevel models in R. I've used the survey package to weight for unequal probabilities of ...
5
votes
0answers
111 views

Compressed sensing: Optimization in $L_1$ norm and total variation with fourier coefficients

I'm reading the article Robust Uncertainty Principles: Exact Signal Reconstruction from Highly Incomplete Frequency Information (Candes, Romberg and Tao, 2004). In this article they are talking ...
5
votes
0answers
224 views

Structure of data and function call for recurrent event data with time-dependent variables

I'm attempting to estimate the effect of 2 drugs (drug1, drug2) on the likelihood of a patient falling (...
5
votes
0answers
2k views

Interpretation of crossed random effect interactions in lme4

I'm considering a model in lme4 in which I am estimating random effects for two crossed factors, very similar to the Machines example in Bates' 2010 draft book ...
5
votes
0answers
196 views

Post hoc tests for robust mixed design ANOVA using R

Is it possible to compute the function mcp2atm with unequal sample size? I ran the robust Mixed Design ANOVA by using tsplit and ...
5
votes
0answers
618 views

Which model for panel data with dependent variables from [0,1]?

I'm stuck with a regression modeling problem. I have panel data where the dependent variable is a probability. Below is an excerpt from my data. The complete panel covers more countries and years, ...
5
votes
0answers
638 views

Stationarity tests for time series

I am currently working on time series modeling, especially on stationarity tests. For this purpose, I am extensively using Pfaff's book "Analysis of integrated and cointegrated time series with R" and ...
5
votes
0answers
544 views

The role of scale parameter in GEE

I am learning the generalized estimating equations (GEE) and the geepack R package. There are some questions that I am a little confused. In a GEE-constructed ...
5
votes
0answers
268 views

Regression line envelope from Census ACS data

Context: I’m working with the Census Bureau’s American Community Survey (ACS) data which are samples (not complete enumerations) aggregated at different spatial scales. Each ACS estimate is provided ...
5
votes
0answers
873 views

What is the confidence interval calculated in a spectral density periodogram in R?

This question is similar to the one posed here: Testing significance of peaks in spectral density In that post, Pantera asks how to test whether a peak in a periodogram has a spike that is ...
5
votes
0answers
387 views

Binomial mid-p value

I've been under the impression that the mid-$p$ values generally control the Type I error, and consequently confidence intervals based on mid-$p$ values control the coverage. However I have checked ...
5
votes
0answers
276 views

Crossed random effects and unbalanced data

I am modeling some data where I think I have two crossed random effects. But the data set is not balanced, and I'm not sure what needs to be done to account for it. My data is a set of events. An ...
5
votes
0answers
772 views

Propagation of uncertainty/standard deviations in biological experiments

I am trying to work out how to propagate standard deviations in a biological experiment, but I have some difficulties. I have the following (semi)fictitious data originating from an image analysis ...
5
votes
0answers
1k views

Mixed model with repeated measures and both of two treatments with lme or lmer in R

I know just enough about lme() and lmer() to get myself by with simple models, and to get myself into trouble with more complex ...
5
votes
0answers
425 views

Canonical correlation analysis on a MICE data set

I am looking to do a canonical correlations analysis (CCA) in R, using the CCA package, on a multiply imputed dataset (obtained from the mice package). I know that ...
4
votes
0answers
40 views

How to calculate uncertainty in bacterial growth rates (or in the slope of any local regression)?

I'm using a plate reader to measure optical density of different bacterial strains so I can compare their responses (growth rates and changes in them over time) to stress conditions. The growth curves ...