Questions tagged [r]

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`.

8,337 questions with no upvoted or accepted answers
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877 views

Fitting custom distributions by MLE

My question relates to fitting custom distributions in R but I feel it has enough of a probability element to remain on CV. I have an interesting set of data which has the following characteristics: ...
15
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6k views

Specify correlation structure for different groups in mixed-effects model (lme4/nlme)

I am trying to account for spatial autocorrelation in a linear mixed-effects model in R with measurements repeated in time. BodyMass has been collected once per <...
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Implementation of CoVaR (a systemic risk measure) in R

I'm trying to estimate CoVaR using bivariate DCC GARCH in R. The concept of CoVaR is the dependence adjusted of VaR, which was first introduced by Adrian and Brunnermeier (2011). However, this ...
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3k views

Gamma hurdle model for continuous response?

I am modelling invertebrate.biomass ~ habitat.type * calendar.day + habitat.type * calendar.day ^ 2, with a random intercept of ...
13
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2k 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 ...
12
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1answer
58k views

Interpreting log likelihood

I have difficulty interpreting some results. I am doing an hierarchical related regression with ecoreg. If I enter the code I receive output with odds ratios, ...
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5k views

How to compute confidence interval in ANOVA with repeated measures?

I made a model using repeated measures univariate ANOVA in R. ...
12
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0answers
1k 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 ...
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3k views

Interpreting and reporting gamm4 result

I am new to gam, and most of my knowledge comes from this document http://www3.nd.edu/~mclark19/learn/GAMS.pdf. Now I am using generalized addictive model with random effects to model some data, where ...
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2k views

How to generate 2 correlated Beta random variables

I was wondering if it might be possible to generate 2 correlated $Beta$ random variables? In other words, I want to generate two Beta random variables which can be said to have come from two Beta ...
9
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1answer
5k views

How to choose bootstrap confidence interval type from boot.ci in R?

The boot.ci documentation in R says there are five different types of confidence interval that boot.ci will return: norm (normal approximation) basic stud (...
9
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1answer
2k views

How to test for the difference in skewness of two samples?

I have two samples. From looking at their densities, one appears symmetrical and the other from some right-tailed distribution. I would like to test that the two do not have the same skewness (...
8
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603 views

The Regularization Path for Smoothing Splines

I've got a potentially interesting question. Does anyone know if R already has a package for calculating the entire regularization path of the smoothing spline? That is, for: $$\hat{f}_{\lambda}=...
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1k views

Negative deviance explained by GAM with betareg in R

I am fitting the following model in "mgcv" package in R using option family=betar to predict a percentage cover response variable (...
8
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1answer
1k views

Random Forest: Class specific feature importance

I'm using the bigrf R-package to analyse a dataset with ca. 50.000 observations x 120 variables, classified into two groups. After growing a forest of 1000 trees, ...
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0answers
3k views

How to use formative indicators in covariance-based SEM with lavaan?

I'm trying to build a covariance-based structural equation model (SEM) using both reflective and formative specifications of latent variables. I use the sem ...
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2k 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 ...
8
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1answer
575 views

Hypergeometric: how do I construct a credibility interval around K (population successes) in R?

I have a problem for which I believe I should use the hypergeometric distribution, but I can't figure out how to do it in R. Say I have a bag of marbles with known number ($N$) of marbles, but the ...
7
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1answer
73 views

How to test the increase of proportions

Let say I've a contigency table as : score <=2 [3-4] >=5 no_event 248 796 288 event 71 419 285 I computed the ...
7
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1answer
461 views

How to judge whether to model a time series additively or multiplicatively?

I don't know how to to identify whether my time series is additive or multiplicative using decompose() command in R. It is a monthly time series.
7
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908 views

How to estimate random-effects for new subjects for predictions (example in GNU R's lme4)

I'm wondering how to make predictions for new subjects from a fitted mixed-effects model (in a frequentist framework). Specifically, we have multiple observations on a set of subjects to which we can ...
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3k views

gam: choosing between cubic and thin-plate splines

I am using gam (mgcv) to model a continuous response (a soil nutrient) in relation to a continuous predictor plus categorical predictors plus site random effects (modest number of sites) with: ...
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568 views

How good is an optimal design (DOE)?

I am looking at an experiment with 5 factors (4 numeric and one nominal) with three levels for each numeric and 2 levels for the nominal. Instead of the 162 runs, I am interested in a small design (30 ...
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1k views

How to fit a function to a CDF in R?

Background: I've been given a dataframe that contains data for a CDF. The column X contains the 250 $X$ values, and the column P ...
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1k views

Relationship between Gumbel and Weibull distribution, accelerated failure time models, and Survreg using R

I have three questions concerning accelerated failure time models (AFT), one statistical, one regarding how to implement these models in R, and one related to finding out information about what R is ...
7
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3k views

Hyper-prior for negative binomial in hierarchical model using JAGS/BUGS

Below I'm using a negative binomial because it is more flexible than a simple poisson model. The data are counts $y$ of events for 16 individuals $x$. There are 14 counts (i.e. counting periods) for ...
7
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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 (http://lme4.r-forge.r-project.org/lMMwR/...
7
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0answers
111 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 ...
7
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1answer
933 views

Using Google Causal Impact package to assess the significance of a planned intervention

I am using the Causal Impact package in R to infer the causal effect of an intervention in some data which are highly correlated and seasonal. Specifically, i got 17 days of hourly data, intervetion ...
6
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1answer
143 views

Confidence Intervals for the Parameters of a Logistic Growth Curve

I'm using the growthcurver library to estimate the parameters from some bacterial growth curves. It fits a logistic equation of the following form: This returns ...
6
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0answers
6k views

Singular fit with simplest random structure in lmer (lme4), is a Bayesian approach the only option?

I'm running a mixed model with the lmer function from the lme4 package in R and ran into some issues with singular fits. I get the warning message 'singular fit', ...
6
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0answers
909 views

When and How to Scale Numeric Interaction Variables in Machine Learning Model

I found one similar question on cross validated, but it was unanswered; my apologies if this has been answered. I'm experimenting with feature interaction in a regression model I'm working on in R. ...
6
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0answers
271 views

when can I substitute an inverse with a pseudo-inverse in an estimator

Short Version: can I substitute the Moore-Penrose generalized inverse of a matrix (R function ginv()) for a matrix inverse (R function ...
6
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0answers
410 views

Mixed models formulation (GAMM, GLS, nlme): from R to mathematical notation

I have just finalised the analysis of a dataset fitting Generalised additive mixed models (GAMMs) with mgcv package in R v3.3.0. But I am having trouble in writing my models into their correct ...
6
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0answers
1k views

Interpolation with radial basis functions (RBF) is failing for some reason

This is not a pure programming question. I am trying to understand what's going on when I try to use RBF with 5 centers. I am using R to exemplify, see below. My data set: ...
6
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0answers
423 views

Gaussian Process Optimization Package in R

Many Gaussian process packages are available in R. For example there is $\textbf{BACCO}$ that offers some calibration techniques, $\textbf{mlegp}$ and $\textbf{tgp}$ focusing on treed models and ...
6
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0answers
735 views

Interpretation of glmmPQL() spatial autocorrelation output

I am modeling binominal data with random effects and spatial autocorrelation using MASS::glmmPQL(). Plotting the residual semivariogram of a model fit without ...
6
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0answers
819 views

Missing value imputation in huge dataset

I have a huge data (4M x 17) that has missing values. Two columns are categorical, rest all are numerical. Given the huge amount of data, running any imputation method runs forever. What should I do? ...
6
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0answers
556 views

Spinograms vs. conditional densityplots

I have a binary response variable (hail) and multiple continuous predictor variables. My aim is to understand the linear/non-linear relationship of the predictors to the response to be able to justify ...
6
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0answers
2k views

Will Tukey multiple comparison be the same for different types of Sum Of Squares of ANOVA for an unbalanced design

I am working on Two-Way ANOVA for an unbalanced design. Will Tukey multiple comparison be the same for different types (I, II & III) of Sum Of Squares of ANOVA for an unbalanced design. I am ...
6
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0answers
800 views

How should I include age in this mixed-effects model?

I've got repeated measures of hearing thresholds for a set of patients who each have a different inner ear measurement. This data is unbalanced, there are a varied number of measurements at varied ...
6
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1answer
727 views

Calculating and plotting confidence interval for Theil-Sen estimator

I'm using Wilcox's R functions (specifically, regplot) to plot a Theil-Sen estimator with a single predictor. However, regplot ...
6
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0answers
1k views

When and why do I have to use “trait” for multinomial multilevel models with MCMCglmm in R?

I want to estimate a multilevel multinomial logit model but I am struggling with the terminology and notation used by the R-package MCMCglmm. There is documentation ...
6
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1answer
597 views

Intepreting p values from R mediate() output

In the output below, the ACME p value shows that it is significant. But the p-value for Prop. Mediated Average is >10%. I thought Prop. Mediate is the proportion of the total effect mediated by the ...
6
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1answer
704 views

Forecasting daily visits using ARIMA with external regressors

I have daily visitors data for the last 10 years. I want to do some basic tests like which is the busiest day, which is the busiest month, busiest week etc. I used ...
6
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0answers
1k views

“weight” input in glm.nb function in R. How exactly does the weight affect the likelihood?

I would like to understand how the weight argument of glm.nb is affecting the likelihood function. I understand that glm.nb find ...
6
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0answers
2k 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: ...
6
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0answers
1k views

R model.matrix and makeContrast. Understanding model and possible contrast

I have measurements from 12 mice, grouped in two conditions. I each mouse I have measurements from 4 tissues. The design is not balanced, 5 mice in condition1 and 7 in condition2. After reading the ...
6
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0answers
608 views

Where can I find resources to learn about change-point analysis ?

Where can I find resources to learn about change-point analysis ? Hopefully, someone can advise me a textbook to read and it will cover both univariate change-point analysis and multivariate change-...
6
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0answers
2k views

Appropriate negative eigenvalue correction for PCoA of genetic distances

I am trying to find the best way to represent genetic distances in a plane so that they may use them as response variables in canonical redundancy analysis (using ...

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