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`.

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280 views

Numerical properties of the logistic growth model for non-linear regression

I am using the nls procedure in R to fit a logistic growth model. In their SSlogis function, José Pinheiro and Douglas Bates chose the formulation ...
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92 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 ...
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464 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 ...
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106 views

How to form a confidence band around the trend fitted from time series data

I have a time series data set. I can decompose it and get the trend but I would like to put confidence ranges around the trend (past) not the forecast-ed component. The decompose function also doesn'...
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551 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 ...
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446 views

Programming a new random effects structure in lme

I am seeking advice on programming a new random effects variance-covariance matrix/structure (pdmat) in R for use in lme()? I've checked out the lme source code (as suggested if you want to program ...
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5k views

When to use longitudinal (panel) weights vs cross-section weights in complex surveys

I'm currently working with a longitudinal dataset, the Kauffman Firm Survey. The survey tracks about 5000 firms starting from 2004 - 2009. Firms die out over the years. It has both cross-sectional ...
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807 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 ...
6
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1answer
672 views

How do I compare date-ranges from a time series?

I have a time series which contains monthly readings for air pollution in a city. The seasonality from this time series has been removed. Given two date ranges, for example Jan-Aug 2008 and Jan-Aug ...
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196 views

Why do PCA and PCoA give the same components but different explained variances?

I'm quite familiar with Principal Component Analysisis, as I use it to study genetic structure. Lately, I was revisiting some of the functions I was using in R (...
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180 views

“Hierarchical” Random forests?

Background I am using Random Forest to classify ~900 objects based on a large number (> 80) predictors. I split these 70:30 for training and testing. The overall model does fairly well, giving an ...
5
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1answer
73 views

Evaluating if time series need differencing

I am a total beginner with time series analysis. I use R. I understand that time series data need to be stationary for analyses like cross-correlation or modeling. I am, however, struggling with ...
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46 views

Non-uniform p-values from hoeffd function in Hmisc when data sets are independent

When using the function hoeffd in the CRAN package Hmisc I get unusual p-values for pairs of data sets that are independent. The function hoeffd is an implementation of Hoeffding's $D$ statistic. ...
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111 views

Why does “mixtools” return the model with highest AIC as the “winner” if lower AIC is better?

Mixtools package is used to fit mixtures of normal/regressions. The package documentation is given here The regmixmodel.sel fits the mixture model for varying ...
5
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1answer
107 views

How do I simulate a random valid correlation matrix of ordinal variables given a list of marginal probabilities?

I am trying to use R to simulate random variations in a real dataset with a known number of categorical and continuous predictor variables, as well as known marginal probabilities for each ordinal/...
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816 views

What is the difference between Lasso regression in glmnet (in R) and Sklearn lasso (in Python)?

A similar post was discussed here regarding Ridge Regression: What are the differences between Ridge regression using R's glmnet and Python's scikit-learn? My question is what is this ...
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214 views

Whether to use EFA or CFA to predict latent variables scores?

I have a dataframe of individual observations, that I partitioned to create a training (0.7 prop) and a test set (0.3 prop). I started by running an exploratory factor analysis (EFA) on the training ...
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107 views

Does it makes sense to calculate a correlation between two binary variables?

I have a data set with 14 binary variables. I conducted a survey and there was a question with 14 elements of a specific method to which the respondents had to check if they used the element. Now I ...
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359 views

Longitudinal mixed model: What random effects are possible?

I'm faced with analyzing the following design: In a longitudinal study, the muscle tissue of about 25 subjects are analyzed at 8 timepoints. Specifically, 7 measurements are taken during a race ...
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554 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. ...
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673 views

Can a factor be regarded as both random and fixed effect?

I have a question about nested mixed effect model. For example I have species A with different populations; these populations belong to two kinds of habitat types (with or without predators). So I ...
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1answer
133 views

How to analyse growth rate in R?

Within the framework of an experiment I followed to growth rate of bird nestlings. I measured them every day for weight and tarsus. I have a number of continuous and categorical explanatory variables, ...
5
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1answer
306 views

Getting ROC curve from markov chain in r

I've been working on some attribution modeling in R, following the markov chain-based methodology described here. In order to compare the sensitivity and specificity trade-offs of using models of ...
5
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1answer
706 views

Multivariate differences between groups controlling for one factor (MANOVA)

I have a sample of 100 participants who have scores on 5 different variables (V1-V5). Some participants took part in a workshop, others did not. I am interested in investigating the influence of ...
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518 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 ...
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545 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? ...
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2k views

Is it possible to do a time series analysis with more than one explanatory variable?

I am working on a project, and I am absolutely new to forecasting and not so strong in statistics. I have an employee data for the last 7 years, along with the other variables like economic growth, ...
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694 views

Seasonally adjusted data used in time series forecasting

I am looking at two time series, from 01/01/2000 to the present: The ISM Manufacturing: New Orders Index, only available seasonally adjusted The manufacturing industry unemployment rate, only ...
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0answers
618 views

creating random variable with certain auto-correlation in R

I want to create a random variable with a given autocorrelation in R. The target autocorrelation is defined by: $$acf_{target}=(lag+1)^{(-b)}$$ with $b=1.41519$ which I derived from a natural ...
5
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1answer
394 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 ...
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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 ...
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193 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
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0answers
394 views

Ideal statistical or machine learning technique to model highly cross-correlated data

I'm trying to build a model that can predict streamflow for an alpine (snowmelt-fed) watershed using snow albedo (roughly, the energy reflectance of the snow) data. Albedo controls the melt of the ...
5
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1answer
166 views

What is the “pdm” stat in the “rms” R package?

I am building an ordinal logistic regression model (ORM). In order to fit my ORM model, I am using the 'orm' function of 'rms' package from R (http://cran.r-project.org/web/packages/rms/rms.pdf). Now ...
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493 views

Solving non-linear equations in R with optimal inital values

I am using the rootSolve package in R to estimate parameters of non-linear equations. The basic formula is ...
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240 views

Quantile regression with censored data. Quantiles not fitted

I'm trying to fit a quantile regression model for rigth censoring data and I'm using R with the package quantreg and its function crq. I'm trying the Portnoy method that it's suposed to estimate the ...
5
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1answer
414 views

testing for mediation of interactions

I am somewhat familiar with various ways of testing mediation for factors in different types of regression analysis. (I'm using R and currently working with a multilevel binary logistic regression.) ...
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519 views

Is this longitudinal data too complicated for GLMM or GEE?

After writing this post, I've realized that I am running around in circles, chasing my tail. Any help approaching this problem would be greatly appreciated, as I think I just need to bounce ideas ...
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2k views

Interpreting MANOVA and redundancy analysis of a canonical correlation analysis

I have done a canonical correlation analysis using the American Community Survey Dataset. The analysis is done between Ancestry and ...
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0answers
268 views

Is the following procedure to measure the quality of an imputation ok?

I'd like to compare different kinds of imputation techniques, i.e. methods which allow to fill missing data fields in a data frame. For now, I'm only using the R package ...
5
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0answers
2k views

Frequency weights, rare events and logistic regression

I'm working on a model that requires me to look for predictors for a rare event (less than 0.5% of the total of my observations). My total sample is a significant part of the total population (50,000 ...
5
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0answers
109 views

R packages that work with biased samples

I'm working with a biased sample of web users. I'm only able to track responses of users who have navigated my site in a certain way, and I'd like to run an analysis to determine how certain factors (...
5
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1answer
2k views

creating contrast matrix (limma) for two factorial in R

I am attempting to construct a contrast matrix that I can run in R, using the limma bioconductor package, but I am not sure that I have coded the contrast matrix correctly. A previous post and the ...
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0answers
626 views

Different estimates of crossed random factor variance using nlme and lme4

I want to fit a model with two crossed random factors that also allow heteroscedasticity. Whereas nlme4 allows non-constant error variance, I was not sure how to ...
5
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0answers
342 views

What is the purpose of working on a logit scale in partial dependence plots?

What is the purpose of working on a logit scale in partial dependence plots (in binary classification)? One could simply go about as follows: Grow a forest Suppose ...
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0answers
8k views

Mixed effect logistic regression in R: choosing random effects

I conducted an experiment which measured a binary response for each subject. The subjects were in 1 of 3 groups. There were two other fixed factors, each of which were continuums (cont1, cont2) ...
5
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148 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 ...
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1k views

Diagnostics for GEE in R

I have been checking out which diagnostics to use for a GEE analysis. It seem that influence measures are appropriate (Preisser, 1996). Does anyone know of a package that can be used in R to examine ...
5
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1answer
2k views

Singularity issues in multinomial logit model with differing choice sets

I am estimating a discrete choice model in which individuals choose which schools to attend. I have a large amount of data on individuals and schools. However, each particular school only appears in ...
5
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0answers
532 views

Studentized residuals and goodness-of-fit with robust linear regression

Could you please advise whether studentized residuals are meaningful when computed on a robust linear regression model using an M-estimator? I'd like to use it to detect outliers by doing something ...