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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365
votes
26answers
132k views

Python as a statistics workbench

Lots of people use a main tool like Excel or another spreadsheet, SPSS, Stata, or R for their statistics needs. They might turn to some specific package for very special needs, but a lot of things can ...
329
votes
10answers
304k views

Difference between logit and probit models

What is the difference between Logit and Probit model? I'm more interested here in knowing when to use logistic regression, and when to use Probit. If there is any literature which defines it using ...
258
votes
2answers
181k views

Interpretation of R's lm() output

The help pages in R assume I know what those numbers mean, but I don't. I'm trying to really intuitively understand every number here. I will just post the output and comment on what I found out. ...
187
votes
4answers
297k views

How to interpret a QQ plot

I am working with a small dataset (21 observations) and have the following normal QQ plot in R: Seeing that the plot does not support normality, what could I infer about the underlying distribution? ...
185
votes
9answers
679k views

How to summarize data by group in R? [closed]

I have R data frame like this: ...
181
votes
2answers
810k views

How do I get the number of rows of a data.frame in R? [closed]

After reading a dataset: dataset <- read.csv("forR.csv") How can I get R to give me the number of cases it contains? Also, will the returned value include of ...
178
votes
9answers
176k views

How to deal with perfect separation in logistic regression?

If you have a variable which perfectly separates zeroes and ones in target variable, R will yield the following "perfect or quasi perfect separation" warning message: ...
174
votes
3answers
97k views

R's lmer cheat sheet

There's a lot of discussion going on on this forum about the proper way to specify various hierarchical models using lmer. I thought it would be great to have all ...
164
votes
21answers
67k views

Does Julia have any hope of sticking in the statistical community?

I recently read a post from R-Bloggers, that linked to this blog post from John Myles White about a new language called Julia. Julia takes advantage of a just-in-time compiler that gives it wicked ...
153
votes
2answers
205k views

How to determine which distribution fits my data best?

I have a dataset and would like to figure out which distribution fits my data best. I used the fitdistr() function to estimate the necessary parameters to ...
148
votes
25answers
117k views

R vs SAS, why is SAS preferred by private companies?

I learned R but it seems that companies are much more interested in SAS experience. What are the advantages of SAS over R?
132
votes
6answers
252k views

Correlations with unordered categorical variables

I have a dataframe with many observations and many variables. Some of them are categorical (unordered) and the others are numerical. I'm looking for associations between these variables. I've been ...
130
votes
3answers
150k views

How are the standard errors of coefficients calculated in a regression?

For my own understanding, I am interested in manually replicating the calculation of the standard errors of estimated coefficients as, for example, come with the output of the ...
111
votes
2answers
55k views

Removal of statistically significant intercept term increases $R^2$ in linear model

In a simple linear model with a single explanatory variable, $\alpha_i = \beta_0 + \beta_1 \delta_i + \epsilon_i$ I find that removing the intercept term improves the fit greatly (value of $R^2$ ...
106
votes
1answer
60k views

Crossed vs nested random effects: how do they differ and how are they specified correctly in lme4?

Here is how I have understood nested vs. crossed random effects: Nested random effects occur when a lower level factor appears only within a particular level of an upper level factor. For ...
102
votes
1answer
59k views

Conditional inference trees vs traditional decision trees

Can anyone explain the primary differences between conditional inference trees (ctree from party package in R) compared to the ...
98
votes
1answer
76k views

Interpreting plot.lm()

I had a question about interpreting the graphs generated by plot(lm) in R. I was wondering if you guys could tell me how to interpret the scale-location and leverage-residual plots? Any comments ...
94
votes
2answers
55k views

How scared should we be about convergence warnings in lme4

If we a re fitting a glmer we may get a warning that tells us the model is finding a hard time to converge...e.g. ...
92
votes
4answers
165k views

What is rank deficiency, and how to deal with it?

Fitting a logistic regression using lme4 ends with Error in mer_finalize(ans) : Downdated X'X is not positive definite. A likely cause of this error is ...
91
votes
4answers
48k views

How to choose nlme or lme4 R library for mixed effects models?

I have fit a few mixed effects models (particularly longitudinal models) using lme4 in R but would like to really master the ...
84
votes
3answers
162k views

An example: LASSO regression using glmnet for binary outcome

I am starting to dabble with the use of glmnet with LASSO Regression where my outcome of interest is dichotomous. I have created a small mock data frame below: <...
84
votes
8answers
62k views

Generate a random variable with a defined correlation to an existing variable(s)

For a simulation study I have to generate random variables that show a predefined (population) correlation to an existing variable $Y$. I looked into the R ...
81
votes
2answers
43k views

Resampling / simulation methods: monte carlo, bootstrapping, jackknifing, cross-validation, randomization tests, and permutation tests

I am trying to understand difference between different resampling methods (Monte Carlo simulation, parametric bootstrapping, non-parametric bootstrapping, jackknifing, cross-validation, randomization ...
78
votes
21answers
43k views

Free resources for learning R

I'm interested in learning R on the cheap. What's the best free resource/book/tutorial for learning R?
77
votes
3answers
60k views

Best way to present a random forest in a publication?

I am using the random forest algorithm as a robust classifier of two groups in a microarray study with 1000s of features. What is the best way to present the random forest so that there is enough ...
75
votes
7answers
125k views

Calculating the parameters of a Beta distribution using the mean and variance

How can I calculate the $\alpha$ and $\beta$ parameters for a Beta distribution if I know the mean and variance that I want the distribution to have? Examples of an R command to do this would be most ...
74
votes
4answers
43k views

What is the difference between R functions prcomp and princomp?

I compared ?prcomp and ?princomp and found something about Q-mode and R-mode principal component analysis (PCA). But honestly – ...
73
votes
15answers
122k views

Good GUI for R suitable for a beginner wanting to learn programming in R?

Is there any GUI for R that makes it easier for a beginner to start learning and programming in that language?
72
votes
15answers
5k views

Complete substantive examples of reproducible research using R

The Question: Are there any good examples of reproducible research using R that are freely available online? Ideal Example: Specifically, ideal examples would provide: The raw data (and ideally ...
71
votes
2answers
444k views

Removing duplicated rows data frame in R [closed]

How can I remove duplicate rows from this example data frame? A 1 A 1 A 2 B 4 B 1 B 1 C 2 C 2 I would like to remove the duplicates based on ...
71
votes
2answers
68k views

Multivariate multiple regression in R

I have 2 dependent variables (DVs) each of whose score may be influenced by the set of 7 independent variables (IVs). DVs are continuous, while the set of IVs consists of a mix of continuous and ...
70
votes
1answer
78k views

How to interpret coefficients in a Poisson regression?

How can I interpret the main effects (coefficients for dummy-coded factor) in a Poisson regression? Assume the following example: ...
68
votes
4answers
19k views

How should tiny $p$-values be reported? (and why does R put a minimum on 2.22e-16?)

For some tests in R, there is a lower limit on the p-value calculations of $2.22 \cdot 10^{-16}$. I'm not sure why it's this number, if there is a good reason for ...
68
votes
4answers
17k views

Why does including latitude and longitude in a GAM account for spatial autocorrelation?

I have produced generalized additive models for deforestation. To account for spatial-autocorrelation, I have included latitude and longitude as a smoothed, interaction term (i.e. s(x,y)). I've based ...
67
votes
9answers
146k views

How to obtain the p-value (check significance) of an effect in a lme4 mixed model?

I use lme4 in R to fit the mixed model lmer(value~status+(1|experiment))) where value is continuous, status and experiment are factors, and I get ...
66
votes
8answers
17k views

Is the R language reliable for the field of economics?

I am a graduate student in economics who recently converted to R from other very well-known statistical packages (I was using SPSS mainly). My little problem at the moment is that I am the only R user ...
66
votes
1answer
63k views

Understanding ROC curve

I'm having trouble understanding the ROC curve. Is there any advantage / improvement in area under the ROC curve if I build different models from each unique subset of the training set and use it to ...
66
votes
3answers
125k views

How to actually plot a sample tree from randomForest::getTree()? [closed]

Anyone got library or code suggestions on how to actually plot a couple of sample trees from: getTree(rfobj, k, labelVar=TRUE) (Yes I know you're not supposed ...
66
votes
4answers
67k views

What do the residuals in a logistic regression mean?

In answering this question John Christie suggested that the fit of logistic regression models should be assessed by evaluating the residuals. I'm familiar with how to interpret residuals in OLS, they ...
64
votes
8answers
41k views

Is PCA followed by a rotation (such as varimax) still PCA?

I have tried to reproduce some research (using PCA) from SPSS in R. In my experience, principal() function from package psych ...
63
votes
5answers
4k views

Why does collecting data until finding a significant result increase Type I error rate?

I was wondering exactly why collecting data until a significant result (e.g., $p \lt .05$) is obtained (i.e., p-hacking) increases the Type I error rate? I would also highly appreciate an ...
63
votes
6answers
11k views

Standard errors for lasso prediction using R

I'm trying to use a LASSO model for prediction, and I need to estimate standard errors. Surely someone has already written a package to do this. But as far as I can see, none of the packages on CRAN ...
62
votes
8answers
100k views

How to simulate data that satisfy specific constraints such as having specific mean and standard deviation?

This question is motivated by my question on meta-analysis. But I imagine that it would also be useful in teaching contexts where you want to create a dataset that exactly mirrors an existing ...
61
votes
5answers
73k views

Using principal component analysis (PCA) for feature selection

I'm new to feature selection and I was wondering how you would use PCA to perform feature selection. Does PCA compute a relative score for each input variable that you can use to filter out ...
59
votes
2answers
124k views

How can I change the title of a legend in ggplot2? [closed]

I have a plot I'm making in ggplot2 to summarize data that are from a 2 x 4 x 3 celled dataset. I have been able to make panels for the 2-leveled variable using ...
58
votes
6answers
49k views

Do the predictions of a Random Forest model have a prediction interval?

If I run a randomForest model, I can then make predictions based on the model. Is there a way to get a prediction interval of each of the predictions such that I ...
58
votes
4answers
34k views

Choosing between LM and GLM for a log-transformed response variable

I'm trying to understand the philosophy behind using a Generalized Linear Model (GLM) vs a Linear Model (LM). I've created an example data set below where: $$\log(y) = x + \varepsilon $$ The ...
57
votes
6answers
18k views

Alternatives to logistic regression in R

I would like as many algorithms that perform the same task as logistic regression. That is algorithms/models that can give a prediction to a binary response (Y) with some explanatory variable (X). ...
57
votes
6answers
42k views

Which permutation test implementation in R to use instead of t-tests (paired and non-paired)?

I have data from an experiment that I analyzed using t-tests. The dependent variable is interval scaled and the data are either unpaired (i.e., 2 groups) or paired (i.e., within-subjects). E.g. (...
57
votes
1answer
15k views

Logistic regression in R resulted in perfect separation (Hauck-Donner phenomenon). Now what?

I'm trying to predict a binary outcome using 50 continuous explanatory variables (the range of most of the variables is $-\infty$ to $\infty$). My data set has almost 24,000 rows. When I run ...

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