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`.
29,252
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Latent growth curve model: should you include predictors if the variance for slope and/or intercept factor is not significant?
Hi I am running a series of latent growth curve models.
I am wondering: can predictors of the slope and intercept factor(s) be included when the slope and/or intercept variance are not significant, or ...
- 115
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21
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zero inflation and endogeneity in logit or probit model
What is the good model for the case of bias in the distribution of the dependent variable? The dependent variable is categorical variable and one categories are dominant (about 90%).
Although I can ...
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13
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When to use factor and ordinal factor?
When modeling a regression (glm.nb) one of my predictors is the number of sides of a road that has forest next to the road. This means my predictor can take one of three values. 0 = no forest on ...
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How to introduce random effects to a GAMLSS model?
I am quite a novice in both R and GAMLSS fitting and could use some help introducing random effects to a GAMLSS model. I want to model the relationship between a variable and subject age. My ...
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Do I need to use a factor for the ANOVA?
The problem:
A psychologist is interested in short-term working memory under (1) sleep deprivation, (2) a strong dose of caffeine, (3) following 8 hours sleep. They conduct a between subjects design. ...
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Sensitivity Analysis selection for nested data?
So the data I'm working with is GPS tracking data of pelicans and Offshore rigs with the goal of seeing if pelicans are positively or negatively affected to the presence of rigs. But before I can do ...
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Interpreting HR when using tt() function
Assuming non-proportional hazards for karno (and based off p 21):
https://cran.r-project.org/web/packages/survival/vignettes/timedep.pdf
How does one interpret the HR for karno?
Is the HR = 0.9590 for ...
- 515
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12
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Generate series with multiple seasonality
I have to simulate time series with multiple seasonality and I don't understand how I can do it.
In particular I have to simulate:
A series with two deterministic seasonality (each with a different ...
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1
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How do I interpret a cox proportional hazard model?
I fitted a cox proportional hazards model in R using the coxph(). My explanatory variables include; gender, residence, antenatal care, tetanus injection, iron tablets, size at birth, place of delivery ...
Sammywills
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Why do some rows in gtsummary output show OR=1 and CI containing 1 but have significant p-values?
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I am using gtsummary to create a table that merges univariate and multivariate regression results. Here's the code I'm using:
...
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56
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whether to adjust or not adjust for baseline in longitudinal RCT
I have a longitudinal RCT data, aiming to compare the superiority of one group with high exercising to the other group with low exercising to see the improving of pain (pain is outcome). Data is ...
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What kind of logrank test is performed by survdiff function in R?
Information added: this question is not duplicate, neither my question nor the question in the link had been solved at all, I added more info to see if you can see the problem
I was trying to ...
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11
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repeated measures with glmer [closed]
I have used glmer before but not for a psychology experiment. So I want to double check if the way I'm using it is correct.
My current design is that for each subject, there are two conditions. For ...
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1
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Appropriate test for comparing categories in two groups?
I have a subset of a data as below: I would like to compare two groups (1/0) for 6 categories for using a medication Every week they could choose more than one option for each question. The number of ...
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How to obtain the KEGG mudule based on KEGG KO? (KEGG mudule enrichment) [closed]
With HUMAnN3, I got the result of the KEGG KO annotation (by humann_regroup_table). What do I need to do if I want to get the KEGG module annotation result? I did not find the relevant guidance/...
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Is it statistically sound to use r mice to predict values instead of classic lm
I have access to a population of around 5 million people. I also have access to multiple social and demographic variables (age, gender, level of education...). I randomly sampled 10,000 people from ...
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How do I move forward to find a better model fit, help interpreting DHARMa residuals
I am trying to test if there is an effect on number of individuals depending on the proportion of a certain land use type and its management. But I don't find a model with a good fit. There seems to ...
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22
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Sampling based on two variables [closed]
I am using R to draw a sample of 111 cases from a database of 188 cases. I have a variable for age groups (there are three age groups) and a variable for geographical region (25 regions).
Example:
<...
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22
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Change the values being operated on in lapply to create a matrix from a list [migrated]
I am running the following code in r to transform correlations I have extracted in wide format (dat7) into a list of correlation matrices.
(The code is my attempt to reimplement http://www.suzannejak....
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Identify the distribution of data [closed]
I did one experiment two times with the same subject. I want to find the repeatability of my result. repeatability in a sense is the fraction of behavioural variation that is due to differences ...
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Help laying out and interpreting multiple regression
Let's say I want to model children's reading scores as a function of family income, type of school (K-6 or K-8), and an interaction. Therefore my model is
\begin{align}
Y = \beta_0 + \beta_1 X_1 + \...
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semPower: Accounting for Clustered Standard Errors in SEM Power Analysis with Fixed Effects Model
I am planning to analyse clustered data with a structural equation model and as I am planning on submitting my project as a registered report, I am first trying to do an in-depth power analysis (it is ...
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Latent growth curve model: The variance-covariance matrix of the estimated parameters (vcov) does not appear to be positive definite
I have run a latent growth curve model in R using lavaan and got the below warning. It would be good to hear suggestions on how to resolve this warning. The full output is below.
Note that I dummy-...
- 115
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13
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incongruences between F-stats in the R cancor package
I'm using the R package candisc to perform canonical correlations.
Since my dataset has missing values (only 36 rows without any NAs out of 88 rows total), I have two options:
I can use the raw ...
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7
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Post-hoc sub-ANOVAS on ezANOVA - how to correct for multiple tests
Using a dataframe which looks like this (with 3 raws per "id"):
...
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10
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modeltuner hyperparameter tunining [closed]
suppose I have a multimodel produced using modeltuner approach with nrounds = 5000 with differet values for alpha alpha = c(0, 0.001, 0.01, 0.1, 1, 10, 30). I have done cross validation on the model. ...
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41
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How to aggregate survival type of data to single measure independent of time?
Thank you for the opportunity to ask this question. Since I do not speak fluently (still learning) the language of mathematics, I explain this in plain English. I understand this is too ideal but I ...
- 267
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26
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Prediction based on new data in the tsDyn package [closed]
I decided to use the tsDyn package to build the model and precision the values. The argument for this package (I previously worked with urca, vars) was the ability to make predictions based on new ...
- 111
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10
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Clustering of Variables around Latent Variables (CLV) over only qualitative data
I'm reaching out today because I have a concern regarding the clustering approach employed with the CLV method introduced by Vigneau and Qannari in 2003. I've noticed that this method is predominantly ...
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37
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Why does nlme::fdHess return NaNs when evaluated at 0? [closed]
Why does the finite-differences gradient/hessian approximation nlme::fdHess return NaNs when seeking the gradient/hessian at 0?
<...
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R deltaMethod(): evaluating a combination of parameters when one cell is empty [closed]
I'm running a linear regression with two categorical predictors and their interaction. One combination of levels does not occur in the data, and as expected, no parameter is estimated for it. I now ...
- 564
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How to specify a linear mixed model (LMM) for a repeated measures design with two categorical predictors and one continuous?
I would appreciate some help figuring whether a linear mixed model (LMM) is a good choice for my data.
My experiment is a 3 (neurostimulation target) X 2 (task block) repeated measures design that ...
- 11
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1
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17
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Best test for comparison of temporal counts
I have a data set of 182 concurrent count observations using two different methods and I was wondering what would be the best test to evaluate how closely related they are to each other.
My data set ...
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0
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20
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Wrong results for (pseudo)median on Wilcoxon paired test in R [closed]
I calculated results for the paired Wilcoxon test, one of which is (pseudo)median.
I tried to reproduce the computation of the ...
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15
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Is there a general way to detect a linear combination? [closed]
I'm new using Rstudio and trying to solve linear algebra exercises made by hand into R-code, but I'm struggling a little bit.
By theory, to detect if there's a linear combination between vector, you ...
Sora
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6
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Use a sequence of bernouli trials to find the possibility of an event happening
I have the data below and We have a game, that has a prize jackpot. The jackpot prize starts at 1,000 credits and every round you play the jackpot increases, until someone wins the jackpot and it ...
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1
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18
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Differences in Regression model for Dummy Coding (factor vs. recode) [closed]
I have the following problem: I generate Dummy Variables with the recode and the factor command. In my regression I got different output for the "lower middle" variable and couldn't explain ...
- 3
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11
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Pairwise t test (holm correction) with ezANOVA output [migrated]
I'm doing data analysis using R (dyplr).
I'd like to perform post-hoc comparisons using the pairwise.t.test() function in R and the output of the ANOVA I performed with ezANOVA() but I don't know how.
...
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7
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How to handle recent variable change resulting in level-switch in time series modeling?
I developed a script to run time series models on people data, and I re-run the Arima model fitting/forecast reconciliation algorithm monthly as new data comes in. I use the grouped/hierarchical time ...
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1
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Interpreting an estimated bivariate VECM
I have used the tsDyn package in R to estimate a VEC model for the data in the graph, and I am unsure about my interpretation of the output.
...
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is LFC shrinkage necessary when using DESEQ differential abundance analysis for microbial abundance data?
LFC shrinkage used to be default in the DESEQ function but it was updated, because it is not always recommended to do. But i cannot find much information on which conditions this is decided.
Are there ...
Tina Tuerlings
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38
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Mixed effects model for prediction
I have a dataset where I collected cortisol samples 3 times a day, for 3 days at 2 timepoints. I am interested in looking at changes in cortisol right after awakening, at 0 min after awakening, 30 min ...
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1
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55
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Specifying a mixed effects model with repeated constructs but cross-sectional observations (crossed vs. nested data at three levels)
I have a question about specifying a mixed model with crossed data across multiple levels. Consider the following situation:
Let’s say I collected data on Americans’ perceptions about the importance ...
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40
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Cox model with ridge term: how to choose value of theta?
The coxph() function in R package "survival" is used to fit the Cox proportional hazards model. This function allows a ridge() term in the formula to penalise selected terms, which requires ...
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165
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Should I use negative binomial GAM?
I'm trying to model a data of presence and absence of birds in nest boxes. I look whether it's zero-inflated and it gave me this:
...
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1
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32
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Understanding the significance level of a confidence interval
I generated 1000 confidence intervals with 95% significance level and I am testing H0: μ = 0 vs H1: μ != 0.
What means if 97.5% of my confidence intervals have the 0 included? It should be exactly 95% ...
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77
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Spatial structure in the random forest residuals
I have a data.frame which includes the response and several predictor variables. The variables were raster data which I converted them into a ...
- 111
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1
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93
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How to Compute Mean Ratios and Their 95% Confidence Intervals in a Bayesian Model
I am working on a Bayesian model using the brm function from the brms package in R, and I am interested in comparing mean responses of different groups. Specifically, I would like to calculate the ...
- 561
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2
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38
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Correlation among 10 binary variables
I have a dataset like this:
All these social determinants are binary variable. How can I find the correlation among them? By chisq.test? Since I have 11 variables and it will be 55 pairs. Is there ...
Louis
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1
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62
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Variances explained by each feature on PC in PCA
I came across this article with an associated Python codebase.
In brief, there is a section "Understanding How Features Contribute to PCs
", where...
One method for understanding which ...
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