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`.
27,350
questions
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Why are my test data R-squared's identical despite using different training data?
I'm fitting two linear models in R, one using a 'big' dataset, the other using a 'small' dataset which is a subset of the big dataset.
When I calculate out-of-sample R-squared from the two models the ...
- 111
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0
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8
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Standardization before clustering is always a good idea?
I'm performing k-means clustering based on 5 features with different scales and Mean > Median. So, I scaled the data before applying kmeans.
The Average silhouette width is therefore maximized for ...
- 1
0
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0
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7
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Problems with in Fisher exact test: results by fisher.test and oddratio function of epitools package
This is my data
mydata <- matrix(c(86,1,14,0), nrow = 2, ncol = 2, byrow = TRUE)
When using fisher.test in R give
...
- 115
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5
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Experience with Kruskal-Wallis versus Zero-Inflated Kruskal-Wallis as nonparametric alternative to one-way ANOVA
I have a data set of 1 categorical predictor (4 levels) and one non-negative continuous response variable (listed as "aphidleaf in histogram). The response variable is not count data and the ...
- 1
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1
answer
16
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How to conduct Cox-regression with time-dependent covariate and estimate K-M plots (including log-rank test)?
I want to conduct a Cox-regression with time-dependent covariate and other control variables and estimate K-M plot with log-rank test result. I will take the heart transplant as an example, some ...
- 31
1
vote
1
answer
19
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ANOVA: RSS > TSS?
I am sure that this is a simple question, but I can't figure out what my mistake is. I am doing an ANOVA project using car::Anova. I presumed that the TSS would be ...
john
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14
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How to trust results of GAM in R
EDITED: I'm new to GAM's and am looking for some advice on if I can trust my model or not.
My dataset (n=200) is examining how a whole suite of environmental variables (15) impact the likelihood of ...
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1
answer
23
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Should I use ordered factor in glm model in R?
I want to fit a generalized linear model (logistic regression) to Titanic dataset. In EDA stage I transformed a variable (Pclass) to ordered factor. Before passing ...
- 61
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4
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Repeated measures covariants in linear model and not outcome
I have a dataset which contains a categorical outcome, 2 repeated measures over time for the same subject and several covariates
...
0
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1
answer
40
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Transformations for zero inflated non-negative continuous response variable in R
Initially, this was going to be a simple analysis of variance (ANOVA) with a categorical predictor (4 levels) and a non-negative continuous response variable (number of aphids on leaves from four ...
- 1
1
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0
answers
11
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Simple regression on subsets vs ANCOVA with interaction term
I'm attempting to predict a continuous variable as a function of one continuous variable and one categorical variable. This led me to an ANCOVA, but I've violated the homogeneity of regression slopes ...
- 198
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11
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Effect Sizes for Unstandardized Estimates in Hurdle Models? [closed]
I used the pscl package in R to run a hurdle model on count data. The output for the hurdle model provides an unstandardized estimate, standard error, Z score, and probability (> absolute value of ...
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0
answers
12
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Interpolation of a multidimensional grid
I am using the ks package to make density kernels for 2D up to 4D data. ks is an excellent package. Lets say I have $(X,Y)$ ...
- 1,020
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0
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27
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Simulating the error term with an AR(2) model
I'm working on some simulations in R where I have a time series in the format
$$y_t=\mu_t+e_t$$
where $\mu_t$ is a trend function that I have defined as $\mu_t=5*t+4*sin(2t)$ and where $t$ goes from $ ...
- 187
2
votes
0
answers
30
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Recreating equation in R returns different value
I am trying to understand an equation that is used to determine sample size. To do this, I am re-creating the example from a tutorial in R. However, when I re-create the example in R I get a different ...
- 31
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5
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How to choose gam base functions, family and splines and how to deal with non-convergence with gam (fam=ziplss, mgcv)?
I am new to this forum and modelling in general. I will try to give a full overview of issue, so bear with me. I am modelling a the habitat use of herbivore species. I have observational data from ...
- 1
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0
answers
12
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mixed effect with logistic regression not working as expected
I found a situation I cannot explain, and I would need some help from specialists.
I am trying to create a Simpson paradox, but for a binary variable, and to solve it with mixed-effect models. This ...
- 211
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0
answers
9
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Interpreting output of a pscl hurdle model in R
I've read several posts on interpreting the output summary of hurdle models, but I'm still struggling a bit to understand the output as its more complicated than models I'm used to. For my data, I'm ...
- 11
1
vote
1
answer
65
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Problems in chisq.test in R
I have two groups of samples, NGHC (n=14) and NHC (n=87). The result of the samples CO.05 should be 0 or 1. For example, the results can be
...
- 115
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0
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17
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K-prototype in R: Error when including missing values
I want to cluster data that includes categorical (dummies and variables with multiple categories) and numerical variables (normalised) and a substantial amount of missing values.
One reason why I want ...
- 1
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0
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15
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Proving that one score is not dependent on the other - interval data - R - Spearman correlation?
I want to attempt to answer the following hypothesis
A continuous scale (measured by an understanding score of 0-2) has a positive influence on consumers’ understanding of an eco-label (understanding ...
- 1
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0
answers
15
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Time Series: Predicting daily count sales data of three different products
I have a data set containing historic daily sales of 3 products pasta, nuts and yeast for one year (2020-01-01 - 2020-12-31).
Pasta and nuts are from store 1, while yeast is from store 2.
The ...
- 445
2
votes
1
answer
39
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Why do arrows of PCA graph have different angles between biplot and ggplot functions?
I'm using R iris data to show my point:
pca = prcomp(iris[,-5],scale=F)
png('irisNS_biplot.png',600,600)
biplot(pca)
dev.off()
...
- 319
0
votes
0
answers
9
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Error in nlrq R function and constraints to the argument [closed]
I've got a model to be estimated through the non-linear quantile regression method. The model is specified in such a way that I have 6 coefficients b1,b2,...,b6. I have constraints for my coefficients:...
- 31
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19
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The math behind svyglm() when we have weights and clusters
I want to apply survey::svyglm() to a scenario that we need to get the robust standard error in both weights and clusters.
There is an example in survey R package:
...
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0
answers
24
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Matrix Completion function in r [closed]
I want to write a matrix completion function for missing values.
I am wondering why the correlation of the output with the true missing values is decreasing when I am increasing the number of ...
- 1
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0
answers
14
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Are the classes between groups in a multiple-group latent class analysis related?
For example, if I run an LCA grouped by sex, and I get male class 1 and 2, and female class 1 and 2- do male class 1 and female class 1 relate in any way? Do they make up some larger/overall class 1, ...
- 21
1
vote
2
answers
14
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Machine Learning outcome with more than 2 categories-caret
I know that there are many algorithms for ML problems where the outcome has 2 categories.
I am wondering kwon if there are algorithms that accept outcomes with more than 2 categories, especially in ...
Daniel Leme
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1
answer
28
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Is the 'Std. Error' provided by lmer in lme4 actually Standard Deviation?
I have been working with lmer in lme4, and wanted to construct a density curve of the slopes produced by my model (rather than just confidence intervals). The model output of lmer produces a slope, ...
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1
answer
39
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Generating data from a hypothetical model
Let say I have below model
$y_{i,t} = 1 + X_1 + X_2 + {\gamma}_i + \epsilon_{i,t}, \epsilon_{i,t} \sim N \left(0, 1 \right), {\gamma}_i \sim N \left(0, \gamma \right)$
Here, the panel it is ...
- 227
1
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2
answers
53
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Cross-validation by hand in R
Trying to teach myself cross-validation on a super simple example, linear regression. My understanding is that when I build a model via CV, it should have a lower RMSE. But I find almost identical ...
- 450
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votes
2
answers
48
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What statistical test is suitable to summarise patient time in hospital with health condition
I am working on a dataset in which I am trying to summarise patient time in hospital by age and any health condition(e.g Cancer, Deprivatin, Depression or any). In my case it's Deprivatin. Patient ...
- 131
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16
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about Feasible GLS and OLS in R
I have question about FGLS and OLS.
If the FGLS coefficients are not much difference with OLS coefficients, which results are more robust in this case?
coefficients of OLS model
...
- 1
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votes
0
answers
21
views
What method to find relation between variable A and B with unequal replicates in different plot
I have an experimental setting as illustrated below.
Two different set of soil variables (say A and B) were taken in multiple plots (Plot1, Plot2, Plot n, those are not properly plot maybe... rather ...
- 1
2
votes
1
answer
31
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What is the effect size `h` in `pwr::pwr.p.test` in `R`?
The R package pwr has a function for calculating the required sample size for a one-sample proportion test (I assume a z-test ...
- 32.4k
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0
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16
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Is Kolmogorov–Smirnov test appropriate for what I describe in this question's body?
I basically have a ranked list of genes (0-1) the higher the score the better. I then want to intersect an independent list of genes to that ranked list, and then I need to calculate a p-value that ...
1
vote
1
answer
21
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Glm with all explanatory variables included gives same probability for all coefficients. Why?
I have a dataset containing the proportion of different land use categories in a circular plot around presence and randomly placed absence points of little owls. The dataset looks like this:
As you ...
- 23
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0
answers
22
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Unexpected wide confidence intervals with lsmeans glm binomial
I have a dataset with 2 factors (sorte / meristemposition) and a binary response (0/1) and ran a glm model in R including the interactions:
...
- 101
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0
answers
11
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Checking the results of the Metropolis - Hastings generated sample
I've generated a sample for the distribuition $f(x) \propto cos(x), x \in [-\frac{\pi}{2}, \frac{\pi}{2}]$ through the Metropolis - Hastings algorithm. For that I've used as candidate distribuition $q ...
- 77
-1
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16
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Can "Heavily Skewed" Predictor Variables be "Useful" to a Model?
In school, we were always told some general/informal "heuristics" about statistical modelling. In particular, we were advised about the following point:
If most of the variable contains ...
- 5,892
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9
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Why does the negative binomial produce multiple threshold parameters in Stata but not in lme4?
Stata produces estimates for the thresholds of a negative binomial regression, as demonstrated here.
However, the same does not happen with lme4 in ...
- 359
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1
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32
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"NA" in multiple regression
I have a question about multiple regression
data$x4 <- with(data, x1+x2) #x4=x1+x2
y = b0 + b1x1 + b2x2 + b3x3
mod1 <- y ~ x1 + x2 + x3 + x4
I ran ...
- 1
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0
answers
16
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nmle:gls with AR or MA terms
I am using nlme:gls to model trends. My understanding is that including AR or MA terms allows the model the correlation structure of the residuals rather than affecting the the regression estimates. ...
- 11
1
vote
1
answer
51
views
Writing mathematical equations (mixed effect models)
I have the following model which i am trying to write the mathematical equation for.
model;
mod = lmer(test ~ IQ + ses + (1 | Class), data = pupils)
I have the ...
- 49
1
vote
0
answers
16
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What does it mean when a feature or variable has non-significant t test statistics but significant p values in F test (anova)?
I ran a linear regression model with 15 features in R. 5 of them are categorical features (converted to factors and first category dropped for each of them). 10 are continuous features (already scaled)...
- 928
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0
answers
17
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Accuracy measures for moving average
I have 12 weeks of sales data and I'm using a moving average to forecast the 13th week of sales. I know that I can do this using the SMA function from the TTR package, the sma function from the smooth ...
- 1
3
votes
2
answers
78
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Summarising and Visualising three attributes in R
I am trying to summarise and visualise three attributes in R:
Patient_Age, Patient_Deprivation and Hospital_Time.
I am trying to summarise the time patients spent in hospital by deprivation(scale 1-5) ...
- 131
1
vote
0
answers
28
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How to conduct a boostrapped or a permutation wilcoxon test (in R)
I have a total of 18 mice, 9 from Healthy group and 9 from Sick group. Since I have a very poor sample size I would like to use boostrapping or permutation test.
Is there a way to conduct a ...
- 467
1
vote
0
answers
41
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Best statistical test to compare outcomes of glm's?
For my thesis, I am comparing the differences in habitat selection of little owls between 2005 and 2022. For both years I have little over 100 presence points (value 1) with a buffer of 50 meters ...
- 23
3
votes
1
answer
56
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Linear model with constraints in R
I have the following problem: I have a simple linear model with 3 independent variables.
...
- 31