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`.
28,853
questions
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How to use MAPE with auto.arima model?
The code below gets a: error in mean(abs((y_true - y_pred)/y_true)) :
argument "y_true" is missing, with no default
I've seen MAPE used on forecasts. Can one use this and similar methods on ...
- 141
1
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1
answer
19
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Calculate log-likelihood of logistic regression
I am trying, without success, to calculate the log-likelihood of the most basic logistic regression model - a constant probability model (i.e. only $\beta_0 \ne 0$).
For the simplest model with 1 ...
- 641
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2
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19
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regression modeling - logistic
My task is to run a logistic regression that models the probability that revenue is non-zero (in the
logistic regression parlance, a positive revenue is a success). Revenue variable is numeric and ...
Sally Nelly
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0
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8
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Use of t_family distribution in glmmTMB
I am trying to use t_family(link="log") distribution from the glmmTMB package. The package allows fixing the shape parameter using ...
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0
answers
7
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Interpret results of a mixed effects model analyzing a 2x2 cross-over study?
I have conducted a randomized 2x2 cross-over trial of 8 participants measuring the effect of a specific diet (intervention) vs normal diet (control) on the number of sleep hours.
The study design ...
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1
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41
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Generate survival data with functional data using R
I am reading this article here and trying to regenerate their simulation study. Here is this scenario here, among others, but if I can figure out one, the rest follow. That is,
Simulation set-up
we ...
- 107
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0
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9
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I am trying to visualize the NHANES dataset using the PAXINTEN of the individual which is intensity recorded by accelerometer [closed]
I am running the following code:
...
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0
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1
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22
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Why does the best fitting Weibull distribution for this survival data deviate further from the actual data than a poorly fit distribution?
I started working with the Gumbel distribution and fit it to the lung dataset to try it out. I then compared it with the survival curve using the Weibull ...
- 463
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15
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What does predict.cv.glmnet actually do with new data? [closed]
This might be a dumb question but I am struggling to figure out what predict.cv.glmnet actually do under the hood, let's say for example for a Lasso regression.
Does it actually train a new model with ...
5
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2
answers
183
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Is there a clean way to derive the start parameters for running the `fitdist()` function for the Gumbel distribution?
I've begun working with the Gumbel distribution and started with the example in the package documentation at https://cran.r-project.org/web/packages/fitdistrplus/fitdistrplus.pdf. For the Gumbel ...
- 463
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0
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18
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Code issue with plot-x and y lengths differ error [closed]
For the code below:
Error in xy.coords(x, y, xlabel, ylabel, log): 'x' and 'y' lengths differ
Traceback:
5. stop("'x' and 'y' lengths differ")
I tried ...
- 1
0
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0
answers
10
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Statistical test for interpreting negative coefficients in multivariate cross sectional analysis [closed]
I wrote a seminar paper on the conditional ß-convergence (income convergence) of the Solow Model and therefore ran several cross sectional regressions in R. Thus, I regressed the variables "GDP ...
1
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0
answers
16
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Bounded uniform prior in R
I have been fitting a bayesian GLM using brms. The code works well but when I loop this over several data and make it a bit more complex, R encounters a fatal error and crashes. This seems to be ...
0
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0
answers
9
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How can I format a double entry table into a long table in R to run a linear model? [closed]
I need to run a linear model of some data. I was given a 'double entry' table. Until today I was not familiar with them. This is how it looks:
Every row has a value of the dependent variable, except ...
- 201
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0
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17
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How to create a dataframe from the result of a for loop in R? [closed]
I want to obtain from a for loop a dataframe in which i can visualize better the result of the code. I'm in the context of Random survival forest, so I leave an example to explain me better.
...
1
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0
answers
17
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Testing signifiance of random effects on large dataset
I want to do a mixed linear model, with two hierarchical random effects. I want to determine wether if these random effects are worth including in the model.
I have tried so far doing :
...
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21
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How to accomodate for missingness in column dependent on value of other column
Please run this code in order to create a reproducible example:
...
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0
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14
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How to simulate variability (errors) in fitting a gamma model to survival data by using a generalized minimum extreme value distribution in R?
As shown below and per the R code at the bottom, I plot a base survival curve for the lung dataset from the survival package ...
- 463
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0
answers
6
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Box Cox Back transformation of coefficients/LSMEANS and confidence intervals IN R [closed]
I have made a simple gls model with a continuous variable as the response and a categorical as the predictor. I have used box Cox transformation to the response because it was highly skewed. How can I ...
- 3
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0
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9
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how to estimate the lognormal distribution 3 parameters using maximum lq likelihood method in R/Rstudio
i've tried to find the equation for lq likelihood equation is:
lq_likelihood <- ((f^(1-q))-1)/(1-q) and with f is pdf of lognormal distribution and q is distortion parameter(i'm using q=1-(1/n))
...
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0
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33
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How do I determine which variables to pick in a binomial GLMM using lme4?
I'm still pretty new to modelling but essentially, the dataset is consists of the following (the first observation only):
...
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0
answers
14
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Computing a variogram in R using a distance matrix [closed]
My question is to an extent a copy of this question, although that question is now 8 years old.
I have geographical data with values distributed according to lattitude and longitude (in degrees).
geoR'...
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1
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1
answer
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Kernel Smoothing for Time Series data
I have generated a time series data set of measurements that are a bit noisy and I want to apply kernel smoothing to the data. My time series data is not regular however, meaning that the time ...
- 111
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15
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Understanding Optimizer Options Using tidysynth
Under the generate_weights() command using the {tidysynth} package for executing the synthetic control method in R, users are given a number of optimization options. However, I cannot find ...
- 519
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2
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641
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How do I deal with many zero values in terms of correlation?
I am currently working on my master thesis. I have determined a simulation model for tax returns and to verify this I would like to use true values.
I would like to determine the correlation between ...
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0
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7
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What's the correct way to report location and spread descriptive stats when you have repeated observations and unequal sampling?
Objective:
Report summary statistics for each treatment x timepoint x condition sub-grouping when there is unequal sampling and repeated observations per subject. It is assumed that all the subjects ...
- 183
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0
answers
14
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dataset used in replication of Bernanke, Boivin and Eliasz (QJE, 2005) in R
I am trying to work on FAVAR model but can't find the dataset used for this replication https://jbduarte.com/blog/time%20series/r/favar/2020/04/24/FAVAR-Replication.html. I looked everywhere but can't ...
- 11
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0
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24
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How to sample from the generalized extreme value distribution in survival analysis?
In the image below and per the code at the bottom of this post, I plot a base survival curve for the lung dataset from the ...
- 463
1
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0
answers
25
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bootstrapped confidence interval for glmer model with identity link
In an experiment Subjects decide as fast as possible whether letter strings presented on screen are real Words or non-words and reaction time (RT) in milliseconds is recorded. We want to know for ...
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9
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What does the neuralnet error reported in plot mean?
When fitting a simple MLP neural net on the Credit dataset by the package neuralnet in R and then plotting it, we get an error reported at the bottom of the plot, ...
1
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2
answers
38
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DAG - why is the path open?
I have this DAG
As I understand it, the paths D <- Ed -> St -> P -> Su and D <- A -> P -> Su are both closed because the contain the collider P. If I condition on P, both these ...
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0
answers
11
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How to test for size (Typ one error probability) on Breusch-Pagan Test in R?
The data i created contains heteroscedasticity. I already calculated the power so my idea was to basically do the same but switch the hypothesis so that H0: Heteroscedasticity and H1: Homoscedasticity ...
user388641
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0
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9
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Can the limma package be applied to Log2 RUV-normalized data? [closed]
So I have a dataset that consists of the batch correction through RUV-normalization of several microarray datasets containing tumoral and non-tumoral samples. The data is in Log2 RUV-normalized ...
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0
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11
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Calculate confidence intervals of ratio calculated from four values using R [closed]
I have four numeric variables (A, B, C, D), each with confidence intervals, and I want to calculate the CI of the ratio between these four values. The ratio is calculated by (A + B)/ (C + D). Is there ...
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0
answers
16
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dev.ratio in glmnet
After running glmnet I can get a pseudo R-squared with glmnet.fit$dev.ratio. Does this take into account the complexity of the ...
- 1,159
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0
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6
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What is a reasonable range of penalty values to try in PELT changepoint analysis?
I have a simulated a time series data set several predictor variables and response class that I created to practice different analytical techniques before I apply methods to my real (very large) ...
- 111
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0
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12
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How to determine contrasts in combinations of categorical variables with emmeans
I have some data with a continuous outcome that is measured among 4 categorical variables: treatment group, gender, collection date, and sub_type. Gender is M/F, collection date can just be Mon/Wed, ...
- 1
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1
answer
20
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Multiple events in Cox PH with time varying data
I study coups d'etat. I would like to understand the relationship between leader/country characteristics and the likelihood of coup attempts.
I have a leader-country-year dataset with one entry for ...
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9
votes
1
answer
369
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Why doesn't R output for a paired t-test match the formula for a confidence interval in the t-distribution?
My understanding is that the formula for a confidence interval when using a t-test is as follows:
$\bar x \pm t_{n-1,\alpha / 2} \frac{S_d}{\sqrt{n}}$
where $S_d$ is the standard deviation of the data....
- 173
2
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1
answer
56
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Non-linear regression. Need some help implementing a model from a paper
I found this paper very useful for my research, however, I'm not familiar with non-linear regressions and I'm finding it tricky replicating it.
Using the first f=model for example:
...
0
votes
1
answer
8
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Feature importance/model exploration in a large survival model
I've built very-well performing survival model (weibull proportional hazards model for interval censored data, modelled with IcenReg) with many covariates, some ...
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0
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16
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Create a graph in R [closed]
Hello I want to create a graph like that in R. Any help with the code I have to write to create it?
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12
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Implementing bootstrap for sequential target trial emulation [closed]
I am currently working on sequential target trial emulation and have been stuck in the step of bootstraping. I would greatly appreciate any assistance, recommendations, or sample code that you could ...
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0
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22
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Autocorrelation returning non-significant values despite an apparent pattern
I have just finished Chatfield and Xing's The Analysis of Time Series, 7th edition and I'm beginning to play around with some simple analysis. I have this graph representing the grand mean value ...
1
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1
answer
30
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How should I scale data that has been assembled from different data sources?
The data I'm woking with consists of 3 types of data:
1- binary features: those features are either 0 or 1. I have about 6 or 7 columns.
2- cells: the values here range from 0 to 0.8 at max. Here I ...
- 409
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0
answers
10
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Running the same mixed model with different contrasts to explore different hypotheses
I'm running the following mixed model to explore the relationship between Condition (3 levels; Predicted, ...
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1
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1
answer
63
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Multiple predictors that measure the same concept in regression
I have used three questionnaires in a study that all measure musical training. Each of these three questionnaires (MT1/MT2/MT3) consist of various Likert scales that are averaged to calculate the ...
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3
votes
1
answer
25
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What are the possible solutions to do matching on very large dataset
Hi I would like to match a group of treated patients with an untreated group. I have about a million patients in the treatment group and ten times that in the control group. Conventional matching ...
- 735
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0
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27
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power analysis for glmer mixed models
I want to know an appropriate way to conduct a post-hoc power analysis for several glmer models built in R using the lme4 package. A reviewer asked for this.
What I did:
I used the R package simr ...
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1
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1
answer
16
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How to convert R output from auto.arima function into mathematical model?
I'm building a model using the auto.arima function in R, and it gives the following output:
...
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