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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0
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0answers
9 views

getting fitted lines with scatterplot matrix in r [migrated]

How do I get a scatterplot matrix which will also show the fitted lines in each plot. I know how to use "abline" function with individual plots but don't know how to implement it in a scatterplot ...
0
votes
0answers
19 views

using biomod2 package with continuous response variables

I am looking to correlate crop area with climate variables and then predict for future if suitability of crop areas will change/remain same under different climate scenarios (in line with species ...
-3
votes
0answers
53 views

About a problem of R in Linux [on hold]

When I use Rscript xxx.r to run a R script in Linux, I found that if I run it twice, the variables I used in the first time will not be kept when running the second ...
1
vote
0answers
18 views

Estimating ARIMA models in SAS [migrated]

I would like to (insert "have to") do some ARIMA modeling in SAS. Normally, I would simply use auto.arima in R and let the function choose the differencing orders and just specify whether to use AICc ...
0
votes
0answers
17 views

z test for difference between 2 proportions using R [on hold]

There is a population with 1,000,000 cases and two equal-sized groups within this population. The p for group 1 is 0.9 and p for group 2 is 0.8. Draw samples of size 500 from this population. Assess ...
0
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0answers
18 views

Using results of Canonical Discriminant Analysis to get overall variable importance?

I have a dataset with thousands of observations pre-assigned to 18 groups and with measures for 8 different variables. I am using canonical discriminant analysis to see how separable my 18 groups are. ...
1
vote
1answer
39 views

Finding cycles in data using a periodogram and Fast Fourier Transform

Problem: Detecting cyclical patterns in daily data using periodogram and FFT. The issue is how to code in R the periodogram to detect monthly, quarterly, semi-annual, annual..etc cyclical patterns in ...
2
votes
0answers
19 views

Regression Model for Binary Matched or Paired Contingency Table Results

This is a follow-up question on a prior thread about the same setup as follows: We have two "Methods" ("A" and "B") to diagnose a medical condition. We are not trying to determine which one is better ...
0
votes
0answers
12 views

How to include a half-Cauchy prior in a Gibbs sampler for a hierarchical model (Rubin's “8 schools”)?

In the third edition of the popular Bayesian Data Analysis, Gelman et al. discuss a variation on Rubin's "8 schools" problem in which only three schools are considered (p. 131). The authors suggest ...
4
votes
1answer
52 views

Null deviance in glm R

This is a question about the difference in calculating the null deviance in a simple Poisson model with and without an intercept. If ...
3
votes
1answer
54 views

lme4: random effects

I have a simulated data set of 4 repeated measurements (measure) for 5 subjects (subj), 20 trials (trl) each. I am trying to fit a model with random slopes for age category with subject and trials ...
0
votes
0answers
3 views

Combined bar plot and points in ggplot2 [migrated]

I would like to plot a "combined" bar plot with points. Consider to following dummy data: ...
1
vote
0answers
17 views

error for using forecasting models inside a loop in r [on hold]

I intended to automate the process of finding forecasts for every 48 hours for an hourly set of data. I simply want to read 3 years of historical data, fit a forecasting model to that and provide ...
0
votes
0answers
14 views

Questionable Output from Time Series Forecast Using MSTS and TBATS from R forecast package

Using historical daily order totals, I'm wanting to forecast the totals of the next 7 days. It's known in my field that these totals fall subject to weekly and yearly seasonal trends. Called ...
0
votes
1answer
20 views

Computing the true effect size from F-values and sample sizes?

I'm trying to extract a bunch of effect sizes from a couple of different studies in for which the authors have performed ANOVAs on their data. More specifically, I'm interested in the main effects of ...
3
votes
1answer
76 views

How is the sigma^2 value (or MSE) for the link function computed in logistic regression in R?

For example, if you have a logistic regression on certain dataset: fit <- glm(y ~ x, data = test, family = "binomial") If you do ...
0
votes
0answers
9 views

Significance of a correlation considering missing data

So I'm dealing with two timeseries, of which one contains quite some missing data (between 10-60%). I'm excluding some datasets which contain exceptional much missing data, but still I would like to ...
1
vote
1answer
53 views

How to document a Random Forest result (final model)?

Using Random Forest to predict dichotomous variables (for classification) I encountered the problem how to best document this model, i.e. I want the user to reproduce/use the final model I created on ...
0
votes
0answers
42 views

Misfitting of drift rate in Wiener model

In a binary-decision experiment, the accuracy and response time of some subjects were recorded. My goal is to fit a Wiener model to response time and accuracy data. The binary experiment has three ...
0
votes
0answers
16 views

R programming. Finding efficient frontier using Black Litterman Model

I'm trying to get Efficient frontier Using Black Litterman model. I'm getting only optimal portfolio using BLCOP Package and i have used this function ...
2
votes
1answer
37 views

simulating data with a lot of predefined constraints in R

how to simulate data (in R) to generate , sample values 1) variables with specific correlation values for a particular model AND 2) with predefined regression coefficients? 3) Can we also set the ...
0
votes
0answers
35 views

R binomial family with identity link

I want to fit a linear model by R with family=binomial(link="identity"), however, binomial family do not have identity link. What should I do?
0
votes
0answers
47 views

How to calculate confidence intervals in R and then plot them? [on hold]

I want to be able to print confidence bands around the dots of the plot for the following data ...
0
votes
0answers
6 views

Accounting for initial values of reponse variable in binomial GLM

R v.3.1.0. Mac OSX 10.9.5. Can somebody please recommend a method to account for initial values of a response variable in binomial GLMM? I am designing an ecological experiment, and am having a hard ...
0
votes
0answers
7 views

Extract ETS method used for automatic forecasts of hierarchical time series with hts package [migrated]

I'm trying to extract the ETS method that is automatically chosen when we apply the forecast function to an hierarchical time series using the hts R package. When I look in the structure of the ...
4
votes
1answer
55 views

Examining trends with interactions and with stratification - obtaining discordant results

I'm examining the effect of income (categorized into quintiles) on a response variable during different years (from 1996 to 2014). I adjust for some other covariates and have repeated measurements on ...
-1
votes
0answers
10 views

r package for non-decimated /stationary wavelet [on hold]

Which r package is should be used for forecasting and plotting stationary wavelet transformation?
0
votes
0answers
12 views

Scatterplot with two different categories of data [duplicate]

I have a text document containing three columns. One column is "sex", and each value is either "M" or "F". The other two columns contain numerical data (my explanatory variable and response ...
0
votes
0answers
13 views

Time series analysis for discontinous years

i have a data of measured values of pH in river water for two years 2004 and 2009 for each month. I want to see seasonal trend ie: are there similarity in summer , winter and monsoon for both year. ...
1
vote
1answer
59 views

What is the reason for this discrepancy between confidence level and probability?

I ran the following R code: library(Hmisc) binconf(x=1, n=70) # PointEst Lower Upper # 0.01428571 0.0007327613 0.07658187 Which is the ...
1
vote
0answers
31 views

Paired homogeneity test: Compare two regression coefficients in R

I have a question about paired homogeneity test. By using Cox regression analysis Im evaluating 2 new biomarkers (A and B) in association with a outcome (X). I developed 2 multivariable models and on ...
0
votes
0answers
46 views

Multiple imputation of conditional variables

I need to impute the missing values of a dataset of medical data in which several variables only make sense if another variable has a specific value. In the questionnaire the data come from they were ...
2
votes
1answer
33 views

partial plots from a Random forest classifier for binary predictors

I'm working on a classification problem with continous and categorical predictors with Random Forests (RF). I'm particularly interested on RF as we avoid the specification of the functional form. ...
1
vote
0answers
12 views

should we check for multicollinearity when building a discrimination analysis?

In fact, I have two questions: 1- do we need to check for the multicollinearity when we deal with linear discrimination analysis? 2- how to solve those variables which are multi-collinear? Lets ...
2
votes
1answer
18 views

Advantages of counterbalancing vs. randomizing stimuli

I'm designing an experiment, in which 40 participants answer 10 questions, 5 in condition $A$ and 5 in condition $B$, and I'm interested in the difference between the two conditions. It's not clear ...
-1
votes
0answers
33 views

Optimal brain damage in R [on hold]

Is there any R package implementing optimal brain damage algorithm or anything similar what can be used to prune neural networks models?
0
votes
0answers
48 views

Setting up a aov model in R for a variant of a 2-way nested ANOVA

I have a rather complex experiment i need to analyse The experiment was an infection trial, where the effect of two different infection methods ("inoculation" and "in-contact infection") were ...
0
votes
0answers
24 views

non-metric multi-dimensional scaling in R: help with plotting and understanding Stress for isoMDS vs. metaMDS

I have a dataframe with 900 observations. There are 11 columns: 9 measured variables and 1 representing region. ...
-1
votes
0answers
10 views

How to calculate average groups and create columns [closed]

I want to write a function for the following table Group1 Group2 Age diffG1 diffG2 A K 12 1.33 1 A K 14 1.33 1 A K 16 1.33 1 B M 12 ...
-1
votes
0answers
12 views

modify Length of Y axis in barplot with R [closed]

I try to do a barplot with R Here the code hommes <- scan() ...
0
votes
0answers
12 views

R language: Can the function rfe of the package caret be used with a mixed effect model [migrated]

I would like to do feature selection with a mixed effect model in R, but I cannot manage to combine the function rfe of the package caret with the function me of ...
6
votes
4answers
119 views

Detecting changes in time series (R example)

I would like to detect changes in time series data, which usually has the same shape. So far I've worked with the changepoint package for R and the ...
0
votes
0answers
13 views

How to do regression model selection if dummy variables are involved?

Original post on stackoverflow: http://stackoverflow.com/questions/28773153/how-to-do-regression-model-selection-if-dummy-variables-are-involved I am trying to do a logistic regression analysis in R ...
0
votes
0answers
9 views

How do I interpret results from calibration using bootstrap in R [closed]

I am using the package rms in R. I want to report results of the statistics found in the function: ...
1
vote
0answers
12 views

Non-recursive regression tree

I would like to construct a regression tree such that each factor appears at most once on each branch. When I use rpart in R, it commonly results in a tree where ...
-1
votes
0answers
39 views

Is the question of outlier detection to fit a model better? [closed]

I was searching to find a package in R which has outlier detection since i am a Matlab User; Anyway, I found several questions in this website which the answers disappointed me very much. this is one ...
1
vote
0answers
18 views

How do I fit a linear mixed model in R with autocorrelation, when the effect of time is of no interest?

I am attempting to fit a linear mixed model with the lme function using R. My data involve repeated measures, but the effect of time is not of interest to me, so I don't want to include it as a fixed ...
0
votes
0answers
13 views

maximizing matrix diagonal elements in R [migrated]

Given a matrix (or table in R ) ...
0
votes
0answers
17 views

Need for correction of persp plot? [on hold]

I have problem with persp and contour plot to visualize PDF and CDF plot of bivariate standard normal plots in R. When I call the generic function persp() and contour() I got wrong plots of PDF and ...
0
votes
0answers
4 views

R Packages for rank-preserving structural failure time model (RPSTM)

I have a randomized clinical trial data that has high percentage(30-40% in both arms) switching over to a different treatment regimen. By browsing through some literature, I am inclined to perform ...