1
vote
0answers
24 views

Plotting fitted values for an nlme model

I just got the output of my lme (nlme) model called shalit5 with syntax: ...
2
votes
0answers
71 views

How to get the regression from a plot?

I have a dependent variable C and an independent variable VPT. VPT is the average volume per ...
2
votes
1answer
92 views

Detecting heteroscedasticity - Can I use Breusch-Pagan Test on binary logistic regression?

I'm currently testing a (binary) logistic regression model, which seems to have at least some issues with multicollinearity. Now I don't really trust the data anymore and would like to also test it on ...
2
votes
0answers
17 views

3D plot of the residual sum of squares in linear regression [migrated]

I'm trying to reproduce Figure 3.2 from the book Introduction to Statistical Learning. Figure describes 3D plot of the residual sum of squares (RSS) on the Advertising data, using ...
0
votes
1answer
43 views

Good way to plot a variable between conditions with multiple measurements

I've a frame containing Participant----Condition----Duration Participant1,One,2000 Participant1,One,2780 Participant1,One,200 Participant2,Two,2000 Participant2,Two,2340 ...
0
votes
0answers
8 views

R plotting on a single figure [migrated]

The question I have to answer is: As an exploratory investigation, visualise the data in a set of pairs plots between the two response variables (ES and NS) and the 5 explanatory variables ...
0
votes
0answers
22 views

Plotting a timeseries in R as stacked bar [migrated]

I have a dataset that look like the following | SUBJECT | ACTION | DURATION | |---------|--------|----------| | 1 | A | 39,57 | | 1 | B | 1,48 | | 1 | B | ...
0
votes
1answer
47 views

Basic R script/package with lots of automated calculations [closed]

Does that exist? A basic R script or package that just needs the data, and it spits lots of “basic” statistics (like the mean, the median, quartiles, make a plot, a boxplot, a histogram, a cumulative ...
0
votes
1answer
67 views

R: plotting a prediction model and understanding results

I am experimenting with developing a linear model lmodel1 which predicts a temp response variable, given three independent ...
2
votes
0answers
29 views

predict() in lmer regression, but I need it only 2 categories [migrated]

I am attempting to estimate a multilevel model. My code is: ...
1
vote
1answer
163 views

Visualizing large dataset with multiple subgroups

I have a large data frame in the following form (I apologize for this formatting): ...
2
votes
0answers
53 views

Analyzing CART type trees in R--options for grouping results, formatting plots

I'm new to using CART trees, but have been asked to do so for a project I'm working on. I've had success running the scripts (from both RPART and PARTY packages) but I can't seem to get exactly what ...
1
vote
0answers
42 views

PCA figure formatting options in R

I've completed PCA analysis, in R with VEGAN package, of some ecological data on tree health. There are 80 trees total (so, 80 'sites') divided into four treatment categories. I've got the data ...
0
votes
0answers
24 views

Plotting Logistic Regression in R [migrated]

How can I plot the logistic regression? I would like to plot the dependent variable on the y-axis and independent on the x. I called the coefficients and got an output, so no errors on the script. ...
4
votes
1answer
112 views

Time series prediction: visualising path uncertainty region

I am predicting a time series' future evolution and am evaluating the path uncertainty using bootstrapping. Is there a good way to visualise the uncertainty that goes beyond simply plotting a pair of ...
-1
votes
1answer
24 views

R plot set scale [closed]

I did some research and didn't find what I was looking for: I have a data set x = 10,100,1000 and y1, y2, y3 respectively, and I want to plot those points. But what is happening is that in the x ...
3
votes
1answer
83 views

Interpreting box plots with one whisker [duplicate]

I have done a boxplot to represent my claim frequency. However make 2 and 4 have only 1 whisker. How do I interpret that?
5
votes
1answer
112 views

Interpret clustering plotted in the first two principal components

I got this plot when I plotted a clustering object in R. If I run km <- clara(data, 2), then plot(km), I get a similar ...
0
votes
0answers
64 views

How to plot binomial regression model in R

I´m trying to visualize a glm model with a binomial response variable, I want to put a line in the plots, but neither lines or ...
3
votes
2answers
94 views

Why do a density plot and a rug plot seem to disagree?

The second peak of the density plot is large in this example. Why does the rug representation of the data--which seems to show few high values--not appear to match ...
2
votes
2answers
88 views

Contour plot for a likelihood function

For the likelihood associated with the mixture model 1/4*Normal(mu1,1)+3/4*Normal(mu2,1) I would like to have a figure as like as following one for a simulated ...
2
votes
1answer
125 views

R ggplot2/ezPlot: Plotting 3x3 RM ANOVA design per quantile of covariate with error bars

First of all, my data: http://www.pastebin.ca/2599202 (I hope this is not too inconvenient, because I fail creating good fitting example data) What I basically need, is a plot like: I plotted the ...
7
votes
2answers
162 views

What are good ways of plotting distributions over time using R?

I have ~400 individuals and >10k timepoints each (simulation results) I would like to be able to monitor as they change over the course of time. Plotting all individuals is too messy, plotting mean ...
5
votes
3answers
232 views

Understanding the confidence band from a polynomial regression

I'm trying to understand the result I see in my graph below. Usually, I tend to use Excel and get a linear-regression line but in the case below I'm using R and I get a polynomial regression with the ...
0
votes
0answers
30 views

Combining Box Plot with frequency count [duplicate]

Are there graphing techniques (certain kinds of plots) that are similar to the Edward Tufte's box plots - shown below - but that consider the distribution of the data points? But instead of a black ...
0
votes
1answer
147 views

Making a cumulative incidence plot in R

Background I have a survival object in R called km. ...
0
votes
1answer
58 views

Project feature vectors into 2D plane for visualization

I would like to project my observations which consist of more than 2 variables into a scatter plot. Some time ago I saw an R package that does this by reducing the dimensions (possibly using PCA and ...
4
votes
1answer
202 views

How to interpret the lasso selection plot [duplicate]

I did lasso selection using lars::lars(), then I got this plot. I have no idea how to interpret it: Could anyone provide a brief explanation? Why does it plot ...
0
votes
1answer
139 views

How to make linear regression model while 'control' confounding variables?

I have data from survey, and Trying to build a linear regression model using R like A~ B however, want to control C, D, E, F, G. like Age, Sex, and other confounding variables. I tried to make some ...
2
votes
2answers
111 views

R - show movement of points

Suppose I have data of the following form t1 = data.frame(a=c(2,3,3,1,5),b=c(6,4,5,2,1)) t2 = data.frame(a=c(3,4,4,1,8),b=c(5,5,5,3,3)) If you consider ...
1
vote
1answer
179 views

How do I correctly produce a prior/posterior plot from MCMC chains in Bayesian hierarchical models?

I'm a beginner at hierarchical modeling and statistics in general and this is confusing me. Question: If I draw a histogram of a posterior distribution from an MCMC chain, do I draw the prior as a ...
1
vote
0answers
121 views

Visualising a linear model using effects package in R

I have ran this model in R: model <- lm(mpg ~ hp + drat + disp, data=mtcars) And I have visualised this model using ...
6
votes
2answers
295 views

How to best visualize one-sample test?

We are currently writing a paper with several one-sample Wilcoxon tests. While visualizing two-sample tests is easy via boxplots, I was wondering whether there is any good way to visualize one-sample ...
2
votes
1answer
473 views

Plot a linear discriminant analysis

Is there a package in R that can do this plot on LDA data graph plot: original question: How does linear discriminant analysis reduce the dimensions?
0
votes
1answer
323 views

In R, how do I fit a student-t distribution to a set of empirical data? [duplicate]

In R, I can fit a Probability Density Function to some empirical data using the following code: ...
11
votes
2answers
543 views

Showing spatial and temporal correlation on maps

I have data for a network of weather stations across the United States. This gives me a data frame that contains date, latitude, longitude, and some measured value. Assume that data are collected once ...
0
votes
1answer
111 views

Problem plotting GLM data of binomial proportional data 2

I am trying to plot the predicting line for a GLM with proportional data. After having troubles with the example from "Crawley" I found this link: Problems plotting GLM data of binomial proportional ...
8
votes
1answer
242 views

Best way to visually present relationships from a multiple linear model

I have a linear model with about 6 predictors and I'm going to be presenting the estimates, F values, p values, etc. However, I was wondering what would be the best visual plot to represent the ...
0
votes
1answer
76 views

Mathematics behind how the normal to the plane is derived from a linear model when plotting with planes3d

I've been experimenting with the rgl library to draw 3d plots of some linear models. The package works really nicely, but I have a question on the math behind how one draws a plane (using planes3d) ...
12
votes
1answer
378 views

How to visualize a 3-D density function?

What is the best way graphically to visualize a 3-D density function? As in I would like to visualize $$z=f_{X,Y}(x,y)$$? Not necessary but R code for this would ...
2
votes
1answer
125 views

What is this horizontal point & confidence graph called?

From page 166 of the Open Intro to Stats, what is this type of graph called? It represents 25 point estimates of a mean, together with their confidence intervals, centered around the actual population ...
2
votes
0answers
140 views

Scatter plots of p-value distribution of gene expression data in R

How do I distinctly represent two data sets on the same scatter plot , to compare the p-value distributions of the genes using R packages? The gene expression values and p-values (obtained by ANOVA) ...
3
votes
0answers
96 views

Plotting fit for binomial lme

I've been asked by a reviewer on a manuscript to provide plots of a model fit for a binomial lme which is specified as follows: ...
1
vote
1answer
473 views

Interpretting LASSO variable trace plots

I am new to the glmnet package, and I am still unsure of how to interpret the results. Could anyone please help me read the following trace plot? The graph was ...
5
votes
1answer
152 views

Visualising a linear model with 6 predictors in R

I've recently been wondering how to visualise a linear model with >1 predictor. Today I came across a paper that managed to visualise a linear model with 6 predictors (and one response variable) in a ...
8
votes
2answers
383 views

Cumulative / Cumulative Plot (or “Visualizing a Lorenz Curve”)

I don't know what such plots are called and thus I just gave this question a stupid title. Let's say I have an ordered dataset as follows ...
3
votes
2answers
127 views

Comparing weights versus time graphically using reshape, vioplot, and ggplot2

I have a group of 200 children who came to clinic at months 0, 1, 2, 3, 6, 9, and 12 this year. At each clinic visit the children were weighed. ...
1
vote
1answer
50 views

Comparing weights versus time graphically with error bars

I have a group of 200 children who came to clinic at months 0, 1, 2, 3, 6, 9, and 12 this year. At each clinic visit the children were weighed. ...
1
vote
1answer
295 views

Performing a Self-Organizing Map on multiple distance matrices in R with a better visualization

I have a number of distance matrices that are related to different elements. Each of these matrices represent a specific distance between these elements. I want to perform a Self-Organizing Map ...
1
vote
2answers
177 views

Drawing smooth 2D curves with 2D spline in R

The problem I am running into here is the following: there is a set of 4 points in 2D, and I need to plot a smooth curve in 2D space that runs through these points. Is there a package in R to do this? ...