Questions tagged [contrasts]
In linear models and particularly in ANOVA, a contrast is a linear combination of parameters with coefficients summing up to zero. It is used to test the corresponding null hypothesis. Contrasts are especially often used with categorical predictors (factors) to make comparisons among the groups (categories). [See also tag 'categorical-encoding']
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Need of p-value adjustment when analyzing all possible pairs of factor levels in linear model
I have a nominal (not ordinal) variable with $K$ levels (these are actualy some groups of patients) and I run linear model in which:
this nominal variable is one of IV's (others are age, sex and so ...
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How to interpret coefficients obtained from an ordinal variable in a linear regression?
I'm following this example https://stats.idre.ucla.edu/r/library/r-library-contrast-coding-systems-for-categorical-variables/
I was wondering what is the correct interpretation of the coefficients ...
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between group contrasts using effect coded dummy variables in regression
I was taught a technique for doing this but can no longer figure out why this works, though using a simple data set I am able to prove it. I will go through that proof here as I think it's the ...
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R - using contrasts to compare all levels of a variable?
I am doing a statistical analysis in R. I made a lmer() model, in which a variable has 4 levels (1,2,3,4).
The script sets up a contrast matrix for these levels.
Basically, The main hypothesis is set ...
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27 views
Fixed/Mixed effects models - emmeans, contrasts, etc
I'm taking a GLMM course and working through some homework that conceptually isn't that difficult, but is very challenging with respect to implementation in R.
The dataset is composed of ...
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22 views
How to compare approximate Bayes Factors (BIC) with glm.nb? (R stats)
I have a situation where I would like to write up an analysis where the statistical significance is non-significant. I wanted to be able to accept the null hypothesis instead of merely 'failing to ...
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How to set up contrasts in a linear regression models that involve averaging over levels of another factor?
For simplicity, assume we have a linear model which looks like this:
Outcome = beta0 + beta1*Treatment + beta2*Time + beta3*Treatment*Time + error
where ...
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Planned Contrasts in Mixed models: group with 3 levels
This analysis is based on data from https://stats.idre.ucla.edu/r/seminars/repeated-measures-analysis-with-r/ with some modifications.
Pulse measurements were made at 3 time points (1,2,3) for study ...
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1answer
39 views
difference between interaction with anova and contrast functions
I'm trying to understand the difference between the interaction with the anova function and the interaction with the contrast ...
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27 views
Can planned contrasts in ANOVA be one tailed tests?
I have an experiment with 3 within-subject conditions: A, B and C. My dependent variable is reaction time. I am interested in comparing A to B and A to C. Using aov() on R I run an one way ANOVA with ...
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Scheffe's S Method - help with finding the absolute value of l
I am trying to understand Scheffe's S Method and how the absolute value of l is found. In the example I am reading, the absolute value of l is |-.836| but I have absolutely no idea how this value was ...
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1answer
118 views
treatment and sum contrasts, inconsistent results
I am fitting a linear mixed effect models with two factors (mPair with 6 levels, and spd_des with 3 levels) and their ...
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112 views
R - Linear Regression with parameters constraint - contr.sum contrast
I am facing a problem with running a simple OLS regression with two categorical independent variable.
I would like to impose that the sum of the coefficients referred to one variable (x in the ...
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1answer
202 views
When is deviation coding useful?
After many years of learning about contrasts in linear models I am curious about the relative usefulness of deviation coding, as it is defined by this website. I would appreciate someone filling me in ...
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1answer
106 views
How to calculate (standardized) orthogonal contrast coding in R?
I want to determine efficient fractional factorial designs and blocked designs for factorial surveys and am using the R library AlgDesign. The criteria I'm using to determine if a design is efficient ...
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1answer
203 views
Difference between Within-Subject Contrasts and Pairwise Comparisons in a Repeated Measures ANOVA
I'm running a two way repeated measures ANOVA, and I'm having trouble finding what is the appropriate output to report (Contrasts vs Pairwise Comparisons).
I have a 2x5 design. Lets say I have ...
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Stratify phylogeny based on variables - e.g. which ST are represented by high % males
So I have tree file and metadata.
Metadata includes sequence type ST (clusters that correspond in most part to the phylogeny), but also some patient data, age, sex etc.
I am trying to identify which ...
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Can and should you avoid implicit pretesting for differences in group means?
Suppose I have a population with four (or more) disjoint sub-populations which differ from one another by traitishness, the union of which is the whole population. I have an outcome measure on the ...
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Simple effects in mixed design with R [closed]
My experiment consists of two factors, one between and one within subject. Time is the between-subjects factor and hold two levels: (low and high). Times is the within-subject factors and hold three ...
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1answer
98 views
Problem with Tuckey correction for planned contrasts with emmeans and pairs() in R
I tried to post my question in Stack Overflow but they suggest me to ask to the statistic expert (you), so here I am!
I have a mixed design with 1 between factor (Group: ASD, CTR) and three within ...
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48 views
Are conditional effects the same as main effects when using orthogonal contrast codes for categorical predictors?
I ran into a presentation discussing the difference between conditional (or simple) effects and main effects when interpreting regression output in the presence of interaction terms.
http://www.lrdc....
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1answer
95 views
Setting up contrasts in lmer?
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I have 139 subjects (ID), with measurements taken at two time points (Time1, Time2), at 148 brain regions, a dependent measure called volume, and a covariate called thickness.
Each subject has 148 ...
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1answer
62 views
Use contrasts in a 2x2 ANOVA to test directional hypotheses
I think I have a rather simple question. I have a 2x2 ANOVA and I am both interested in the main effects and their interaction. Usually, I'd simply run the ANOVA (type 3) to see whether main effects ...
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changing the coding system from helmert coding to difference coding changes regression results?
EDIT: I think I have mistaken the names of the coding systems, so I changed it (in bold). The content has not changed at all, though, so I would still appreciate any answer.
END EDIT
I'm running ...
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42 views
Orthogonal contrasts, ANOVA, why are there only as many contrasts there are degrees of freedom?
For example, if I have the data
$$
\begin{array}{l|l|l|l|l|l|l}
A & low & & medium & & high & \\ \hline
B & standard & new & ...
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Predictor removed because of rank-deficiency in “lmer” model? [duplicate]
In my current research project, I am looking at the impact of different within-subject experimental manipulations on distance perception.
The experiment comprised 40 subjects each providing 144 ...
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2answers
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How to model repeated measurements with mixed effect models - lme4
I have a dataset of temperature measurements within a day 6 am, 6 pm, for two groups of patients health and flue,
There are repeated measurements on the same patient and same timepoint - measurements ...
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How to analyze contrasts? (Factorial and One-way ANOVA)
I have a statistics exam soon. I've been plowing through all kinds of statistical tests but I'm blocking hard on one "process" relevant to ANOVA's. I just don't understand, and I will give you one ...
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1answer
30 views
How to break down a 2-way factorial interaction into an interaction contrast
Assume the following dataset:
...
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59 views
Negative variance of linear combination of regression coefficients
I'm going crazy over this so I hope someone can help me.. First a presentation of my case:
I have a complex multiple regression model with 4 predictors (some terms that don't concern this issue are ...
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1answer
19 views
Is it okay to combine dummy coding and sequence coding?
I have a model with two categorical variables. Each one has three levels. Iv1 has a natural reference category so I would like to use dummy coding, and compare level 2 to level 1, and level 3 to level ...
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1answer
690 views
Differences between Simple Effects, Pairwise Comparisons, and planned/post hoc comparisons?
I am very confused as to the differences between simple effects, pairwise comparisons, and planned/post hoc comparisons. From what I understand, after running an ANOVA, you would use one of these to ...
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2answers
55 views
Significant main effects lost during ANCOVA due to interaction terms. Is type III the way to go?
I have some experimental data which I am analysing using step wise multiple regression (ANCOVA) in R using the step function. The response data (wp) is the leaf ...
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129 views
What's special about orthogonal contrasts?
In my Design and Analysis class we talked about orthogonal contrasts when it comes to running an ANOVA for one factor of several levels. I understand what it means for two contrasts to be orthogonal. ...
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1answer
63 views
Combining successive and treatment contrasts in lmer
I am running a lmer mixed effects model with three fixed effects parameters, each having multiple levels:
predic1: HH LR RR LD (4 levels)
predic3: L1 L2 L3 L4 (4 levels)
predic2: A B C D E F (5 ...
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1answer
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Does it make sense to do a polynomial contrast on a continuous time variable?
I tried running a few polynomial contrasts in SAS for a continuous time variable for linear, quadratic, cubic and quartic contrasts and the F values for each were the same. When I used categorical ...
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1answer
129 views
Dummy coding versus contrasts: which compares treatment with control?
I have a data set where I want to compare different treatments with a certain baseline. So I basically have a linear model (ANOVA) like this:
outcome = b_0 + sum_i(b_i * x_i)
with b_i the fitted ...
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39 views
Fit GLM using part of the data
I have a single-cell RNA-seq experiment with five different treatments. The treatments are likely to result in different cell types, although this isn't known at this stage of the analysis. Regardless,...
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1answer
230 views
significance of slope (different than zero) in triple interaction (with factors) for mixed model
I have the following mixed model (package {lme4} in R) :
...
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144 views
How to perform general linear hypothesis test on fitted model with treatment contrasts in R?
How should I perform a general linear hypothesis test in R on the coefficients of a fitted model that are represented by treatment contrasts? In particular with regard to the differences between the ...
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Multiple contrasts [closed]
We are currently doing 2 contrasts for a condition variable (3 levels)
...
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101 views
Custom contrasts in lmer - reference group?
I am a student working on data and am very confused about custom contrasts in a linear mixed model. I have tried it two ways.
Method 1 (inverse contrast matrices):
...
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24 views
Means and standard deviation of factor levels in mixed models
I have a response variable (ovs.m <-number of UV-reflecting scales on a lizard individual) and a factor with five levels (Morph: o, ow, w, y, yo). Using Rmisc, I can summarise the mean, sample size,...
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1answer
106 views
Specifying contrasts using afex
I would like to understand how to specify a contrast in a follow-up analysis using the afex package. Below I included code from the documentation and explain why I ...
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227 views
How to perform post-hoc tests with the package emmeans [closed]
After running a generalised linear mixed effect model I have estimated the logit probability by using "emtrends" from emmeans package.
The variable Condition is a factor with 3 levels(old,lure,new), ...
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1answer
228 views
Post-hoc testing in emmeans for mixed-effects models (lme4) with interactions in R
I have a linear mixed effects model (say AxBxC), where all of the 2-way interactions are significant but the 3 way interaction is not, and I want to perform post hoc contrasts on the 2 way ...
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48 views
reporting means and standard errors of multiple categories based on lm output
Lets say I have a variable that I model based on two categorical predictors. Here is code to generate data in R:
...
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189 views
Please help me understand my contrasts in an lmer model?
I have subjects in four groups and want to compare their scores on a measure called LD. The groups are called DD, DE, GD and GE. At the moment I'm only interested in the contrasts DE versus DE, and GD ...
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Linear mixed model: Setting custom contrasts for interactions and main effects with glht in R
I am currently learning statistics with R, and I am a bit confused about how to set custom contrasts for interaction effects. I tried removing the intercept from my model:
...
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3answers
877 views
Specify contrasts for lme with interactions
I have used lme to generate a mixed effect model of the response of cells to a certain stimulus. The stimulus is applied 3 times in a row (coded by the Exposure ...
