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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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Can the probability of a hypothesis be tested by contrasting posterior predictions against simulated data?

I have a query regarding contrasts of posterior predictions. I have generated three sets of predictions from a model using data from animal orientation experiments. The data were modelled according to ...
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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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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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35 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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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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72 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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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
122 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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59 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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75 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
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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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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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Setting up contrasts in lmer?

0 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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48 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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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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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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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
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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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442 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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Planned contrasts after ANOVA

I ran a one way ANOVA and after that a planned contrast to examine differences between the control group and 5 other treatments (n=10 per treatment). I got these results: F5,54=8.62, p<0.001. ...
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2answers
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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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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
38 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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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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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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135 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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61 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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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
93 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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202 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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194 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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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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133 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
715 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 ...
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1answer
366 views

What statistical test does -contrast- use after regression in Stata?

I am using the -contrast- command to generate p-values for trend test in Stata. I've reviewed the documentation on contrast but cannot find information on what statistical test is being used behind ...
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147 views

Planned contrast ANOVA with mixed effects in R?

I am looking to analyze variables (e.g., wood calcium concentration in a tree) as it relates to forest age classes. Each of four forest age classes has 2 replicate "sites". In each site I make ...