A contrast is a linear combination of parameters or parameter estimates, with the coefficients in the linear combination known. Often used to test focused hypotheses.

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How can I make an ANCOVA in R (Prior to a Cox ph model)?

I want to make an ANCOVA analysis of the survival rate of flies after being on a bad diet for the first 21 days of their lives compared to those always on a normal diet. I have studied the responses ...
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2answers
27 views

R lm() nested formulas give different results

Online sources show two supposedly equivalent ways to write an R linear model formula with nested factors: ...
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2answers
68 views

How to compare nested factor levels to mean, not to first level, and how to test the last nested level in R lm()

I have two factors j (with 3 levels A, B, C) and k (with 3 levels M, N, O), with k nested within j. Level A of j is the reference level and it has only one k level, M, in it. What I want to test ...
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3 views

contrasts between two grouped levels and the other six levels in a mixed 3x3 ANOVA in SPSS

I have a mixed ANOVA with 3 between subjects groups (control, m, s) , and 3 within subjects factors of stimulus type (3 levels), orientation (4), eccentricity (8 levels). i would like to investigate ...
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25 views

Why do contrasts or contrast sum of squares have one degree of freedom?

I have repeatedly seen that contrasts or contrast sum of squares are mentioned to have one degree of freedom. I'm wondering why this is the case. Is there an obvious explanation? Shouldn't they have ...
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1answer
62 views

Justification for default contr.poly() polynomial contrasts in R

In R, one can use contr.poly() to create a set of orthogonal contrast codes for testing linear and higher order effects of categorical factors: ...
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0answers
29 views

non-orthogonal contrasts in R

I am running ANOVA and doing non-orthogonal contrasts. Non-orthogonal contrasts are not supposed to completely partition the sum of squares of treatments. But what I got from R is not what is supposed ...
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28 views

Comparing linear contrast or slopes

I have a very simple question that is bothering me for a while. Imagine if you have a group with N participants, tested on an indice of performance (such as reaction times RT) according to I various ...
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29 views

How to do contrasts with weighted observations in R's linear model function lm()

As part of a simple simulation study, I have the following lines of code in R: ...
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27 views

How to get the significance of the last group in effect coding (contr.sum in R)?

I built in R a model similar to: ...
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10 views

Significance of a group of variables

I know how to do a significance contrast of a group of variables but if I see a lack of significance in two variables (for example in R the t test show when you type summary(lm(y~x1+x2+...+xk))) ...
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1answer
60 views

How do I contrast code for a factor where one level is the application of both of two others?

I have a factor 'Music' that has four levels: none, piano, guitar, and mixed. Subjects gave a response hearing no music, piano only, guitar only, or piano and guitar, so I want to create an lmer model ...
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83 views

Interaction with contrast and dummy coding

I have a question regarding the interpretation of an interaction using categorical variables where one is dummy coded (0, 1) and the other is contrast coded. The variables are: Var1: 3 levels, ...
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103 views

Specifying interaction contrasts for within x between terms in SPSS

I am trying to analyse a dataset with 3 groups of subjects and one repeated measure with 6 levels (accuracy at identifying 6 different emotions). I am using the GLM command from SPSS to do this, which ...
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0answers
70 views

How to create dummy variables for interaction term between categorical variables?

I'm building a logistic regression model estimating the probability of hospitalization based on several predictor variables, including indicator variables for various diagnosis categories (coded as ...
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0answers
46 views

Possible to code contrasts comparing each level to grand mean with no reference category?

I'm working on a health care outcome regression model using the deviation contrast scheme described on the UCLA SAS help page here for a collection of dichotomous predictor variables measuring medical ...
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2answers
72 views

Forcing nlme to give the results for the levels of a treatment as “absolute” values instead of contrasts

I am using a nonlinear model to fit an equation to data using nlme in R. Several values (one by treatment) are estimated for a fixed effect. As usual, by default ...
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1answer
43 views

Refitting with different contrasts vs. pairwise comparisons

Say, I fit a linear or generalised linear model in R with dummy coding (contr.treatment for ...
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0answers
141 views

How to do planned comparisons on repeated measures (GLM repeated measures) using SPSS?

I have issues figuring out how to perform planned comparisons using a GLM for repeated measures analysis. More specifically, I have one group of subjects, assessed with 2 different scales (3 subscores ...
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49 views

SPSS Contrasts for a Five-Way Within-Subjects ANOVA (Yes, You read correctly)

I have a 4 x 4 x 2 x 2 x 2 repeated measures design and I'm trying to test a contrast for just the first variable (here called "SOA"), averaging over the others, in SPSS. Initially, I thought it ...
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231 views

Linear trend in SAS using contrast

I've been struggling with this problem for a couple of hours, and I could use some advice. I have a linear regression model with two continuous predictors and a categorical one (with 4 levels). I ...
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1answer
149 views

Orthogonal contrasts for four levels - are Helmert contrasts orthogonal?

I am planning to do a 2-way mixed ANOVA with the within-subjects factor having four levels. Since the exact data do not matter, I hope to suffice by only providing a general question. On my ...
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1answer
177 views

Design of matrix of contrasts in R

I am doing some post-hoc comparisons (in lme4, but here I'll just present a simple linear model), and I am having a hard time making sure that I am building the right matrix of contrasts to test ...
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46 views

Specific contrasts in mixed model with interaction

I have a dataset consisting of two groups tested across three days. Therefore I run a linear mixed model as follows: ...
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345 views

R model.matrix and makeContrast. Understanding model and possible contrast

I have measurements from 12 mice, grouped in two conditions. I each mouse I have measurements from 4 tissues. The design is not balanced, 5 mice in condition1 and 7 in condition2. After reading the ...
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46 views

Logistic regression: Trying to use mean logit as reference group

Question I would like to do a logistic regression where the independent variables are compared to the mean logit, rather than the logit being compared a certain reference group. Example The example ...
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32 views

combining and contrasting time course GLMs using R

I am analyzing some time course data in which I have set up a GLM using R for each subject. Each GLM I want to run is an attempt to extract estimates of different behavioral conditions effects on the ...
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62 views

R lm without intercept strange contrast

I am actually doing a linear regression without intercept lm(y~ -1 + a + b + c + d ), where b, ...
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20 views

counfounded batch effects in microarray dataset - can I do partial experiment redesign?

I'm working with a microarray data set where the batches are completely confounded treatment time, i.e. time t1 is all in batches b1 and b2, and time t2 is all in batches b3, b4, and b5. I know this ...
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28 views

Testing linear contrast in an unbalanced longitudinal design (R)

I'm experiencing some conceptual problems in testing a linear contrast in an unbalanced longitudinal design. I have performed some correlation analysis with brain imaging data. These analysis ...
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1answer
248 views

Polynomial contrasts for regression

I cannot understand the usage of polynomial contrasts in regression fitting. In particular, I am referring to an encoding used by R in order to express an interval ...
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42 views

Can one perform trend analysis with ANOVA?

I'm using the multcomp package in R to do a trend test as part of an ANOVA. I am wondering if it is possible to not only ask "is there a trend" within one of the treatments but also "are the trends ...
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58 views

How to reconcile SAS hazard ratio standard error with actual value

I am trying to replicate the "C3 Contrast" (Output 66.3.7) at the bottom of: http://support.sas.com/documentation/cdl/en/statug/63962/HTML/default/viewer.htm#statug_phreg_sect048.htm I am able to ...
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38 views

How to perform a constrast in R for a cox proportional hazards model

I have the following model fit: ...
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1answer
47 views

Non-omnibus ANOVA test

Let's say I have $N$ groups that are mutually independent ($X_1,\ldots,X_N$). What I am looking for is a p-value to test the null hypothesis "$\mu_1=\mu_2\vee\mu_1=\mu_3\vee\ldots\vee\mu_1=\mu_N$", if ...
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1answer
153 views

Tests of within subjects contrasts in R

I have run a split splot model in SPSS (via repeated measures function) and I would like to reproduce my results using R. To do so I used ezANOVA function from ez package to obtain sphericity tests ...
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21 views

Testing contrast between low/high and high/low

I'm trying to understand the results published in Sagristano, Trope, and Liberman (2002). Specifically, I don't understand what analysis produced the result highlighted in the screenshot below. The ...
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59 views
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2answers
40 views

How to code and interpret a regression with 4-level categorical variable and continuous covariates

I have a problem in which 4 groups of people are compared in their performance on a certain test. One way anova shows that they are in fact different. But I also know that my groups are different in ...
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1answer
124 views

What is a “contrast” in a Principal Component Analysis (PCA)?

I have been studying how to interpret principal components. I recently came across an example of a particular eigenvector: $$e_j^T = \left[ \frac{\sqrt{2} }{2}, \frac{-\sqrt{2} }{2}, 0, \dots,0 ...
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1answer
193 views

How to define weights when testing an exponential trend?

In a linear model including ANOVA one can test a trend (e.g., linearity, quadratic effect, etc.) among the ordered effects (regression coefficients or factor levels) through assigning proper weights. ...
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0answers
83 views

How to run a power analysis for a repeated measures (all within-subjects) with combined contrasts?

I am looking for a little help on determining the correct way to run a power analysis on a within-subjects repeated measures design (i.e., no between subjects variable) with combined contrasts. ...
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140 views

Repeated measures logistic regression

I have a dataset that features a binary outcome, a binary predictor, and an unordered factor with 7 levels, and 120 subjects. Each of the 120 subjects were asked a binary question on seven issues, ...
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1answer
146 views

Contrasts with interactions

I have a couple of questions about contrasts but would also appreciate any suggestions for relevant literature. I am carrying out a GLM (binomial). There are 3 Factors (A,B,C) - A has 3 levels, B ...
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93 views

SPSS/Stata Repeated Measures - Contrast question

I have data from 8 subjects collected at 5 time points. I would like to see if there is a difference between time points (1 + 2) and (3 + 4 + 5) using either SPSS or Stata. When in SPSS I use ...
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2answers
338 views

Contrast to test significant interaction - why not include main effect?

Given a data set with a continuous outcome variable $Y$ and two nominal IV $X_1$ and $X_2$ which have 4 (A,B,C,D) and 3 (E,F,G) levels respectively, we can assign the first level of each as a ...
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1answer
772 views

Specifying contrasts for lme in 3x3 repeated-measures design

I would like to test the effects of two categorical variables, each with 3 levels, on some continuous data. Three groups of participants completed the same task for 3 types of stimuli, so it's a 3x3 ...
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392 views

Contrast matrix definition

What exactly is contrast matrix and how exactly is contrast matrix specified? I.e. what are columns, what are rows, what are the constraints on that matrix and what does number in column ...
5
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0answers
188 views

Interpretation of intercept in Helmert coding

I have a general, presumably simple, question, but I couldn't find a conclusive answer so far. Assume I have a simple case of a General Linear Model with one categorical predictor variable, that has ...
4
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1answer
163 views

GLMM model specification help gender effects + an effect that is nested only within female

Main question: "What are the contributing variates to daily movement distances?" Specifically my question today relates to: "What is the contribution related to gender, and then within female what ...