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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3
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2answers
42 views

Test for one coefficient doubled another one?

I want to run a regression in order to test ( thinking of the $t$-test ) the null hypothesis that one coefficient ($b_2$) is twice another coefficient ($b_3$), so $b_2= 2 b_3$, The variable for $b_3$ ...
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0answers
4 views

Control the composition of scored data based on certain variables

So imagine you had some sample with the following demographic breakdown: Gender: 30% Female 70% Male HHI: 30% Less than 50K/year 50% 50K - 100K 20% More than 100K and you want to build a ...
2
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0answers
22 views

Confused about F-contrast and F-test in statistical software

Let's say I have an estimated parameter $\beta$ from a general linear model for 2 subject groups (with the $\beta$s corresponding to their means). If I wanted to do a two sample t test in a ...
0
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0answers
13 views

How to specify these contrasts in R

Can anyone tell me how to create the following contrasts in R? ...
0
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0answers
24 views

Linear mixed effects models for longitudinal, unbalanced data

I want to use linear mixed effects models (lme4::lmer) for the selection of features (dependent variables, >1000) on significant differences between specific groups ...
0
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1answer
49 views

Mean Differences in Poisson Regression

I performed a Poisson regression. My dependent variable is number of days and my independent variables are all binary indicators (e.g. facility = facility1 facility2, facility3 and severity = ...
0
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0answers
23 views

More than three independent contrasts in PERMANOVA

I try to create more then three independent contrasts in PERMANOVA with 4 factors without success. I need to use all possible pairwise combinations of factor levels in my contr2df object. There are ...
0
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0answers
14 views

Changing contrasts for AOV doesn't seem to change anything?

My data set acidity.data has 10 observations each for 3 regions. The regions are listed in the Group column as ...
1
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0answers
30 views

User defined contrast coding with 2 categorical and 1 continuous predictor

I would really appreciate if someone could confirm that the contrast matrix that I defined with the glht package for my model is correct and that the continous ...
0
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0answers
34 views

Beta regression using GAMLSS: how to do post-hoc contrasts?

I have compliance rate data [0,1] from a mixed design study, which examines compliance rate over time for people receiving different types of incentives. I looked this up and thought that the beta ...
0
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0answers
22 views

Factor in linear mixed model is significant, but none of the contrasts?

So I have a linear mixed model with two fixed factors, let's call them A and B, A has three levels (A1,A2,A3) and B two (B1,B2). There is also a random effect, let's call it subject. Over likelihood ...
0
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0answers
17 views

Defining Contrast Matrix

Suppose I have a binary Covariate $X$ which is defined as $$ X = \begin{cases} 1, & \text{if treatment group} \\ 0, & \text{if placebo group} \end{cases}$$ The model is $$\mathbb E[Y] = ...
0
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0answers
36 views

Contrasts for hypothesis test in linear mixed model with repeated measures in R

I have data from an experiment in which we measured electromyographic (EMG) activity of 4 muscles before and after an emotion induction, in 71 participants. I have my data in long format, so I have ...
0
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0answers
10 views

Testing time trend theories using contrasts

I am planning analyses for a study in which I have 5 different groups who take measures at four time points. I plan to conduct my analyses in a two step process. First, I want to find which ...
0
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0answers
35 views

Planned contrasts in ezANOVA

I have a data set that is 3 x 5 and I can easily run a repeated measures ANOVA using ezANOVA in R. I now wish to have planned contrasts going into the ANOVA. The data consists of one control ...
0
votes
0answers
6 views

Doubts regards the contrast between two samples to analyze their expected values

I have this two samples: pob1<-rchisq(90,12) pob2<-rchisq(50,7) For making a contrast to see whether if I can guess that their expected values are equal or ...
0
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0answers
8 views

Making a contrast of two samples

Having this pob1<-rchisq(90,12) pob2<-rchisq(50,7) How can I make a "contrast" to see if I can guess that both of their expected values are equal against ...
0
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0answers
20 views

Interpretation of orthonormal contrasts in ANOVA/regression

Is there an intuitive substantive or geometric interpretation of regression coefficients associated with categorical predictor variables coded with orthonormal codes? For a simple example, say we are ...
0
votes
1answer
57 views

How to preserve order of factor levels in R [closed]

I have an unbalanced longitudinal data for glucose levels of some patients coming to a hospital. My data looks like id, date, glucose_level. As I want to find the ...
1
vote
1answer
69 views

Contrasts in ANOVA in R

I have conjured up a dataset here: ...
1
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0answers
39 views

Appropriate test for two test groups, one control group and binary outcome

I have the following problem: We send our Clients an email and offer them some new product. Let's say we want to test 2 email designs. Additionally, we need a control group, since some of the clients ...
0
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0answers
16 views

contrast testing in binomial GLM when variance = zero

I am trying to use GLM (family = binomial) to to test for differences in gene frequency among treatments. The data is binary (gene is present or absent). Its a simple one way model,but with quite a ...
0
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0answers
17 views

Calculate contrast given the estimate and standard deviation

I am analyzing results for a before-after control-impact experiment on species richness. I've used the 'vegan' package to calculate species richness using species accumulation curves, using the ...
0
votes
0answers
28 views

How to construct contrasts for a linear model with interactions?

I have trouble figuring out how to set up contrasts for a linear model with interaction terms. In the following example, how do I construct contrasts so that I test for the differences of species A - ...
1
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0answers
48 views

Complex Factorial Manova in R/SPSS

Hello I have been struggling for many days with this problem. The situation and data set are following. The data set comes from an experiment that asked subjects (ID) to compare several CVs on ...
0
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0answers
34 views

Occupancy analysis in Rmark: how can I calculate contrasts for BACI (Before-after-control-impact) experiment?

I'm analyzing presence/absence data using Rmark occupancy analysis (i.e. Rmark is the package which runs Program MARK in R). This is for a BACI (before-after-control-impact) design and I want to ...
2
votes
1answer
69 views

Zero-inflated Poisson regression: how can I calculate contrasts for BACI (Before-after-control-impact) experiment?

I am analyzing count data with a lot of zeros and found that although the data do not fit a poisson glm, they fit the zero-inflated poisson (ZIP) regression significantly better than the standard ...
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0answers
32 views

what are the consequences if a contrast is non-orthogonal?

everywhere I read about orthogonal contrasts. I know what they are, but I see nowhere why it matters if they are orthogonal or not. What are the consquences? Thank you!
0
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0answers
21 views

Strong differences in p-values depending method used to set contrasts with TukeyHSD in multcomp

I am currently running multiple comparisons following ANOVA. For this I want to set my own contrasts in TukeyHSD to exclude comparisons not of interest. So the first thing I did is test whether my ...
0
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0answers
48 views

How do I report Helmert contrast when running ANOVA?

I am a German student, so my English might not be perfect. Sorry for that. I would like to know how I do report Helmert contrast. I ran a two-way ANOVA and I wanna write down my contrasts in my thesis ...
0
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0answers
4 views

Sum Squares not adding up with testFactor

For some unknown reason the SS for the orthogonal contrasts I created with testFactor in the phia package do not add to the SS for the factor. Any ideas? Here is how I created the contrasts: ...
0
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0answers
19 views

contrast mean difference between intervention and control group

I'm studying a case of a quasi-experimental design, and have two groups. The Intervention Group and the Control Group. An answer for each individual was measured before and after the intervention ...
0
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0answers
13 views

how to (not) plot all pvals if many contrasts are done

I have run an ANOVA and then a Bonferroni test, using 8 groups. Therefore, the significant pvalues are many and showing them in a plot is messy. How would you recommend to approach this ...
0
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0answers
25 views

Compare one level vs the others in regression

we have a set of esclusive mutations on a set of genes. We would like to estimate the influence of such mutations on a certain syndrome. Our main problem is how to model the comparison between ...
7
votes
2answers
179 views

Why do some regression estimates differ by a change of sign, but others don't, when I change reference level?

Suppose I have a continuous outcome y and two factorial predictors, each with two levels. One of my categorical predictors, ...
0
votes
0answers
31 views

Orthogonal contrasts in a logistic mixed-effects model with unbalanced dataset

I have a dataset containing a dichotomous outcome variable Y, and 3 independent variables: ...
0
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0answers
11 views

Polynomial Contrast and Syntax in R

I read an example on ANOVA where the response variable is continuous and there are three independent factors, namely, machine (1, 2, 3), temp (low, high) and time (short, mid, long). The question ...
0
votes
0answers
292 views

Helmert contrasts: Each level compared to mean of subsequent levels, or mean of previous levels?

My question is what is the accepted definition of Helmert (and Reverse Helmert)? UCLA stats define Helmert contrasts thus: "Helmert coding compares each level of a categorical variable to the mean of ...
0
votes
1answer
200 views

R function survfit(): give newdata reference values for factors with >2 levels?

The goal is to plot separate survival curves for each level of a categorical variable in R, using a coxph model including the variable and a second categorical variable with >2 levels. If the second ...
2
votes
1answer
466 views

How to set custom contrasts with lmer in R

I am using lmer in R to check the effect of condition (cond) on some result. Here are some made up data, where s is the subject identifier and ...
1
vote
0answers
65 views

Choosing contrast coding in R

I am working on a data set with categorical variables. To apply ANN, I want to apply contrast coding to those variables. But how do I choose between coding functions in R (sum, helmert, treatment ...
1
vote
1answer
71 views

Why does “orthogonality” matter when using poly(x,degrees=1)?

I think I understand why orthogonality matters when doing regression with polynomial fits (so that the linear and quadratic, cubic, etc... can be evaluated independently). However, I don't understand ...
0
votes
0answers
102 views

Contrasts / Post Hoc Tests for three way repeated measures ANOVA

I have three factors A B and C with 2, 2 and 3 levels. A and C have significant main effects, B is not significant, interaction A*C is significant, the others are not. Now I want to know how to ...
2
votes
1answer
74 views

Testing linear restriction of parameters of ordered logistic regression models

Given the ordered logistic regression model: $outcome=\beta_0+\beta_1X_1+\beta_2X_2+\beta_3X_1*X_2$ Can I test linear restrictions on the parameters? For example I would like to test $H_0: ...
0
votes
0answers
14 views

Hypothesis Testing $\mu_{..}$ vs $\mu_{i.}$ for all $i$ In Context of Sample Surveys

I have been tasked with creating a table of p-values, where each cell is a p-value testing $\mu_{..}$ = $\mu_{i.}$, for each level of $i$. Essentially, $\mu_{..}$ is total average and $\mu_{i.}$ is an ...
1
vote
1answer
62 views

successive difference (aka repeated) contrasts with reference group

I have data from an experiment where performance y on two different devices was measured over three successive sessions. The 2x3 design is completely within-subject (see simulation code at the ...
1
vote
0answers
60 views

Imposing restriction over some regressors in a linear model?

I have the following problem: Starting with a multivariate linear model $Y=\beta_1x_1+\beta_2x_2+\beta_3x_3+\beta_4x_4+\alpha_1x_5+\alpha_2x_6+\alpha_3x_7+\alpha_4x_8+\epsilon$ and $$X=\begin{pmatrix} ...
1
vote
2answers
200 views

Why the discrepancy between the classic definition of contrast and that in R

According to Wikipedia, contrast is defined as follows: Let $\theta_1$,$\ldots$,$\theta_t$ be a set of variables, either parameters or statistics, and $a_1$,$\ldots$,$a_t$ be known constants. ...
1
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1answer
45 views

Why don't the following contrasts and linear models behave as I expected?

I am trying to understand how contrasts work, so I ran a small simulation using the following R code: ...
0
votes
0answers
30 views

Performing Interaction Contrasts on mixed-models in R

I need to run interaction contrasts on the following data set. It is a mixed design with the dependent variable a questionnaire score measured across five test days (within-subjects variable 'Day'). ...