# Tagged Questions

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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### Design/Contrast Matrices and Unestimable Coefficients

I am trying to analyse microarray data from samples with the following characteristics: one of two genotypes, a procedure either carried out or not carried out, and, in the case that the procedure is ...
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### Interaction Contrasts in SPSS

I am trying to run a 2x2 MANOVA with two sets of categorical independent variables (V1: healthy weight vs. overweight) (V2: binge eating diagnosis vs. healthy controls), on continuous dependent ...
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### Contrasts are giving wrong estimates using glht in R

The problem: glht is giving the direct differences between the estimates of the summary table (i.e., not summing each estimate with the intercept to obtain the estimated value). ...
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### Repeated Measures MANOVA with contrasts?

The data that I am using consists of 74 people that answered three DV once (each of them once). I had a 2x2 design, with Context x Intensity as IVs. I have done a MANOVA on the data but my supervisor ...
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### Is the Scheffé test of contrasts the “best-case” for post-hoc tests?

I am reading through Explaining Psychological Statistics, 4th Edition and am stumped after the following passage: ScheffĂ© (1953) understood that the best anyone can do when creating a complex ...
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### Statistics, R: Build linear regression model with differently contrast-coded variables

I want to build a linear regression model where I predict a mean of a group of participants (how they rate something on average). Predictors should be age (continuous) origin (deviation coded, each ...
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### Planned contrast through factor-based vs. model-parameter-based approach

I have two questions concerning planned contrasts: I would like to know how factor-based contrasts (obtained through an interaction term) compare to model-paramter-based contrasts (obtained by ...
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### Logistic regression with 2 predictive variables

I need some advice for choosing the correct model. I have 3 binary variables: Risk (0 = the person doesn't take financial risks, 1 = the person takes financial risks), gender (0 = female, 1 = male), ...
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### Using contrasts in Poisson regression

The question is about using contrasts in regression analysis (here, Poisson regression with robust error variance). We have devided the participants in our sample into 6 groups, according to their ...
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### Advantage/acceptability of using contrast codes to conduct pair-wise comparison vs. t-test on subset of data?

I conducted a study with three conditions (A, B, and C) and I want to test the difference between A and C. My default approach would be to run a t-test (or its equivalent) on a subset of the data (...
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### Permutation test for repeated measures (in time)

I have the measurements of a quantity, observed every day for 60 days Usually, this quantity is really near to 0, apart from 3 days where it is (significantly?) greater than 0 I thought it would be ...
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### Repeated measures ANOVA contrasts

I'm running a repeated measures ANOVA with a 3-level DV. Now what I've read is that you only look at the post-hoc test if the within-subject (overall) effect is significant. What about the within-...
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### Application of Anova/Manova

I have a dataset providing information about head and leg injuries for drivers and passengers . The dataset contains the following variables Head.IC: Head injury criterion(number) Chest_decel: Chest ...
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### Anova and contrast

How do we use ANOVA and Contrast to compare multiple dependent variables with multiple independent variables in R. Have watched few videos in you-tube but am really confused. How do I compare ...
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### Compare the coefficients of two independent variables within a model, representing 2 diff independent variables are statistically different?

I'm trying to show that two coefficients within a model are statistically different from each other. These variables measure two similar, but different variables, price increase and price decrease. ...
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### condition specific differentially expressed genes

I have log2 transformed gene expression data set. ...
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### How to set sum contrasts for unbalanced factors

Let's say that I have a model where the response time depends on accuracy (0/1, coded either as categorical or numerical) and another categorical variable (pres: idem/diff), both interacting with the ...
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### 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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### 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 ...
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### 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 ...
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### How to specify these contrasts in R

Can anyone tell me how to create the following contrasts in R? ...
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### 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 ...
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### 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 = extreme,...
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### 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 ...
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### 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 ...
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### 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 ...
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### 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 ...
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### 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 ...
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### Defining a contrast matrix to test the null hypothesis $H_0: \beta_5=\beta_6=0$

In the book Applied Longitudinal Analysis, 2nd Edition there is an example in the chapter "Marginal Models: Generalized Estimating Equations (GEE)" in "Muscatine Coronary Risk Factor Study" sub-...
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### 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 ...
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### 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 theory/...
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### 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 ...
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### 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 ...
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### 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 ...
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### 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 ...
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### 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 ...
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### Contrasts in ANOVA in R

I have conjured up a dataset here: ...
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### 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 ...
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### 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 ...
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### 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 ...
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### 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 - ...
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### 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 ...
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### 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 ...
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### 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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### 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!
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### 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 ...
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### 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 ...
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### 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: ...