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Setting Contrasts for ANOVA in R [migrated]

I've been attempting to perform an ANOVA in R recently on the attached data frame. My question revolves around the setting of contrasts. My design is a 3x5 within-subjects design. There are 3 ...
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0answers
17 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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2answers
15 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
63 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
89 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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27 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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0answers
36 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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0answers
14 views

Testing batch differences in GWAS

I have some genotyping (~half a million response variables) data that was run in 4 batches (190 total samples, spread over 4 batches). The samples are from a case-control study (95 cases, 95 ...
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0answers
28 views

What happens with covariates when doing contrasts?

I am doing an analysis of covariance (in SPSS) but can't find anywhere how does SPSS treat the covariates when producing the analysis for the special contrasts I specified. Does it take them at their ...
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1answer
91 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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0answers
42 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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0answers
33 views

What is the default contrast coding for the interaction test in a 3x2 ANOVA?

As far as I understand it, the interaction term in a traditional 2x2 ANOVA is great for detecting a disordinal interaction, because the test assumes that the interaction is of form (-2, -2, 2, 2) ...
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2answers
218 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
135 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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0answers
74 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 ...
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0answers
70 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 ...
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0answers
41 views

Contrasts for one factor in a repeated-measures ANOVA

I am trying to set custom orthogonal contrasts for a repeated-measures design using R. Is it possible to set contrasts just for one factor? The model looks like this: ...
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1answer
125 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 ...
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1answer
64 views

Looking for the 'Elbow' in data

Subitization is the rapid, accurate enumeration of low-numerosity displays, distinguished from counting by a sharp non-linearity in the plot of response times. Below is a representative plot, from ...
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0answers
40 views

One factor repeated measures where first time point is a control

Patients were randomized to two groups (control and intervention). Each patient is evaluated at 3 time points. The first time point is taken pre-intervention, so it should have the same mean response ...
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1answer
87 views

Non-Orthogonal Planned Comparison: How to correct for alpha?

I have a data set containing three groups (A, B, C). Group A and Group B have undergone two different types of training designed to improve the same thing. Group C is my control group with no ...
2
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1answer
119 views

Inverse matrix for contrast coding

I'm trying to understand how "user defined contrast coding" works. My question refers to the example from http://www.ats.ucla.edu/stat/r/library/contrast_coding.htm#User: ...
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0answers
51 views

User-defined contrast on Generalized Estimating Equations

I am running a GEE on SPSS as well as Stata on choice data with the following structure: Each subject completed 32 trials in 4 ...
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0answers
77 views

Computation of polynomial contrast variables

Please give me idea how to efficiently recode a categorical variable (factor) into the set of orthogonal polynomial contrast variables. For many types of contrast variables (e.g. deviation, simple, ...
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94 views

Testing certain contrasts: Is this provably a hard problem, or not?

I posted this to mathoverflow and no one's answering: Scheffé's method for identifying statistically significant contrasts is widely known. A contrast among the means $\mu_i$, $i=1,\ldots,r$ of $r$ ...
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2answers
165 views

Defining contrasts in ANOVA to compare mean differences

I would like to run an analysis of variance (parametric or not) with two factors; each factor having two levels. So if x, y is are the levels of the first factor and 1, 2 the levels of the second I ...
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0answers
24 views

Orthogonal contrasts given MLEs and log-likelihoods

I have a parametric distribution for which the MLE must be obtained numerically, with optimization routines. My functions return the $\hat\beta$s and the log-likelihood. To test the hypothesis that ...
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0answers
77 views

A contrast suggested by the data

One approach to testing hypotheses suggested by the data is Scheffé's method. According to the Wikipedia article, the contrast $C = \sum_{i=1}^r c_i \mu_i$ (where $\sum_{i=1}^r c_i=0$) is estimated ...
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0answers
59 views

How to Partition An Interaction SS in ANOVA

I'm a new user of R and I'm trying to replicate Table 6.18 on page 262 in Statistical Procedures in Agricultural Research, By K. A. Gomez and A. A. Gomez. New York, Chichester, etc.: Wiley (1984). ...
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0answers
68 views

How to avoid regression to the mean in a simple comparison

This is a pretty simple question but I haven't been able to find a clear answer to it. I have some data from a behavioral experiment taken under two conditions (A and B); within each condition, each ...
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2answers
662 views

Plotting predicted values in GLM in R

I am trying to find a more aesthetic way to present an interaction with a quadratic term in a logistic regression (categorisation of continuous variable is not appropriate). For a simpler example I ...
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0answers
55 views

Checking for differences in time trends

I have two waterbodies that were sampled for a single water quality variable over time. Both waterbodies were sampled in the fall of each year from 2009-2012. In each year of sampling, 5 replicate ...
0
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1answer
264 views

Checking confidence intervals on user defined contrast (one-way ANOVA)

Hi is anyone able to help - I am doing this all in R Code: I have run one way analysis on some data and set up 2 contrasts (Liberarts-Finearts and also Engineering-science). I now need to calculate ...
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1answer
751 views

How to specify a contrast matrix (in R) for the difference between one level and an average of the others?

I have a regression model that looks like this: $$Y = \beta_0+\beta_1X_1 + \beta_2X_2 + \beta_3X_3 +\beta_{12}X_1X_2+\beta_{13}X_1X_3+\beta_{123}X_1X_2X_3$$ ...or in R notation: ...
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0answers
217 views

How do I conduct an analysis of an interrupted time series design with a comparison group?

I am not sure if this is the right place to ask this question (if not, please refer me to the right place), but it would be nice if someone could help me: Description of the Data/the Scenario: I ...
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2answers
818 views

Effect size in contrast analysis

I'm running 2-way repeated measures ANOVA (3 and 5 levels) with planned contrasts afterwards. I'm interested in comparing 1)levels of the first factor among themselves (e.g. A1B with A2B, A2B with ...
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2answers
233 views

Contrasts in mixed model

Suppose I have a data frame like this (four groups, for each n = 12): ...
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1answer
270 views

Questions about the glht function for planned comparison

I have a nested model with the following effects fixed: treatments random: experiment_date I used lme() to model the data ...
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0answers
429 views

Orthogonal contrasts in R

I am having somewhat of a problem setting up contrasts from an anova in R. I have done this in the past, but at the moment I don't seem to be able to get R to use my contrast matrix instead of the ...
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2answers
1k views

Contrast for hypothesis test in R (lmer)

I'm running a lmer mixed effects model with a four-level factor (levels "0","10","100","1000") as the fixed effect. lmer(free ~ reward.f + (1|S), longdata) I ...
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1answer
524 views

Contrasts in repeated mesures ANOVA in R

I am a refugee from SPSS in the process of re-learning how to do everything in R. Mostly it's been fun, as R is great for a lot of things but I've run into a snag that I can't seem to find a solution ...
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1answer
681 views

How to define contrast coefficient matrix?

I have this data ...
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1answer
396 views

How to examine interactions between factor and covariate in a mixed effects model?

I have 2 factors A and B (5×3) and one covariate X in a within subject design. Here's ...
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0answers
472 views

Calculating standard errors for contrasts of parameter estimates of a (multiple) linear regression

I am running regression analyses in matlab with glmfit and calculate significance of contrasts of parameter estimates by using standard errors. Somehow however, the results I get are not consistent ...
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0answers
311 views

Seeking an effect-size measure for simple effects in binary logistic regression in SPSS [closed]

I am trying to get an effect-size measure for simple effects in a binary logistic regression. I am using the GENLIN procedure in SPSS; here is the syntax: ...
0
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1answer
244 views

Non-significant MANOVA with significant planned contrasts [duplicate]

Possible Duplicate: Not-significant F but a significant coefficient in multiple linear regression How can you have a non-significant multiple regression model w/ significant predictors? ...
4
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2answers
583 views

How to interpret these custom contrasts?

I am doing a one way ANOVA (per species) with custom contrasts. ...
6
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2answers
246 views

Refugee from SPSS having issues with fit.contrast in R

I'm trying to wean myself off of SPSS and switch to R for psych statistics and I'm mostly getting there, but I've run into a real roadblock with fit.contrast from ...
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2answers
1k views

Confused about sum and treatment contrasts

I'm currently studying for an Experimental Design exam. I feel like I'm missing something quite fundamental... I've attached a minimal example to illustrate my confusion at ...