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21 views

Triple nested cross validation

I have read several very informative posts including the link about the nested/double cross validation, which can determine (sub)optimal hyperparameter values as well as make an unbiased estimate of ...
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54 views

including interactions in a mixed linear model in R (lme)

I'm trying to test for the effect of soil moisture on transpiration rates. I have plot-level data for 18 plots in 6 different stands of trees (3 plots x 6 stands). I want to treat "stand" as a random ...
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19 views

Assessing the effect of related variables using lmer in R

I am trying to run a model to describe the rate of water table drawdown in the soil. The predicted variable is rate, and I am interested in the effect of two categorical variables: (1) if the water ...
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2answers
72 views

What is the right way to analyze a nested design in R?

I know that there are already a host of questions about nested designs but many of them haven't been answered or come from biological domains which I sometimes find hard to transfer to my domain. I ...
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0answers
83 views

Random Effects Tobit Model

I'm studying the effect of various criminal case and court district characteristics on sentence lengths. I was planning on running xttobit in Stata because I have individual defendants/cases within ...
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1answer
21 views

Nested ANOVA in SPSS / Science Education

I am analyzing student performance on a pre/post test designed to assess gains for a week long high school biology curriculum on natural selection. After comparing pre/post performance using a ...
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0answers
32 views

Unstable models, repeated crossvalidation, feature selection

I'm still trying to classify few (about 200) samples in a high dimensional feature space (dim=19) into 3 (very unbalanced) classes. I use an implementation of Least Squares SVM with one vs one coding ...
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0answers
42 views

Nested logit program in R

My question is specific to transportation modelling using a nested logit (NL) model. I wonder how to make a program including a t-parameter, t-value, and likelihood in R. I did estimation in a ...
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2answers
94 views

What to do AFTER nested cross-validation?

I've searched exhaustively on this forum and elsewhere, and have come across a lot of great material. However, I'm ultimately still confused. Here's a basic, concrete example of what I'd like to ...
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1answer
85 views

Random factor nested in two fixed factors

I have read Random effect nested under fixed effect model in R, but I have a doubt: My data is on germling survivorship, I have Temperature as a fixed factor (2 ...
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0answers
30 views

Including nested random effect in a GAM

We have 6 transects at 6 different sites (6 transects per site). Each site subdivided into two zones therefore in our model we have: Site (fixed categorical factor) and Zone (random categorical factor ...
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0answers
35 views

Can all the p-values from drop1 models be high even when the p-value for the full lm model is low

I have used the R lm() function to fit a model with one numeric and ten categorical variables. The p-value reported for the regression is very low: Residual standard error: 2.459 on 320 degrees of ...
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0answers
38 views

Data Mining Methods with Nested Data

I have three general questions that I am really struggling to answer: a) When we have nested data (e.g. employees nested in departments which are nested in companies which are in specific ...
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48 views

question about multi-level modelling with nested data (R/Stata/SPSS)

I have a dataset composed of observations taken from 16 separate experimental panels, each nested into one of 4 conditions (Treatment A Level 1, Treatment A Level 2, Treatment B Level 1, Treatment B ...
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2answers
340 views
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0answers
79 views

Mixed model, repeated measures, nested?, nominal data

I am not sure how to approach the statistical analysis of the following study. Any insights would be greatly appreciated. Thanks! So, I have two independent groups, group A and group B. I am ...
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0answers
88 views

Nested ANOVA: Unequal sample sizes? Variance components?

I am completely out of my depth on this, and all the reading I try to do just confuses me. I'm hoping you can explain things to me in a way that makes sense. (As always seems to be the case, "It ...
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0answers
36 views

Poisson Regression Nested Design

At the moment, I'm trying to do a 'Poisson Regression'. I have several years (2004 to 2012) with four seasons in each year. My dataset consists of the amount of carcasses found every 10 days, and the ...
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0answers
19 views

Nested Design, Split-plot or ANOVA

I have general statistical question concerning the analysis of two-factorial experiments. I would like to compare several response variables (biovolume, richness etc.) of two experiments (homogeneous ...
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52 views

Including a nested factor as random effect in a GLMM

Good afternoon, I'd like to ask for advice on including a nested factor as a random effect in a GLMM. I've read other threads in this forum, but still am not able to answer my question. Any help is ...
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1answer
34 views

Is a model nested within itself before collapsing categorical variables?

If I have a model with a categorical variable $X_1=\{0,1,2,3\}$ and a continuous variable $X_2$, and I have a regression model that includes an interaction between $X_1$ and $X_2$, then I decide I ...
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0answers
15 views

How do I test for equal variances in a nested design?

I've got a dataset where stations (3) are nested within beaches (5). Every station is replicated 6 times per beach, so that I have a total of 90 observations. I now want to test for equal variances, ...
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1answer
128 views

Linear regression - are my models nested or non-nested?

I’ve got two main groups, which I am comparing, a) rats and b) rabbits. Each group consists of two subgroups – breed 1 and breed 2. Using linear regression, I would need to find out, does a model ...
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0answers
97 views

Fixed, random effect and nested factor in lme

I have a dataset with the following variables: Treatment : (fixed,3 levels) Location : (fixed, 4 levels) Sample (random, 5 levels): 5 samples are taken in each location (randomly) Subsample ...
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0answers
20 views

How to analyze data with a lot of missing data (including covariate, nesting and blocking)

I have data set that was haphazardly collected to test grazing impact on soil. To test the grazing impact, 6 replicate soil samples were collected from inside a fence and 6 replicates were from ...
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1answer
15 views

SVMs for nested/prioritzed text document classes.

Let's say A, B, C, D, E, F are classes of text documents (i.e. sentences). Usually they occur distinctively, say: one document is precisely C. But sometimes one document is C AND A, at the same time. ...
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27 views

Need help with proper syntax for SPSS Mixed [closed]

I am having trouble building my model properly, and I was hoping I could get some advice here. I have a 2 (S: P vs. D) x 3 (ET: CA vs. CO vs. AD) between-subjects design. Participants were run in ...
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64 views

Very Low ICC in HLM

I ran a HLM analysis (One Way ANOVA with random effects model). I calculated my ICC and it is very small (00.1%). I understand this means that there is basically no meaningful level-2 variability in ...
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0answers
71 views

Mixed model regression with non-independent (nested?) data in r

I am having trouble modeling a regression with seemingly non-independent, nested observations. I am examining the effect of relatedness on proportion of offspring in cases of multiple males ...
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1answer
66 views

Nested design with pairing

I have been asked to help a colleague with analysing the following experimental design. 2 treatments (fixed), 5 time points (fixed) with 4 animals (random) at each time point. The animals within each ...
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0answers
25 views

How do you control FWER when testing multiple nested models with likelihood ratio tests?

Suppose I have three different models $M_1, M_2$ and $M_3$, these models are nested such that $M_1 \subseteq M_2 \subseteq M_3$. I perform two likelihood ratio tests, $M_1$ against $M_3$ and $M_2$ ...
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0answers
118 views

Dealing with nested factors and correlation structure in a GEE model

This question is of a previous one that has not been answered yet (see the details of our experiment and question here). We are now exploring a GEE (Generalized estimating equation) approach that ...
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0answers
34 views

How to analyse spatially and temporally dependent data?

I would be very grateful if anybody has some suggestion about how to deal with the statistics of the following experiment. I am planning to study soil characteristics under different trees in soil of ...
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0answers
20 views

Compare variance and point statistics in a 3 way group

I need some help on this analysis. I have 3 groups of individuals, different the level and kind of physical activity. For each individual I have the heart rate, taken every minute for ~24h. (each ...
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76 views

Nested Anova Question:

I've a dataset for measurement of protein marker abundance for two groups of individuals, Treatment and Control. Within these two groups there are several subjects and for each subject there are three ...
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1answer
142 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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0answers
53 views

What to use: Nested Case-Control or Case-Cohort?

I am following a cohort of patients over time from which I am planning to sub-sample a sub-group of patients to pilot a new intervention. The plan is to compare the effectiveness of the new ...
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0answers
59 views

Why variances from nested random effects appear identical?

Could anyone shed some light on a slightly confusing result from a lmer4 model in R? I have a nested random effect, but the variance explained by each level seems identical, and I can't see why. I ...
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1answer
141 views

The test statistic in the likelihood ratio test for nested linear models

Imagine that we have a family of probability disributions with p.d.f $f_{\theta}(z)$ where $\theta \in \Theta$. We also know that there is a linear dependence between parameters. As a consequence we ...
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0answers
94 views

nested design after anova tukey

so I analyzed a nested design (split-plo, 2x4 factorial) with ANOVA and it indicated that there are differences in the levels of factor b. I went on with t-tests comparing the means depending on ...
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1answer
281 views

Why can't likelihood ratio tests be used for non-nested models?

More specifically, why do the likelihood ratio tests have asymptotically a $\chi^2$ distribution if the models are nested, but this is no longer the case for the not-nested models? I understand that ...
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1answer
274 views

Using AIC to select between models that use nested and non-nested variables

I'm using SPSS to try and find a mixed model that adequate explains the data that I have. Two of the explanatory variables are closely related ('Sample group' and 'individual'), as an individual is ...
0
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1answer
149 views

From dummy coding to ordinal variable

I have read from multiple sources (like this pdf) that in a linear regression model, an ordinal variable can be obtained by imposing linear restrictions on its dummy coding. e.g. $x$ is an ordinal ...
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0answers
106 views

GLM with quasipoisson nested distribution

I want to make a GLM with a quasipoisson response distribution. My response variable is inflorescences by plant and my explanatory variable is coverage. For inflorescence counts, I used the average ...
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1answer
1k views

Structuring a linear mixed model in R with nesting

My ecological question is: "What are the trends in percent coral cover by island and depth across the state of Hawaii from 1999 to 2012?" I am trying to analyze this hierarchical data set using R ...
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0answers
61 views

Is this a nested model?

I have a dataset with explanatory variable $X$ and response variable $Y$. Besides, there is a two-level factor $S_{j}, j=1,2$. The random error variance might be different between these two strata. I ...
2
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1answer
150 views

Is this a nested model and can I use the likelihood ratio test?

I have a data set, total_data and I applied a model to it. For instance, the model has one parameter $\beta$, and I calculated the log-likelihood of the fitted model (using maximum likelihood method). ...
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0answers
440 views

Nested Logit model in r

I am trying to run a nested logit using mlogit in R to analyze data from choices people made. There are 4 possible alternatives they could choose from, but in any given choice situation a person had ...
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0answers
131 views

Nested test to remedy pseudoreplication

Data structure: I have two datasets from two protected areas that differ in protection status. Both areas contain 43 and 37 sites each. Question: I would like to know which test would be the best ...
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1answer
641 views

How do I set up a multivariate hierarchical multiple linear regression in R?

I have two continuous DVs (measurements taken on individual fish), one continuous individual level IV (fish's size), and two site-level IVs (PC1 and PC4). Sites are either take or no take. There are ...