# Questions tagged [separation]

Separation occurs when some classes of a categorical outcome can be perfectly distinguished by a linear combination of other variables.

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### emmeans differences in logistic regression give wrong significance in case of complete separation

Suppose (fictitious example) we have a logistic model for dependent "Happy" (0/1), and factor "Age" ("young", "middle", "old") as independent variable ...
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### Generalized mixed effect logistic regression model and strange p values (maybe separation of data)? [duplicate]

I'm running a mixed effect logistic regression model (function glmer from the package lme4) in RStudio with two random ...
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1 vote
101 views

### GLMER and p values when all outputs are 1: strange results?

I'm running a mixed effect logistic regression model (function glmer from the package lme4) in RStudio with two random ...
• 165
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### Is it possible to run a zero-inflated negative binomial model with complete separation? [duplicate]

I am trying to analyze how the number of events Y is influenced by three factors A (4 levels), B (2 levels) and C (2 levels) and the interactions between the three. Initially trying a poisson ...
49 views

### Warning: Hauck-Donner effect detected in the following estimate(s): INTERCEPT

This is a quick question because I could not find an answer online. I ran a truncated Poisson model and I got the warning in the title (perfect separation?) affecting my intercept. The output is: <...
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1 vote
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### estimating effect with marginaleffect package

I want to estimate ATE. first of all I used MatchIt package for full matching for propensity score and then I used logistic regression with all of variable in propensity score model after that I used ...
273 views

### Is G*Power reliable for logistic regression? It does not seem to account for Hauck-Donner

I've just been introduced to G*Power. The only option I could find for analysing logistic regression is described as: Options: Large sample z-Test, Demidenko (2007) with var corr That seems to ...
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### What method should be used if the clusters contains different classes?

Assume that you having $N$ clusters. Each cluster have multiple classes. So we know the class ID for every major clusters, but not the class ID for the data points inside the major clusters. Each ...
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### glm.fit: fitted probabilities numerically between 0 and 1 warning [duplicate]

I am currently writing my master's thesis and am doing a logistic regression with the following glm formula in R: ...
1 vote
102 views

### Perfect separation, perhaps? In binary outcome and repeated measure (random effect) with multiple independent variables (using R)

(Using R) - this is my first time posting a stats question online, so please let me know if I'm on the wrong forum or haven't provided enough information and I'll do my best to fix it! About the data ...
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1 vote
412 views

### DHARMa residuals plot vs. binned residuals using stan_glm object

I am quite a newbie in R and even more so in Bayesian regression. I have fit a stan_glm binomial model with 1689 observations, 12 variables and two interaction ...
632 views

### What is the proof that non-linearly separable data can't become linearly separable with the results of PCA?

Give a non-linearly separable dataset $X,$ I want to proof that after performing PCA on it, the resulting dataset is guaranteed to be still non-linearly separable. I think we could argue that we still ...
466 views

### fitting a gam with constraints on parameters to deal with separation in parametric terms

I am trying to fit a gam using mgcv which has a mix of smooth and parametric terms. The model is for some count data on fish catches. I am modelling variation in location and time, but also ...
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### Do neural networks create a separating hyperplane?

https://colah.github.io/posts/2014-03-NN-Manifolds-Topology/ mentions that neural networks learn a representation of the data so as to make the classes linearly separable. What I fail to see is how ...
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### How to find a mapping to a higher dimension that separates the data, given a data set

We have the following dataset: $$\begin{bmatrix} x_1 & x_2 & y\\ +1 & 0 & +1\\ -1 & 0 & +1\\ 0 & +2 & +1\\ 0 & +1 & -1 \end{bmatrix}$$ I was asked to find ...
1 vote
115 views

### Logistic regression difficulty with multi-level factor and many 0 outcomes

My dataset describes the presence/absence of an animal in a number of different plant species. Below is a table of plant species Vs animal presence/absence, i.e each row show the number of animal ...
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### Logistic regression - Exp (B) = 0? and sig is 0.999 or 1? [duplicate]

I'm having an issue with binary logistic regression for a project I'm working on. For some of the variables, I'm receiving a significance value of 0.999 and exp(B) of 0. Is this normal?
1k views

### Proportion data with number of trials known (and separation?): GLM or beta regression?

I perform a lot of bioassays in which I score mortality not on individuals, but on groups of individuals as a proportion (the denominator, i.e., number of trials, is known): Sample Data: ...
296 views

### Unexpected weights in Gradient descent algorithm (linear classification) in python

I am attempting to implement a back propagation algorithm that can efficevley read from a file of features and there targets and predict there outputs correctly, however for sake of testing I am hard ...
765 views

### Hauck-Donner effect in ordinal generalized regression

I am running a series of ordinal regressions on a rather large data set (n=3640). With some predictors I had issues with violations of parallel lines assumptions, so I decided to run those with a ...
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1 vote
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### Pooling Profile Penalised LTRs in multiple imputation

I am analysizing data from a clinical trial. I used multiple imputation to impute the (binary) outcome variable, which is the only variable with missing data. All of the covariates are categorical and ...
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371 views

### Binomial (1/0) response, Factor explanatory variable: why can't GLM estimate effect when one factor level has all 1s in response?

I have a dataset with a binomial response variable (1/0) and a single explanatory categorical variable with 2 levels. For one level, the response is all 1s and no 0s (e.g. ...
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### For the Logistic model, why is the objective function unbounded below if two sets are linearly seperated?

I am reading Approximate linear discrimination via logistic modeling in the Section 8.6.1 of B & V's Convex Optimization book. On Page 428, $$\operatorname{minimize} \ -l(a, b) \tag{8.27}$$ ...
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### Why PCA is not considered in the taxonomy of blind source separation approaches?

Blind source separation (BSS) approaches are divided in the literature into four methods, including independent component analysis (ICA), sparse component analysis (SCA), and non-negative matrix ...
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1 vote
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### Is the sum of 3 bits a linearly separable task?

In other words can a linear classifier learn to correctly assign a class (label 0 to 3) for an input of 3 bits? Intuitively this cannot work, since the half-adder circuit contains an XOR block, which ...
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287 views

### Hidden vs Firth vs Shen-Gao logistic regression: dealing with the Hauck-Donner effect

In 1993 a version of penalized logistic regression was introduced by Firth in order to reduce the bias due to outliers and/or (quasi-)perfect prediction in logistic regression: Bias Reduction of ...
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### On the use of the sampling year as fixed-effect

I have my database in temporal blocks (so I have my occurrence sites into the year of sampling of a few years with maximum 7 years). In order to fix the complete separation problem that I also have, ...
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### Is there any impact on the results of random forest if we have perfect separation in the database?

I'm having a perfect separation in my database. One of the solutions is to switch randomly some of the values of the dependent variable to the opposite for the variables that cause the problem this ...
• 155
523 views

### Dealing with quasi-complete separation in General Additive Model?

I am modelling influence of fire on occurrence of certain bird species (count response variable) in Before/after control/impact experiment design. I've got intact and burned sites and count data both ...
1 vote