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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On the detection of the predictors responsible for the separation in logistic regression

I'm using multiple glmm models and I have separation and pseudo-separation situations. I want to know if there are any tools in R to extract the predictors ...
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13 views

On the test of significance under penalized likelihood estimation

I start using brglm2 package to implement logistic regression under a perfect separation problem. Is there any way to test the significance of the parameters using ...
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10 views

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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1answer
17 views

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 ...
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23 views

significance of pvalue for logistic regression [duplicate]

I'm trying to understand how to interpret the significance of logistic regression If I use the standard iris dataset, the Petal Length is a significant predictor for the Setosa classification. If I ...
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1answer
125 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 ...
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50 views

How many percentage to randomize and how many iterations in a “what-if analysis”?

I've got complete separated data as such: ...
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27 views

Options when model complexity and separation causes non-convergence in logistic regression

I have created an example data set here My data represent the presence/absence of a particular animal species (data$outcome) and measurements of trees. I would like ...
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3answers
775 views

Analysis of Danish mask study data by Nassim Nicholas Taleb (binomial GLM with complete separation)

Recently, Nassim Nicholas Taleb made this post about the recent Danish mask study, a randomized controlled trial which concluded that the proportions of newly diagnosed coronavirus infections was not ...
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306 views

Are these two 2D datasets the same and can they be separated with the XOR NN?

I'm a very beginner in the neural network topic. So I ran into a problem. I see on the online lectures: Famous example of a simple non-linearly separable data set, the XOR problem (Minsky 1969) in the ...
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1answer
96 views

Using Chi-squared test when perfect separation in logistic model?

My dataset is similar to this; it describes the presence/absence of a parasite in six species of animal from two locations. Each row in the dataset represents a different individual animal. I would ...
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47 views

penalised logistic regression with brglm - warnings

I've built a logistic model to predict a binary response. I've got four categorical predictors. One of them (posicion) has 6 levels, 3 of which occur not too frequently and are ALWAYS (by definition) ...
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60 views

How to use the kernel trick on a XOR-like dataset

Let's say that I have the following data: I want to find a transformation of this dataset that will make it linearly separable. My thought was to bring the data around the origin and then multiply $...
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Perfect separation of a dummy variable with the dependent variable in a binary logistic regression produces high insignificant estimates [duplicate]

I have the following setup: I have a binary logistic regression analysis with a couple of independent variables. They include a nominal variable that is coded in a dummy form with $k-1$ predictors. It ...
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8 views

Identify two points from a set as similar

I'm trying to build a model to asses different physiological parameters (Dry weight, yield, Nitrogen concentration, one model for each) from a field based on reflectance from different wavelengths i.e....
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1answer
76 views

Unexpected behaviour of logit regression with glm in R

I recently was puzzled by the behaviour of R's glm when trying to compute a logistic regression ...
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25 views

Separation and Correlation

In a logistic regression setting, can there be a relation between the fact that covariates are highly correlated and the problem of perfect(quasi-perfect) separation?
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137 views

What is the cause of this very high standard error in my logistic regression model?

I am running a logistic regression model where the outcome variable is Neurologic Complications, and there are various factors who's impact I am examining. One of the factors (HTN_new1), a categorical ...
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1answer
93 views

Probability of linear separation in a dataset with categorical response

I am simulating datasets to which I fit polytomous logistic regression models. The maximum likelihood estimator of this model is undefined when all categories are linearly separated (and it is quite ...
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1answer
64 views

What does it means getting p-values equal to 1 and complete separation in logistic regression? [duplicate]

I was really confused if I should ask this here or in Stackoverflow, but I'll give a shot here. I ran a logistic regression using statsmodels library in Python. However, two things went wrong here (...
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1D representation for 2D toy data (about linear separability)

suppose there is a dataset with 2 features x1, and x2. the points (-1;-1); (1; 1); (-3;-3); (4; 4) belong to class 1 and (-1; 1); (1;-1); (-5; 2); (4;-8) belongs to class 2. I am confused in terms of ...
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32 views

Separating hardly distinguishable classes for easier classification

I apologize for this seemingly basic question, but I was just thrust into this data science role and would like to get some advice from some experts. I have a dataset with a small number of features ...
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1answer
114 views

Logistic Regression assumption

In Logistic Regression, the assumption is that the data must be linearly separable, but if the data is not linearly separable then we can't apply Logistic Regression?
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1answer
20 views

Fourier analysis to retrieve components of individual spectra

I have a basic, simple question, I am a physics student, and searching internet gives me a lot of signal processing theory but couldn't find this basic answer, which I plan to implement in my speech ...
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123 views

Cumulative explained variance between scaled and unscaled data

I was writing a small piece of code to portray the difference between scaled and unscaled data when doing PCA and (as expected) I found that the separability of classes was better by doing the ...
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1answer
171 views

instability of logistic regression

I am reading Introduction to Statistical Learning and it is said (as in other websites) that Logistic Regression is unstable compared to Linear Discriminant Analysis in well separated cases. ...
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1answer
53 views

Doubt on d-separation

In the book: Bayesian Networks With Examples in R, the author shows three examples of d-separation: He cites: Then, just a few lines below, the author uses the dsep function, which returns FALSE for ...
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Which theorem in Cover's 1965 paper is actually referred to as Cover's Theorem?

Cover's Theorem is stated on Wikipedia (and similarly elsewhere) as A complex pattern-classification problem, cast in a high-dimensional space nonlinearly, is more likely to be linearly separable ...
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1answer
50 views

likelihood ratio test for logistic regression with a complete separation

Can likelihood ratio test be used for logistic regression in the case of complete separation? I understand that individual parameters can go to infinity so Wald's test is not recommended, but does ...
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1answer
39 views

Clustering Proof of Equation

Greetings! Could anyone enlighten me about the validity of this equation? I'm trying to prove it without success. $K$ is the number of clusters, $C_i$ is the $i$-th cluster, $m_i$ is the number of ...
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34 views

Relationship between Cohesion and Separation

Hello! May someone explain to me please how to prove the equation depiicted with the red line? Thank you in advance!
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1answer
45 views

Doesn't separation in data affects Random Forest?

I'd like to know if separation in data points given by a certain variable will affect Random Forest in terms of "being a correct built model"? For example, logistic regression is highly vulnerable in ...
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1answer
409 views

Why one result is so wide in this logistic multiple regession

I am doing multiple logistic regression with data with 24 predictor variables and 193 rows. All predictor variables have values of 0 or 1 and outcome variables (OUTVAR) also has only 2 possibilities. ...
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52 views

Is A ⊥ B | C where one path active but another inactive?

I'm trying to determine if A ⊥ B | C? I see two paths flowing through elements of C: (1) B <- C - > A (all variables unobserved, active triple; independence cannot be guaranteed for this path) (...
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90 views

Cutting dendrogram at certain point

I have a question about cutting dendrogram like that It shows some hierarchy in the prison I have to cut it to separate the group. Is it possible to cut not all dendrograph at the same height like ...
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55 views

What is the *formal* definition of separation in *binary* logistic regression?

I am trying to understand complete and quasi complete separation in the context of logistic binary regression. However, I have not found a clear source. I know the seminal paper https://www.jstor....
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1answer
254 views

Seeking to understand using the Firth correction in Generalized Estimating Equations to deal with quasi-complete separation

In order to deal with complete separation in my data someone suggested that I run penalized GEE (PGEE) by adding a Firth-type penalty term in R. Although I have read many papers on the Firth ...
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1answer
78 views

Quasi/Complete separation due to huge and infinite values

(R statistics) My question is regarding this warning. My data contains patients and healthy subjects. Exponential decay is my outcome measure. I have a example dataset here I managed to run ...
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1answer
1k views

If logistic regression is a linear classifier why does it fail on linearly separable data?

Logistic regression is a linear model, decision boundary generated is linear. If the data points are linearly separable, then why does Logistic regression fail? Shouldn't it perform better on data ...
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36 views

Linear separation in higher dimension [duplicate]

I am having a problem comprehending with the relation of kernel, weight and linear separation. I have a case where I am given a kernel $k_1$. that has a corresponding mapping $\phi_1$. And we ...
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48 views

anomaly detection : check the separability of normal and abnormal data

I'd like to develop an anomaly detection. I have historical data from sensors in the form of time series. The time series can be divided into data of a normal state and data of an abnormal state i.e. ...
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1answer
262 views

Handling quasi-perfect separation in a zero-inflated negative binomial regression in R

I want to run a zero-inflated negative binomial regression in R, but one of my variables exhibits quasi-complete separation and throws errors for both the negative binomial and logistic pieces. I've ...
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1answer
42 views

Dealing with Complete Separation in Logistic Regression when Reporting [duplicate]

I have a question regarding how one would deal with complete separation in logistic regression when reporting the outcome for statistical analysis. For a study, we have group participants into 4 ...
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1answer
22k views

glm.fit: fitted probabilities numerically 0 or 1 occurred however culprit feature is numeric

I've been receiving the warning message in the title and have reviewed posts such as e.g. this one. I would like to understand how this feature has perfect separation with the target variable, since ...
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36 views

Does separation of data matter in Bayesian power calculations with logistic regression models?

I know that, when performing power calculation based on logistic regression model, under the regular frequentist approach, power calculations become unstable if it is based on the model that causes ...
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1answer
231 views

A priori contrast for binomial GLM

after much reading I decided to write because I cannot find a solution to my question. I already did a priori contrasts before for a continuous variable with normal distribution. Now I have another ...
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1answer
74 views

Is there an upper bound on number of logistic regression responses that yield infinite estimates

Suppose a logistic regression problem has N observations of {0, 1} and that there are p parameters. Also assume the design matrix, X, is full rank with p < N. We know that there will be certain ...
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113 views

Logistic regression with separation and nested design in R

Data: An item can be in the state 0 or 1 (binary). Each year, it starts in the state 0 and then changes to state 1. I have data of 4 seasons (2010 -2013). Each year I sampled the (same) individuals ...
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2answers
320 views

GLMM for count data using square root link in lme4

I have data from a field survey. The objective of the study is to relate number of seedling (respond variable, count data), landform (exploratory variable, categorical variable with 3 levels) and ...
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1answer
179 views

Kullback-Leibler Divergence as the class separation measure

I am trying to use KL divergence as the separation measure between the classes. I have the positive, negative samples for 2 distributions and want to adjust the algorithm parameters to get the best ...