Questions tagged [partial-plot]

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Random forest classification: Interpreting variables importance and partial dependence plots

I have been performing diagnostic of my random forest model. The model has three classes with eight predictors, as follows: ...
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1answer
66 views

Y-axis value (class probability) more than 1 in a Random Forest PDP

Sometimes I am getting such PDPs from a Random Forest classification (two-class) model. Why Y-axis probability is more than 1 here? What might have caused it?
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41 views

Partial plots for Gaussian Process: definition and computation

How do I make partial plot (or partial dependence plot) for Gaussian Process classification? I mean plot which would show a dependence of a response probability to a single covariate variable? ...
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12 views

Reversing normalized values on a partial dependency plot in R

I am trying to explain my MARS model (for classification). I created a partial dependency plot based on my model: As you can see I have monthly income feature on the x-axis and customer churn ...
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0answers
113 views

Am I getting the definition of partial residual plot right?

I am trying to make a partial residual plot of one quadratic predictor in GLMM (glmer in R). I tried to do it manually, from how I understood the definition of ...
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0answers
304 views

leverage.plot() R - CAR package

I'm trying to complete a homework regarding added-variables and leverage plots using the CAR package. In the documentation of the ...
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1answer
1k views

Partial Effects Plots vs. Partial Dependence Plots for Random Forests

One method for interpreting the relationship of a predictor X to the response variable Y in a fitted multivariate regression model is a Partial Effects (PE) Plot. This can be generated by holding ...
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0answers
450 views

Component Plus Residual Plot: How do they work?

How does component plus residual plot work? You create these plots by plotting: But how do they work? The books says that you want to get rid of the influences from other predictors. A linear ...
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0answers
39 views

The law of large numbers mediates predictor-outcome relation, what to do?

I am conducting a random forest analysis in which a predictor is naturally correlated to the outcome. That is, the predictor is the amount of sunlight a patient received during his admission in a ...
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0answers
163 views

About Partial dependence for Poisson GLM

Can someone tell me what would be the expression for calculating the partial dependence on a GLM model with family specified as Poisson? From applying Friedman partial dependence estimation ...
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0answers
168 views

Why do partial dependence plots look different with same model but different data?

I've got a randomForest model object from the R package randomForest and am using the function partialPlot to generate partial dependence plots. I know that normally one would create these using the ...
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2answers
5k views

Interpreting Partial Dependence Plots in GBM

I am using gbm to fit a model and partial dependence plots to interpret parts of the model. There seems to be some differences between partial dependence plots for ...
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0answers
208 views

Quantifying uncertainty when fitting a statistical model to partial effects/dependencies from a random forest (or other machine learning model)

Question: I estimate the partial dependence of $y$ on one predictor in a fitted random forest (RF). I want to now fit a parametric model to this partial dependence. How can I estimate my uncertainty ...
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3answers
24k views

R: What do I see in partial dependence plots of gbm and RandomForest?

Actually, I thought I had understood what one can show a with partial dependence plot, but using a very simple hypothetical example, I got rather puzzled. In the following chunk of code I generate ...
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0answers
3k views

Generating and interpreting partial dependence plots [closed]

I am trying to mimic partial dependence plots as explained in R's pdp package (https://journal.r-project.org/archive/2017/RJ-2017-016/RJ-2017-016.pdf). The second ...
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1answer
3k views

Best way to visually present relationships from a multiple linear model

I have a linear model with about 6 predictors and I'm going to be presenting the estimates, F values, p values, etc. However, I was wondering what would be the best visual plot to represent the ...
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0answers
1k views

Partial regression plots for regularized (L2) linear regression

I'm trying to get to grips with multiple linear regression and partial regression plots. The answer to this question from @Silverfish really helped initially, so I had a go with my own data using ...
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1answer
5k views

Partial Dependence Plot interpretation

This question regarding the partial dependence plots obtained from random forest model. I am trying to do classification modelling. I see negative probability in the y-axis . How to interpret this?
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1answer
9k views

Meaning of y axis in Random Forest partial dependence plot

I am using the RandomForest R package and am confused at how to interpret the values of the Y-axis in their partial dependence plots. Help docs state that the plot ...
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0answers
1k views

Interact.gbm : Friedman's H statistic

I really need help to understand how the function interact.gbm (gbm package) can compute Friedman's H statistic to assess the relative strengh of interaction ...
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1answer
3k views

Random Forest partial plot

I have the following graph generated after I used the partial plot function of Random Forest in R. Now from this image, my understanding says that temperature has a linear relationship with my ...
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0answers
3k views

Trying to understand partial residual plots

When I launch this code (sorry, I cannot post my data): ...
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0answers
406 views

How can I compare GBM feature importances to GBM partial dependence plots?

I am having trouble reconciling the difference between the indicated "importance" from a GBM that I am calculating with what is shown in the partial dependence plots. I would expect higher ...
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0answers
396 views

How to explain the value of y-axis in Partial Dependency plot

sample numbers = n number of classes = 2 The function is $$F(x) = \sum_{i = 1}^nf(x,x_{ic}) $$ where $$f(x,x_{ic}) = \log p_1(x,x_{ic}) - \frac{(\log p_1( x,x_{ic} )+\log p_2( x,x_{ic}))}{2}$$ In the ...