Questions tagged [partial-plot]

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Calculating partial dependence function of many variables

In this answer How o calculate partial dependence when I have 4 predictors? there is a great example on how to calculate the partial dependence function for $X_s$ when $X_s$ accounts only for one ...
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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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199 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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523 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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Partial residual plot for GLMs

I'm trying to understand how exactly partial residual plots are computed for Generalized Linear Models. Lets say you have a response variable $Y$ and three explanatory variables, where a Poisson error ...
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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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105 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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177 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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2k 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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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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806 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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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
4k 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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4k 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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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
6k 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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2k views

Trying to understand partial residual plots

When I launch this code (sorry, I cannot post my data): ...
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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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398 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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378 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 ...
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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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1answer
2k 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 ...