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Questions tagged [partial-plot]

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GAM partial response plot interpretation

I've made the gam in the code below (in R), but I'm struggling to interpret the results. Specifically, the partial response plots for all but one of the variables is linear, and the CI lines cross in ...
blitz1259's user avatar
1 vote
0 answers
115 views

Flat smooth term but significant relashionship GAM

I am using GAMs to model the occurrence of a species across 7 sites. I specified Site as a factor, and the response to each variable (smooths) is allowed to vary across sites. See a sample of code ...
Timelate's user avatar
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2 votes
1 answer
1k views

Creating a partial dependant plot for a prediction function [closed]

I am working on creating a partial dependant plot for one of my features (B). The problem is that I didn't use any model to predict my output (R). I've used a ...
X0-ZXC's user avatar
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0 votes
1 answer
460 views

Partial Dependence Plot PDP for machine learning

I have used two regression models from ML for a specific problem. Now I want to study some features importance using the the partial dependence plot "PDP". My question is: do I need to ...
jojo's user avatar
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1 vote
0 answers
367 views

Understanding partial dependence plot from XGBoost in R

I have developed an xgboost model in R using the package 'xgboost', with a binary outcome being predicted. I'm looking at a partial dependence plot of one of the important features, and I'm confused ...
Ben's user avatar
  • 11
1 vote
0 answers
623 views

Partial Residual plots for Zero-Inflated Negative Binomial Models?

I am looking for guidance on how to create partial residual plots for zero-inflated negative binomial (ZINB) models in R. I am quite new to R and have done a lot of research on my questions but have ...
batgirl's user avatar
  • 11
0 votes
1 answer
366 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?
Arif Masrur's user avatar
3 votes
2 answers
252 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? ...
Tomas's user avatar
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2 votes
0 answers
568 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 ...
Tomas's user avatar
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1 vote
0 answers
1k 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 ...
Hans Meier Ruth's user avatar
6 votes
1 answer
3k 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 ...
Brian Blackwell's user avatar
3 votes
0 answers
238 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 ...
iPolaco's user avatar
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0 answers
564 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 ...
ecologist1234's user avatar
5 votes
0 answers
269 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 ...
mkt's user avatar
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2 votes
0 answers
4k 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 ...
Gaurav Bansal's user avatar
0 votes
0 answers
41 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 ...
FtD's user avatar
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1 vote
0 answers
2k 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 ...
JamesS's user avatar
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3 votes
0 answers
398 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 ...
Giorgos's user avatar
  • 31
4 votes
1 answer
6k views

Partial Dependence Plot interpretation

This question is regarding the partial dependence plots obtained from a Random Forest model. I am trying to do classification modelling. I see negative values in the $y$-axis. How to interpret this?
Shudharsanan's user avatar
3 votes
2 answers
7k 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 ...
Danib90's user avatar
  • 427
2 votes
0 answers
2k 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 ...
Stats9415's user avatar
18 votes
1 answer
16k 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 ...
jacobsap's user avatar
  • 181
8 votes
1 answer
3k views

Random Forest partial plot for a binary predictor

I'm not sure how to interpret a partial dependence plot for a categorical variable. For instance, the partial dependence (command ...
utobi's user avatar
  • 11.9k
4 votes
0 answers
4k views

Trying to understand partial residual plots

When I launch this code (sorry, I cannot post my data): ...
Tomas's user avatar
  • 6,211
5 votes
1 answer
4k 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 ...
show_stopper's user avatar
1 vote
0 answers
439 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 ...
joe's user avatar
  • 255
2 votes
0 answers
440 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 ...
user46841's user avatar
17 votes
3 answers
30k 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 ...
user7417's user avatar
  • 1,033
16 votes
1 answer
4k 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 ...
AMathew's user avatar
  • 1,060