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 gbm and the extension dismo - but that might be saved for a different post.

Anyways, when using gbm I am having a hard time interpreting what the y-axis is. See image below.

To give a little bit of background - I am building a model with Biomass as my response over ~ 30 predictors.

Looking at this image - I thought that the y-axis was the response (biomass) when only FvFm is being used in the model. So this would mean that lower FvFm values are usually indicative of higher biomass. However, this is incorrect - as we would expect there to be lower biomass with lower FvFm (especially at values < 0.3) and higher biomass at medium to higher values of FvFm.

My question would be: How can I interpret the y-axis? Is it actually my response variable or does it have different meaning?

enter image description here

  • 3
    $\begingroup$ Partial dependence plots do not ignore the effect of all the other predictors, they average out the effects of the other predictors from the full model. This means the partial dependence can defiantely go against the association you see in the data when looking at just FvFm and the response, just like how in linear regression the sign of a coefficient in the fill regression can be different than the one when it is the only predictor. $\endgroup$ Commented Sep 1, 2016 at 14:52
  • $\begingroup$ @MatthewDrury I know it has been some time, I have been trying to figure out ways around this but to no success. I was wondering if there is anyway to fix this? Or can you provide any literature that support partial dependence showing the opposite of what expected? $\endgroup$
    – Danib90
    Commented Dec 5, 2016 at 15:12
  • 2
    $\begingroup$ Can you be a bit more clear about what there is to fix? It doesnt seem to me that anything is broken. $\endgroup$ Commented Dec 5, 2016 at 16:02
  • $\begingroup$ @MatthewDrury I guess nothing is broken. I am trying to publish this for my thesis though and I think I might get eaten alive in peer-review if they see this figure. So I guess I need it to show what the actual data shows or I need to have some literature that explains that partial dependence plots can go against what the raw data shows. $\endgroup$
    – Danib90
    Commented Dec 5, 2016 at 16:22

2 Answers 2


?plot.gbm doesn't ignore the effects of the other predictors, rather it

Plots the marginal effect of the selected variables by "integrating" out the other variables.

You may wish to review section 8.2 of Friedman (2001), which is cited by ?plot.gbm when it states:

plot.gbm produces low dimensional projections of the gbm.object by integrating out the variables not included in the i.var argument. The function selects a grid of points and uses the weighted tree traversal method described in Friedman (2001) to do the integration.

Looking at the bottom of p. 27 of the paper ("For regression trees based on single-variable splits..."), I think a partial dependency plot of $y$ on $x$ can be simplified as the tree traversal:

  • Create a sequence of values for $x$: $x_1$ through $x_r$ (see the parameter continuous.resolution).

  • For each value of $x_i$ in this sequence:

    • Start at the root node of the tree
    • Set weight $w$ = 1
    • Traverse tree as follows:

      • If the node is a split on $x$, take the branch corresponding to the value $x_i$ and keep $w$ unchanged.
      • If the node is a split on a variable other than $x$, visit both child nodes:

        • Left child gets weight: $w_{left}$ = $w_{parent} * p_{left}$
        • Right child gets weight: $w_{left}$ = $w_{parent} * p_{right}$
        • where $p_{left}$ is the proportion of the training observations at the parent node that continue to the left child, similarly for right
      • If the node is a terminal node, return $w_{term} * f(x_i)$ , where $f(x_i)$ is the predicted value* at that terminal node.

    • Return $\bar{F}(x_i)$ which is simply the sum of returned weighted values from the terminal nodes.
  • Repeat for each of $M$ trees, then calculate the average $\bar{F}(x_1)$ through $\bar{F}(x_r)$ :

  • Plot this average function

*The predicted value is what appears on the y-axis.

Since you have a continuous outcome variable (biomass), this predicted value is your response variable.

However - if you had a Bernoulli or Poisson outcome variable, you would need to use type="response" to plot the response variable. (See ?predict.gbm)


If the trend of the FvFm variable is not what you would expect it to be after fitting the gradient boosting model you can constrain the feature. The gbm object has the following parameters:

gbm(formula = formula(data),
    distribution = "bernoulli",
    data = list(),
    var.monotone = NULL,
    n.trees = 100,
    interaction.depth = 1,
    n.minobsinnode = 10,
    shrinkage = 0.001,
    bag.fraction = 0.5,
    train.fraction = 1.0,
    keep.data = TRUE,
    verbose = "CV",
    n.cores = NULL)

You can use the var.monotone parameter to constrain the FvFm feature to force it to have the trend you would expect. This may be a solution in the event that an issue arises during the peer-review process. Constrained models are common in the credit industry where there are governance and regulatory concerns.

  • $\begingroup$ How are you addressing the plots? $\endgroup$ Commented Jun 28, 2018 at 16:09
  • $\begingroup$ @MichaelChernick Danib90 expressed concerns that the Partial Dependence plot for FvFm did not look as expected. My suggestion would impact the trend of the plot if they would constrain the feature. My recommendation does not explicitly address the main question but clarifies that a person has the option of forcing the gradient boosted model to treat a feature a certain way and therefore affect the PD plot. I would have left this as a comment, but I don’t have the reputation points. $\endgroup$
    – ecampana
    Commented Jun 28, 2018 at 17:17

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