Screeplot fails for PCA in R and Python

[exalate-issue-sync]

Python fails:

{code:python}from h2o.estimators import H2OPrincipalComponentAnalysisEstimator

Import the birds dataset into H2O:

birds = h2o.import_file("https://s3.amazonaws.com/h2o-public-test-data/smalldata/pca_test/birds.csv")

Split the dataset into a train and valid set:

train, valid = birds.split_frame(ratios = [.8], seed = 1234)

Build and train the model:

birds_pca = H2OPrincipalComponentAnalysisEstimator(k = 5,
use_all_factor_levels = True,
pca_method = "glrm",
transform = "standardize",
impute_missing = True)
birds_pca.train(training_frame = train)

birds_pca.screeplot()

{code}

---

KeyError Traceback (most recent call last)
in
----> 1 birds_pca.screeplot()

~/anaconda3/envs/py_36/lib/python3.6/site-packages/h2o/model/dim_reduction.py in screeplot(self, type, **kwargs)
104 """
105 # check for matplotlib. exit if absent.
--> 106 is_server = kwargs.pop("server")
107 if kwargs:
108 raise ValueError("Unknown arguments %s to screeplot()" % ", ".join(kwargs.keys()))

KeyError: 'server

R fails:

{code:r}h2o.varimp(birds_pca)

Warning message:

“This model doesn't have variable importances”{code}

[exalate-issue-sync]

Tomas Fryda commented: [~accountid:5dc4f5bbb6e6b50c58af0624] The problem with python is easy to solve (currently it expects that a user always provides the {{server}} keyword which should be optional).

The R part seems to me that is correct, I didn’t find any mention in the documentation that {{varimp}} should be supported in R. You can use {{birds_pca@model$importance}} or {{summary(birds_pca)}} to display the “varimp”.

Maybe I am missing something, I looked just in [https://docs.h2o.ai/h2o/latest-stable/h2o-docs/data-science/pca.html#faq|https://docs.h2o.ai/h2o/latest-stable/h2o-docs/data-science/pca.html#faq|smart-link] and the {{varimp}} is there mentioned only for python to get the same result as in R’s {{@model$importance}}.

[h2o-ops]

JIRA Issue Details

Jira Issue: PUBDEV-8167
Assignee: Tomas Fryda
Reporter: Neema Mashayekhi
State: Resolved
Fix Version: 3.32.1.4
Attachments: N/A
Development PRs: Available

[h2o-ops]

Linked PRs from JIRA

#5517