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ncss-tech / soilReports

An R package that assists with the setup and operation of a collection of soil data summary, comparison, and evaluation reports. These reports are primarily used by USDA-NRCS soil scientists in both initial and update mapping.
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explore other ordination methods #18

Closed dylanbeaudette closed 8 years ago

dylanbeaudette commented 8 years ago
  1. tried other MDS methods:
    • MASS::sammon() fails when there are duplicates in the initial configuration
    • vegan::monoMDS() gives similar results as MASS::isoMDS()
    • MASS::isoMDS() is the fastest, most stable algorithm I have tried
    • tried tsne algorithm (https://lvdmaaten.github.io/tsne/), slow and runs out of memory with large datasets
dylanbeaudette commented 8 years ago

consider using MDS via randomForest()

dylanbeaudette commented 8 years ago

consider vegan::betadisper(), there are decent plot methods and summary functions.

dylanbeaudette commented 8 years ago

vegan::betadisper() seems to be the most flexible method, and it provides useful summary and testing options. See vegan::betadisper() for some ideas.