nonmetric multidimensional scaling (Plantae)

Knowledge graph centered on nonmetric multidimensional scaling (Plantae) with 67 nodes and 130 connections. Top connected: Hummingbird, Bombus, Ipomopsis, Ligusticum porteri, I. aggregata.

Method synopsis

PERMANOVA testing of volatile composition differences across species and years, with NMDS visualization of chemical dissimilarity patterns.

Synthesized from method descriptions across 3 papers using this protocol.

Procedure from a recent peer-reviewed implementation

Steps below were extracted from the most recent peer-reviewed implementation of this protocol in the corpus — Traditional plant functional groups explain variation in economic but not size related traits across the tundra biome (2018), Global ecology and biogeography. Implementations in other papers (listed below) may differ.

1. Test trait variation explained by functional groups
   Used PERMANOVA analysis to test the significance of and variance explained by functional groups to estimate how well traditional functional groups represent trait characteristics. Used Euclidean distance with 999 permutations for the combination of all six traits using the 'adonis' function in R package 'vegan'.
   Quantities: 999 permutations used in PERMANOVA analysisDuration: Not specifiedConditions: Analysis conducted using all six traits simultaneously
   Equipment: R package 'vegan'
2. Compare explanatory power across trait combinations
   Repeated PERMANOVA analysis for every possible multivariate combination of traits to test whether particular trait combinations were well differentiated by functional groups. Differentiated between size-related and economic traits, reflecting two major dimensions of trait variation amongst global plant species.
   Quantities: All possible combinations of 6 traits tested, with mean variance explained calculated over 999 replications for each combinationDuration: 999 replications for each trait combinationConditions: Economic traits: SLA, LDMC, LN; Size-related traits: PH, SM, LA
   Equipment: R statistical software

Typical Equipment

• R-Studio
• Vegan Package

Output Measurements

• multivariate composition differences
• ordination scores
• statistical significance

Papers Using This Protocol (3)

Species Studied With This Protocol