Nematode (version 0.2.0)

summary.NMDS: Summarize NMDS Results

Description

Provides a concise summary of Non-Metric Multidimensional Scaling (NMDS) analysis results, including stress value, PERMANOVA (adonis2) and ANOSIM test statistics.

Provides a concise summary of Principal Coordinates Analysis (PCoA) analysis results, including PERMANOVA (adonis2) and ANOSIM test statistics.

Usage

# S3 method for NMDS
summary(object, ...)
# S3 method for PCoA
summary(object, ...)

Value

A list containing:

• stress - NMDS stress value

• points - Sample coordinates in the reduced space

• adonis2 - PERMANOVA results (R2, p-value, significance)

• anosim - ANOSIM results (R statistic, p-value, significance)

A list containing:

• points - Sample coordinates in the reduced space.

• eig - Variance explained by each principal coordinate axis.

• adonis2 - PERMANOVA results (R2, p-value, significance)

• anosim - ANOSIM results (R statistic, p-value, significance)

Arguments

object

An object of class "PCoA" produced by runPCoA function.

...

Additional arguments (currently not used).

Examples

# Example with default Bray-Curtis distance
data <- data.frame(
  Cephalobus = c(10, 20, 30, 1, 6, 5),
  Eucephalobus = c(5, 10, 12, 30, 1, 6),
  Acrobeloides = c(1, 2, 3, 12, 30, 1),
  Caenorhabditis = c(5, 8, 15, 2, 3, 12),
  Aphelenchus = c(5, 13, 11, 15, 2, 3),
  Leptonchus = c(3, 10, 15, 0, 15, 11),
  Pratylenchus = c(9, 2, 15, 15, 0, 15),
  Tylenchus = c(5, 0, 15, 11, 15, 2),
  Mesodorylaimus = c(7, 10, 18, 3, 12, 30),
  Discolaimus = c(1, 10, 25, 10, 18, 3),
  row.names = c("Sample1", "Sample2", "Sample3", "Sample4", "Sample5", "Sample6")
)
group_df <- data.frame(
  group = c("A", "A", "B", "B", "C", "C"),
  row.names = c("Sample1", "Sample2", "Sample3", "Sample4", "Sample5", "Sample6")
)

# Example for summary.NMDS
nmds <- runNMDS(data, group = group_df)
summary(nmds)

# Example for summary.PCoA
pcoa <- runPCoA(data, group = group_df)
summary(pcoa)