enveomics.R (version 1.9.1)

enve.df2dist: Enveomics: Data Frame to Dist

Description

Transform a dataframe (or coercible object, like a table) into a dist object.

Usage

enve.df2dist(
  x,
  obj1.index = 1,
  obj2.index = 2,
  dist.index = 3,
  default.d = NA,
  max.sim = 0
)

Value

Returns a dist object.

Arguments

x

A dataframe (or coercible object) with at least three columns:

1. ID of the object 1,

2. ID of the object 2, and

3. distance between the two objects.

obj1.index

Index of the column containing the ID of the object 1.

obj2.index

Index of the column containing the ID of the object 2.

dist.index

Index of the column containing the distance.

default.d

Default value (for missing values).

max.sim

If not zero, assumes that the values are similarity (not distance) and this is the maximum similarity (corresponding to distance 0). Applies transformation: \(distance = (max.sim - values)/max.sim.\)

Author

Luis M. Rodriguez-R [aut, cre]

Examples

# A sparse matrix representation of similarities as data frame.
# The column "extra_data" is meaningless, only included to illustrate
# the use of the obj*.index parameters
sim <- data.frame(
  extra_data = c(0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.5),
  query      = c("A", "A", "A", "B", "C", "C", "D"),
  subject    = c("A", "B", "C", "B", "C", "B", "A"),
  similarity = c(100,  90,  60, 100, 100,  70,  10)
)
dist <- enve.df2dist(sim, "query", "subject", "similarity", max.sim = 100)
print(dist)