toWide: toWide

In neotoma2: Working with the Neotoma Paleoecology Database

toWide

Description

Obtain a wide table with information regarding of samples grouped by variablename and depth/age.

Usage

toWide(
  x,
  variablenames = c(),
  ecologicalgroups = c(),
  elementtypes = c(),
  unit = c(),
  groupby = "age",
  operation = "prop"
)

Arguments

x	dataframe object with samples
variablenames	Optional vector to filter by specific variable names.
ecologicalgroups	Vector stating the ecological groups to be filtered by, e.g "DIAT", "TRSH"
elementtypes	Label of element type to filter by, e.g. "pollen", "valve"
unit	Label stating which units to filter by, e.g. "NISP"
groupby	Group by 'age' or 'depth'
operation	label or vector of operations to be chosen from: 'prop', 'sum', 'presence'.

Value

wide data.frame obtained from long samples data.frame

Examples

fourcorners <- '{"type": "Polygon",
"coordinates": [[
[-109.36060497194846, 37.69552879956651],
[-107.813845732192, 37.69552879956651],
[-107.813845732192, 36.80303716260222],
[-109.36060497194846, 36.80303716260222], 
[-109.36060497194846, 37.69552879956651]
]]}'

# Download all vertebrate localities within a bounding box.
fc_sites <- neotoma2::get_sites(loc = fourcorners[1])
fc_ds <- neotoma2::get_datasets(fc_sites) %>% 
neotoma2::filter(datasettype=="vertebrate fauna")

fc_dl <- neotoma2::get_downloads(fc_ds)
fc_dl1 <- fc_dl[[1]]

fc_smp <- samples(fc_dl1)
toWide(fc_smp, ecologicalgroups=c('AVES', 'RODE'), 
elementtypes='bone/tooth', unit='present/absent')

neotoma2 documentation built on May 29, 2024, 6:21 a.m.