mudata (version 0.1.1)

mudata: Create a MuData object

Description

Create an object describing multi-parameter spatiotemporal data in the (mostly) universal data format. This format is a collection of tables as described below. For an example of data already in this format, see the kentvillegreenwood dataset.

Usage

mudata(data, locations = NULL, params = NULL, datasets = NULL,
  columns = NULL, dataset.id = "default", location.id = "default",
  defactorize = TRUE, validate = TRUE, expand.tags = TRUE,
  retype = FALSE)

Arguments

data

The data table, which is a molten data frame containing the columns (at least) 'dataset', 'location', 'x', 'param', and 'value'. The 'dataset' column can be omitted if there is only one dataset contained in the object (its name can be specified by passing the parameter dataset.id). The 'location' column can be omitted if there is only data for one dataset and one location (its name can be specified by passing the parameter location.id).

locations

The locations table, which is a data frame containing the columns (at least) 'datset', and 'location'. If omitted, it will be created automatically using all unique dataset/location combinations.

params

The params table, which is a data frame containing the columns (at least) 'datset', and 'param'. If omitted, it will be created automatically using all unique dataset/param combinations.

datasets

The datasets table, which is a data frame containing the column (at least) 'dataset'. If omitted, it will be generated automatically using all unique datasets.

columns

The columns table, which is a data frame containing the columns (at least) 'dataset', 'table', and 'column'. If omitted, it will be created automatically using all dataset/table/column combinations.

dataset.id

The dataset id to use if the datasets table is omitted.

location.id

The location id if the locations table is omitted.

defactorize

Pass FALSE to suppress coersion of 'dataset', 'location', and 'param' columns to type 'character'.

validate

Pass FALSE to skip validation of input tables.

expand.tags

Pass FALSE to collapse non-required columns to a single column (called 'tags'), with key/value pairs in JSON format. See expand.tags.

retype

Pass TRUE to retype columns based on the 'type' column of the 'columns' table. This is useful when reading data from disk, where date/time columns may be stored as text.

Value

A mudata object

Examples

# NOT RUN {
library(reshape2)
library(dplyr)
data(pocmaj)

# melt data and summarise replicates
datatable <- pocmaj %>%
  melt(id.vars=c("core", "depth"), variable.name="param") %>%
  group_by(core, param, depth) %>%
  summarise(sd=mean(value), value=mean(value)) %>%
  rename.cols("depth"="x", "core"="location")

# create mudata object
md <- mudata(datatable)
summary(md)
plot(md, yvar="x", geom=c("path", "point"))

# }