make_do_matrix: Make matrix of dissolved oxygen data

In OTUtable: North Temperate Lakes - Microbial Observatory 16S Time Series Data and Functions

Description

Takes a given sample ID and converts the dissolved oxygen data in data(metadata) from long format into a matrix. This is useful for plotting using plot_column()

Usage

make_do_matrix(sampleID, field_data)

Arguments

sampleID	A regular expression used to select a group of samples
field_data	A dataset of DO profiles in long format. Column names must be the same as the metadata file provided with this package

Details

Also fills in NA values with the average of the depth above and below the missing value. If the value is at the bottom of the water column, the second deepest is substituted.

Value

Returns matrix of DO data with depth in rows and date in columns

Note

This is mainly used for generating contour plots. In general, long format is easier to work with. In the metadata file included in this package, each DO measurement is listed twice, once under the epilimnion sample name and again under the hypolimnion sample name.

Author(s)

Alexandra Linz <[e-mail]>

Examples

data(metadata)

dissolved_oxygen <- make_do_matrix("TBE.....07", metadata)

Example output

OTUtable documentation built on May 1, 2019, 10:51 p.m.