Return metadata attributes from a single spectrum or a collection of spectra
as a data.frame. A wrapper on add_attr2tb providing an
alternative order of formal parameters and constrained functionality.
Usage
spct_metadata(
x,
col.names = NULL,
idx = "spct.idx",
na.rm = is.null(col.names),
unnest = TRUE
)Arguments
- x
generic_mspct or generic_spct Any collection of spectra or spectrum.
- col.names
named character vector Name(s) of column(s) to create.
- idx
character Name of the column with the names of the members of the collection of spectra.
- na.rm
logical Flag controlling deletion of columns containing only NA values.
- unnest
logical Flag controlling if metadata attributes that are lists of values should be returned in a list column or in separate columns.
Details
Each attribute is by default copied to a column in a tibble
or a data.frame. If the argument for tb is NULL, as by
default, a new tibble will be created. If an existing
data.frame or tibble is passed as argument, new columns are
added to it. However, the number of rows in the argument passed to
tb must match the number of spectra in the argument passed to
mspct. Only in the case of methods add_attr2tb() and
spct_metadata() if the argument to col.names is a named
vector, the names of members are used as names for the columns created.
This permits setting any valid name for the new columns. If the members of
the vector passed to col.names have no names, then the value is
interpreted as the name of the attributes to add, and also used as name for
the new column.
Valid values accepted as argument to col.names are NULL, or a
vector containing one or more of the following character strings:
"lon", "lat", "address", "geocode",
"where.measured", "when.measured", "what.measured",
"how.measured", "comment", "normalised",
"normalized", "scaled", "bswf.used",
"instr.desc", "instr.sn", solute.properties,
"filter.properties", "Tfr.type", "Rfr.type",
"time.unit", bswf.used, multiple.wl. Invalid character
values are ignored with a warning.
Note
The order of the first two arguments is reversed in
add_attr2tb(), when_measured2tb(), what_measured2tb(),
etc., compared to attribute query functions, such as spct_metadata,
when_measured(), what_measured(), how_measured(), etc.
This is to allow the use of add_attr2tb() and related functions in
'pipes' to add metadata to summaries computed at earlier steps in the pipe.
See also
add_attr2tb for more details.
Other measurement metadata functions:
add_attr2tb(),
getFilterProperties(),
getHowMeasured(),
getInstrDesc(),
getInstrSettings(),
getSoluteProperties(),
getWhatMeasured(),
getWhenMeasured(),
getWhereMeasured(),
get_attributes(),
isValidInstrDesc(),
isValidInstrSettings(),
select_spct_attributes(),
setFilterProperties(),
setHowMeasured(),
setInstrDesc(),
setInstrSettings(),
setSoluteProperties(),
setWhatMeasured(),
setWhenMeasured(),
setWhereMeasured(),
spct_attr2tb(),
subset_attributes(),
trimInstrDesc(),
trimInstrSettings()
Examples
# collection of spectra
spct_metadata(sun_evening.mspct)
#> # A tibble: 5 × 11
#> spct.idx lat lon address when.measured what.measured how.measured
#> <fct> <dbl> <dbl> <chr> <dttm> <chr> <chr>
#> 1 time.01 60.2 24.0 Viikki, H… 2023-06-12 18:38:00 cosine.hour.9 "Acquired w…
#> 2 time.02 60.2 24.0 Viikki, H… 2023-06-12 18:39:00 cosine.hour.9 "Acquired w…
#> 3 time.03 60.2 24.0 Viikki, H… 2023-06-12 18:40:00 cosine.hour.9 "Acquired w…
#> 4 time.04 60.2 24.0 Viikki, H… 2023-06-12 18:41:00 cosine.hour.9 "Acquired w…
#> 5 time.05 60.2 24.0 Viikki, H… 2023-06-12 18:42:00 cosine.hour.9 "Acquired w…
#> # ℹ 4 more variables: normalized <dbl>, multiplier <dbl>, time.unit <Duration>,
#> # bswf.used <chr>
spct_metadata(sun_evening.mspct, na.rm = FALSE)
#> # A tibble: 5 × 17
#> spct.idx lat lon address when.measured what.measured how.measured
#> <fct> <dbl> <dbl> <chr> <dttm> <chr> <chr>
#> 1 time.01 60.2 24.0 Viikki, H… 2023-06-12 18:38:00 cosine.hour.9 "Acquired w…
#> 2 time.02 60.2 24.0 Viikki, H… 2023-06-12 18:39:00 cosine.hour.9 "Acquired w…
#> 3 time.03 60.2 24.0 Viikki, H… 2023-06-12 18:40:00 cosine.hour.9 "Acquired w…
#> 4 time.04 60.2 24.0 Viikki, H… 2023-06-12 18:41:00 cosine.hour.9 "Acquired w…
#> 5 time.05 60.2 24.0 Viikki, H… 2023-06-12 18:42:00 cosine.hour.9 "Acquired w…
#> # ℹ 10 more variables: normalized <dbl>, multiplier <dbl>, f <lgl>,
#> # range <list>, target <dbl>, cols <chr>, time.unit <Duration>,
#> # bswf.used <chr>, Tfr.type <chr>, Rfr.type <chr>
spct_metadata(sun_evening.mspct,
col.names = "geocode",
unnest = FALSE)
#> # A tibble: 5 × 2
#> spct.idx geocode
#> <fct> <named list>
#> 1 time.01 <tibble [1 × 3]>
#> 2 time.02 <tibble [1 × 3]>
#> 3 time.03 <tibble [1 × 3]>
#> 4 time.04 <tibble [1 × 3]>
#> 5 time.05 <tibble [1 × 3]>
spct_metadata(sun_evening.mspct,
col.names = c(when.measured = "time", "what.measured"))
#> # A tibble: 5 × 3
#> spct.idx time what.measured
#> <fct> <dttm> <chr>
#> 1 time.01 2023-06-12 18:38:00 cosine.hour.9
#> 2 time.02 2023-06-12 18:39:00 cosine.hour.9
#> 3 time.03 2023-06-12 18:40:00 cosine.hour.9
#> 4 time.04 2023-06-12 18:41:00 cosine.hour.9
#> 5 time.05 2023-06-12 18:42:00 cosine.hour.9
# multiple spectra in long form
spct_metadata(sun_evening.spct,
col.names = c("geocode", "when.measured"))
#> # A tibble: 5 × 5
#> spct.idx lat lon address when.measured
#> <fct> <dbl> <dbl> <chr> <dttm>
#> 1 time.01 60.2 24.0 Viikki, Helsinki, FI 2023-06-12 18:38:00
#> 2 time.02 60.2 24.0 Viikki, Helsinki, FI 2023-06-12 18:39:00
#> 3 time.03 60.2 24.0 Viikki, Helsinki, FI 2023-06-12 18:40:00
#> 4 time.04 60.2 24.0 Viikki, Helsinki, FI 2023-06-12 18:41:00
#> 5 time.05 60.2 24.0 Viikki, Helsinki, FI 2023-06-12 18:42:00
# single spectrum
spct_metadata(sun.spct,
col.names = c("geocode", "when.measured"))
#> # A tibble: 1 × 5
#> spct.idx lat lon address when.measured
#> <fct> <dbl> <dbl> <chr> <dttm>
#> 1 spct.name 60.2 25.0 Kumpula, Helsinki, FI 2010-06-22 09:51:00