Description Usage Arguments Details Value See Also Examples
Get and set global opm options, or get list of predefined parameter names of interest for the user
1 2 3 4 5 6 7 8 9 10 11 | ## S4 method for signature 'character'
opm_opt(x)
## S4 method for signature 'list'
opm_opt(x)
## S4 method for signature 'missing'
opm_opt(x, ...)
## S4 method for signature 'character'
param_names(what)
## S4 method for signature 'missing'
param_names(what)
|
x |
Character scalar or list or missing. If not
given, all current settings are returned (as a named
list). If If |
... |
Optional arguments. If |
what |
Character scalar indicating the parameters of interest. See ‘Details’. |
The following keys can be used with the following kinds of values:
Default colour set
used by the OPMS
method of
xy_plot
and other plotting functions.
Character vector with default colour
borders between which level_plot
interpolates to obtain a colour palette.
Used by functions that support combination of metadata entries converted to data-frame columns immediately after their selection. Sets the character string that is used when joining old names to new name. Should normally only be a single character.
Used by functions that support
combination of metadata entries converted to data-frame
columns immediately after their selection. Sets the
character string that is used when joining old values to
new values. Should normally only be a single character;
must be a single character when used by
opm_mcp
.
Character
scalar indicating the default type of contrast used by
opm_mcp
.
Character scalar.
Default CSS file linked by
phylo_data
when producing HTML
output. Ignored if empty.
Character
vector with names of entries of csv_data
be
used by include_metadata
. Should be kept a
subset of opm_opt("csv.selection")
.
Character vector with names of
entries of csv_data
(must be a valid
‘keys’ argument) to be extracted by
collect_template
.
Character scalar. Default
‘subset’ argument of extract
and the
plotting functions.
Character scalar.
Default ‘subset’ argument of
do_disc
. It is usually not advisable to
change it.
Integer scalar. Number of digits used by some functions generating output text.
Character scalar. Character encoding
in input files as assumed by read_opm
.
Character scalar. Template used as
‘format’ argument by split_files
.
Character scalar indicating whether
read_opm
and other IO functions based on it
automatically convert to this plate type. If empty,
nothing is changed.
Character scalar
used as column name for trivial groups (either all items
in the same group or each item in a group of its own)
created by extract
.
Colour palette used by
heat_map
.
Used by
phylo_data
for automatically creating
HTML ‘title’ and ‘class’
attributes.
Integer vector
indicating the preferred order when trying to read
CSV files with read_single_opm
.
See there for details.
Used by
metadata
and some other functions that must
be in sync with it for joining metadata keys used in
nested queries (because the resulting object is
‘flat’).
Integer scalar that
can be used for identifying an
OmniLog(R)
instrument. Useful for collect_template
if
several such machines are in use.
Integer scalar used when abbreviating
full substrate names. See wells
for an
example.
Default name of the key to be treated as overall running time in the metadata. Currently only relevant for easing the inclusion of the total measurement duration in the metadata.
Default name of the key to be treated as ID in the metadata. Currently only relevant for easing the inclusion of plate-specific IDs in the metadata.
The first value to inserted next as ID value in the metadata. Currently only relevant for easing the inclusion of plate-specific IDs in the metadata.
Used when making discretisation results
uniform within a group. The minimum proportion the most
frequent value much reach to be used for representing all
values (if less, frequent, NA
is used). Must be a
numeric scalar between 0 and 1.
Character scalar indicating the default
output format used by phylo_data
.
Character scalar indicating the default
splitting characters used by separate
.
Logical scalar indicating whether
OPMD
objects can only be created if the
discretised data are consistent with the parameter from
which they have been estimated.
Numeric
scalar indicating the default threshold used by
annotated
.
Character
scalar indicating the time zone to be used when parsing
setup_time
entries. This is relevant for
merge
, which by default attempts to sort by
parsed setup times
Character vector
indicating the time formats used for parsing the
setup_time
entries (in the given order). Also
relevant for merge
by default. It is
advisable to put the more specific formats to the front
because otherwise information such as an ‘AM’ or
‘PM’ indication might be lost. A wrong format
might well match a given entry, causing opm to
misinterpret the time or even the date.
Issue a warning if
read_single_opm
reads a multiple-plate
old-style or new-style CSV file.
The following kinds of parameter names applied by
opm cannot be modified by the user (but displayed
using param_names
):
Names of the estimated curve parameters used internally and in the output.
Alternative name used to select discretised values instead.
Names that should not be used in
metadata entries because they are used as predefined
column names by functions such as flatten
.
The name of the column in data frames
generated by extract
that separates data
from metadata.
The name of the column that
holds the overall running time when extract
is used to obtain it.
List or atomic vector. If one to several values are set, the previous entries are returned invisibly.
base::options base::getOption
Other auxiliary-functions: separate
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 | # fetching a value
(digits <- opm_opt("digits"))
stopifnot(digits == 4)
# setting a value; previous value is returned as list
(old.opts <- opm_opt(digits = 5L))
stopifnot(is.list(old.opts), length(old.opts) == 1L)
stopifnot(old.opts$digits == 4)
# fetching the value again: should now be changed
(digits <- opm_opt("digits"))
stopifnot(digits == 5)
# resetting the value
(old.opts <- opm_opt(old.opts))
stopifnot(is.list(old.opts), length(old.opts) == 1L)
stopifnot(old.opts$digits == 5)
(digits <- opm_opt("digits"))
stopifnot(digits == 4)
## reserved parameter names
(x <- param_names())
stopifnot(is.character(x), length(x) > 1, identical(unique(x), x))
(x <- param_names("reserved"))
stopifnot(is.character(x), length(x) > 1, identical(unique(x), x))
stopifnot(param_names("split.at") %in% x)
|
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