metadata.set {opm} | R Documentation |
Set the meta-information stored together with the data.
For most kinds of arguments the WMDS
and
MOPMX
methods set the meta-information
stored together with the measurements for all plates at
once. But they can address the plates individually if
value
is a data frame, and they can address
metadata keys individually if value
is a formula.
## S4 replacement method for signature 'MOPMX,ANY,ANY' metadata(object, key) <- value ## S4 replacement method for signature 'MOPMX,ANY,data.frame' metadata(object, key) <- value ## S4 replacement method for signature 'MOPMX,missing,ANY' metadata(object, key) <- value ## S4 replacement method for signature 'MOPMX,missing,character' metadata(object, key) <- value ## S4 replacement method for signature 'MOPMX,missing,data.frame' metadata(object, key) <- value ## S4 replacement method for signature 'MOPMX,missing,logical' metadata(object, key) <- value ## S4 replacement method for signature 'OPM,missing,character' metadata(object, key) <- value ## S4 replacement method for signature 'OPM,missing,logical' metadata(object, key) <- value ## S4 replacement method for signature 'WMD,ANY,ANY' metadata(object, key) <- value ## S4 replacement method for signature 'WMD,character,ANY' metadata(object, key) <- value ## S4 replacement method for signature 'WMD,character,WMD' metadata(object, key) <- value ## S4 replacement method for signature 'WMD,character,WMDS' metadata(object, key) <- value ## S4 replacement method for signature 'WMD,character,data.frame' metadata(object, key) <- value ## S4 replacement method for signature 'WMD,list,WMD' metadata(object, key) <- value ## S4 replacement method for signature 'WMD,list,WMDS' metadata(object, key) <- value ## S4 replacement method for signature 'WMD,list,data.frame' metadata(object, key) <- value ## S4 replacement method for signature 'WMD,list,list' metadata(object, key) <- value ## S4 replacement method for signature 'WMD,missing,FOE' metadata(object, key) <- value ## S4 replacement method for signature 'WMD,missing,WMD' metadata(object, key) <- value ## S4 replacement method for signature 'WMD,missing,WMDS' metadata(object, key) <- value ## S4 replacement method for signature 'WMD,missing,character' metadata(object, key) <- value ## S4 replacement method for signature 'WMD,missing,data.frame' metadata(object, key) <- value ## S4 replacement method for signature 'WMD,missing,list' metadata(object, key) <- value ## S4 replacement method for signature 'WMD,numeric,WMD' metadata(object, key) <- value ## S4 replacement method for signature 'WMD,numeric,WMDS' metadata(object, key) <- value ## S4 replacement method for signature 'WMD,numeric,data.frame' metadata(object, key) <- value ## S4 replacement method for signature 'WMD,numeric,list' metadata(object, key) <- value ## S4 replacement method for signature 'WMDS,ANY,ANY' metadata(object, key) <- value ## S4 replacement method for signature 'WMDS,ANY,WMD' metadata(object, key) <- value ## S4 replacement method for signature 'WMDS,ANY,WMDS' metadata(object, key) <- value ## S4 replacement method for signature 'WMDS,ANY,data.frame' metadata(object, key) <- value ## S4 replacement method for signature 'WMDS,character,WMDS' metadata(object, key) <- value ## S4 replacement method for signature 'WMDS,character,data.frame' metadata(object, key) <- value ## S4 replacement method for signature 'WMDS,missing,FOE' metadata(object, key) <- value ## S4 replacement method for signature 'WMDS,missing,WMD' metadata(object, key) <- value ## S4 replacement method for signature 'WMDS,missing,WMDS' metadata(object, key) <- value ## S4 replacement method for signature 'WMDS,missing,character' metadata(object, key) <- value ## S4 replacement method for signature 'WMDS,missing,data.frame' metadata(object, key) <- value ## S4 replacement method for signature 'WMDS,missing,list' metadata(object, key) <- value ## S4 replacement method for signature 'WMDS,missing,logical' metadata(object, key) <- value
object |
|
key |
Missing, numeric scalar, character vector, factor, or list.
|
value |
Character vector, list, data frame, formula,
|
This method can easily be used to copy (selected parts
of) the csv_data
to the metadata; see there
for details.
map_metadata
can also be used to modify
metadata but it will return a novel object. See
edit
for manually modifying metadata.
value
.
Other metadata-functions: edit
,
include_metadata
,
map_metadata
, map_values
,
metadata
, metadata_chars
## WMD methods # WMD/missing/list method copy <- vaas_1 new.md <- list(Species = "Thermomicrobium roseum") metadata(copy) <- new.md stopifnot(identical(metadata(copy), new.md)) # WMD/missing/formula method (operates on previous entries!) copy <- vaas_1 metadata(copy) <- Organism ~ paste(Species, Strain) (x <- metadata(copy, "Organism")) stopifnot(is.null(metadata(vaas_1, "Organism")), !is.null(x)) # WMD/numeric/list method copy <- vaas_1 metadata(copy, 1) <- list(Authors = "Vaas et al.") stopifnot(length(metadata(copy)) > length(metadata(vaas_1))) # WMD/list/list method copy <- vaas_1 stopifnot(identical(metadata(copy, "Species"), "Escherichia coli")) # You can use this to translate the keys on-the-fly... metadata(copy, list(Organism = "Species")) <- list( Organism = "Bacillus subtilis") stopifnot(length(metadata(copy)) == length(metadata(vaas_1))) stopifnot(identical(metadata(copy, "Species"), "Bacillus subtilis")) stopifnot(is.null(metadata(copy, "Organism"))) # this was not set! # ...but you need not metadata(copy, list("Species")) <- list(Species = "Yersinia pestis") stopifnot(length(metadata(copy)) == length(metadata(vaas_1))) stopifnot(identical(metadata(copy, "Species"), "Yersinia pestis")) # Names need not be duplicated metadata(copy, list("Species")) <- list("Gen. sp.") stopifnot(length(metadata(copy)) == length(metadata(vaas_1))) stopifnot(identical(metadata(copy, "Species"), "Gen. sp.")) # ...but this would delete the entry because nothing would be found in # 'value' metadata(copy, list("Species")) <- list(Organism = "E. coli") stopifnot(length(metadata(copy)) < length(metadata(vaas_1))) stopifnot(is.null(metadata(copy, "Species"))) # ...this yields a general mechanism for metadata deletion by providing an # empty list as 'value'. # WMD/character/any method copy <- vaas_1 metadata(copy, "Strain") <- "08/15" stopifnot(length(metadata(copy)) == length(metadata(vaas_1))) stopifnot(metadata(copy, "Strain") != metadata(vaas_1, "Strain")) # WMD/factor/any method metadata(copy, as.factor("Strain")) <- metadata(vaas_1, "Strain") stopifnot(metadata(copy, "Strain") == metadata(vaas_1, "Strain")) ## WMDS methods # WMDS/missing/list method copy <- vaas_4 (metadata(copy) <- list(x = -99)) # will replace all of them stopifnot(identical(unique(metadata(copy)), list(list(x = -99)))) metadata(copy[2]) <- list(x = 1) # will replace those of 2nd plate stopifnot(identical(unique(metadata(copy)), list(list(x = -99), list(x = 1)))) # WMDS/missing/WMD method (metadata(copy) <- vaas_1) # will also replace all of them stopifnot(identical(unique(metadata(copy)), list(metadata(vaas_1)))) # WMDS/missing/formula method copy <- vaas_4 metadata(copy) <- Organism ~ paste(Species, Strain) (x <- metadata(copy, "Organism")) stopifnot(length(x) == length(metadata(vaas_4, "Organism")) + 4) # WMDS/ANY/ANY method copy <- vaas_4 (metadata(copy, "Species") <- "Bacillus subtilis") # will set all of them stopifnot(identical(unique(metadata(copy, "Species")), "Bacillus subtilis")) stopifnot(!identical(metadata(copy), metadata(vaas_4))) metadata(copy) <- vaas_4 # reset metadata(copy) stopifnot(identical(metadata(copy), metadata(vaas_4))) (metadata(copy) <- vaas_1) # set everything to metadata of vaas_1 stopifnot(identical(unique(metadata(copy)), list(metadata(vaas_1)))) # WMDS/character/data frame method copy <- vaas_4 (x <- data.frame(Type = grepl("T$", metadata(vaas_4, "Strain")))) metadata(copy, "Type") <- x # one-column data frames are simplified stopifnot(identical(metadata(copy, "Type"), x$Type)) # if keys match, a partial selection of the data frame is used (x <- cbind(x, Notype = !x$Type)) metadata(copy, "Type") <- x stopifnot(identical(metadata(copy, "Type"), x$Type)) # if keys do not match, the entire data-frame rows are included metadata(copy, "Type2") <- x stopifnot(!identical(metadata(copy, "Type2"), x$Type)) # WMDS/missing/character method: setting unique IDs metadata(copy) <- opm_opt("md.id.name") # set IDs metadata(copy, opm_opt("md.id.name")) # get these IDs stopifnot(is.integer(metadata(copy, opm_opt("md.id.name")))) # to reset the start point to the number n, use opm_opt(md.id.start = n) # WMDS/missing/character method: setting the running time metadata(copy) <- opm_opt("md.duration") # set it metadata(copy, opm_opt("md.duration")) # receive it stopifnot(is.double(metadata(copy, opm_opt("md.duration")))) # WMDS/missing/logical method: storing or deleting csv_data() entries copy <- vaas_4 metadata(copy) <- TRUE # store them stopifnot(ncol(to_metadata(copy)) > ncol(to_metadata(vaas_4))) metadata(copy) <- FALSE # remove them again stopifnot(identical(metadata(copy), metadata(vaas_4)))