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#' @md
utils::globalVariables(c(".", "element", "taxonid", "symmetry", "taxongroup",
"elementtype", "variablename", "ecologicalgroup", "element", "taxonid"))
# Start "c" methods
#' @title c Method - Combine objects, including NULL
setClassUnion("missingOrNULL", c("missing", "NULL"))
#' @title Add a new chronology into an existing collectionunit.
#' @param object A collection unit object
#' @param x A chronology object generated using \code{set_chronology()}
#' @param y A data.frame of sample ages, with required columns:
#' `"analysisunitid"`, `"age"`, `"agetype"`, `"ageolder"`, and `"ageyounger"`.
#' @returns `chronologies` with new added chronology
#' @description Given a collunit, add a new chronology object to the unit
#' with both the chronology metadata and the age information (as `y`)
#' @details When undertaking analysis we may wish to add a new chronology to
#' existing records within Neotoma. To do this we must first build the
#' chronology, but also link it to existing analysis units within the
#' collection unit.
#' For examples from this function, see the
#' [Complex Workflows](https://open.neotomadb.org/EPD_binder/complex_workflow.html)
#' documentation online.
#' @export
setMethod(f = "add_chronology",
signature = signature(object = "collunit",
x = "chronology",
y = "data.frame"),
definition = function(object, x, y) {
existingIds <- as.data.frame(object@chronologies)$chronologyid
existinganalysisIds <- purrr::map(object@datasets@datasets,
function(x) {
map(x@samples@samples,
function(y) {
y$analysisunitid
}) %>%
unlist()
})
if (x$chronologyid %in% existingIds) {
stop("There is already a chronology with the same ID as your
new chronology. Please change the new chronologyid.")
}
assertthat::assert_that(all(c("analysisunitid", "age",
"agetype", "ageolder",
"ageyounger") %in% colnames(y)),
msg = "The data.frame for sample ages must
contain the columns analysisunitid,
age, agetype, ageolder and ageyounger.")
if (!any(unlist(existinganalysisIds) %in% y$analysisunitid)) {
stop("There is no overlap between the existing analysis units and
the anaysis units in your new sample ages data.frame.")
} else if (!all(unlist(existinganalysisIds) %in% y$analysisunitid)) {
warning("Not all of the existing analysis units are represented in
the new sample ages data.frame. Analysis units without
ages will have NA values assigned.")
}
object@datasets@datasets <- map(object@datasets@datasets,
function(z) {
z@samples@samples <- map(z@samples@samples, function(a) {
auid <- a@analysisunitid
if (auid %in% y$analysisunitid) {
sampleagerow <- y %>% dplyr::filter(analysisunitid == auid)
a@ages <- data.frame(age = sampleagerow$age,
agetype = sampleagerow$agetype,
ageolder = sampleagerow$ageolder,
ageyounger = sampleagerow$ageyounger,
chronologyid = x$chronologyid,
chronologyname = x$chronologyname) %>%
rbind(., a@ages)
}
return(a)
})
return(z)
})
object@chronologies <- c(object@chronologies, x)
if (x@isdefault == 1) {
object@chronologies <- set_default(object@chronologies,
x$chronologyid)
}
return(object)
})
#' @title c Method for NULL values
#' @param x NULL object
#' @param y sites/collunits object
#' @returns concatenated `collunits` object
#' @export
setMethod(f = "c",
signature = "missingOrNULL",
definition = function(x = "missingORNULL", y) {
y
})
#' @title Show the collection unit information
#' @param object collunits object
#' @return null used for side effects. Printing a data.frame
#' @export
setMethod(f = "show",
signature = signature(object = "collunits"),
definition = function(object) {
result <- purrr::map(object@collunits, function(x) {
as.data.frame(x)
}) %>%
bind_rows()
print(result)
})
#' @title Show the collection unit information
#' @param object collunit object
#' @return null used for side effects. Printing a data.frame
#' @export
setMethod(f = "show",
signature = signature(object = "collunit"),
definition = function(object) {
result <- as.data.frame(object)
print(result)
})
#' @title Get or remove sites by numeric index
#' @param x The collunits object
#' @param i The numeric index
#' @description Retrieve sites by numeric index
#' @return null used for side effects. Printing a data.frame
setMethod(f = "[",
signature = signature(x = "collunits", i = "numeric"),
definition = function(x, i) {
new("collunits", collunits = x@collunits[i])
})
#' @title Slicer
#' @param x collunits object
#' @param i iteration in collunits list
#' @description Obtain one of the elements within a collunits list
#' @returns sliced `collunits` object
#' @export
setMethod(f = "[[",
signature = signature(x = "collunits", i = "numeric"),
definition = function(x, i) {
if (length(i) == 1) {
out <- new("collunit", x@collunits[[i]])
} else {
out <- purrr::map(i, function(z) {
new("collunit", x@collunits[[z]])
})
out <- new("collunits", collunits = out)
}
return(out)
})
#' @title Get slot names
#' @param x A collection unit object.
#' @description Get all names for named elements within a `collunit` object.
#' @returns NULL. Shows the names of the slots
#' @export
setMethod(f = "names",
signature = signature(x = "collunit"),
definition = function(x) {
slotNames(x)
})
#' @title Insert collunit
#' @param x collunits object
#' @param i iteration in collunits list
#' @param value The value to be used
#' @description Obtain one of the elements within a collunits list
#' @returns Modified `collunits`
#' @export
setMethod(f = "[[<-",
signature = signature(x = "collunits"),
definition = function(x, i, value) {
collunitset <- x@collunits
collunitset[[i]] <- value
out <- new("collunits", collunits = collunitset)
return(out)
})
#' @title Assign collunit field by numeric index
#' @param x The collunit object.
#' @param i The column indicator.
#' @param value The value to be used.
#' @returns sliced element
setMethod(f = "[<-",
signature = signature(x = "collunit", i = "character"),
definition = function(x, i, value) {
for (idx in 1:length(i)) {
slot(x, i[idx]) <- value[idx]
}
return(x)
})
#' @title Assign collunit field by numeric index
#' @param x The collunit object.
#' @param i The column indicator.
#' @param value The value to be used.
#' @returns sliced value
setMethod(f = "[<-",
signature = signature(x = "collunit", i = "numeric"),
definition = function(x, i, value) {
slots <- slotNames(x)
for (idx in 1:length(i)) {
slot(x, slots[i[idx]]) <- value[idx]
}
return(x)
})
#' @title Assign collunit field by numeric index
#' @param x The collunit object.
#' @param name name of the slot.
#' @param value The value to be used.
#' @returns assign a new value to a slot
setMethod(f = "$<-",
signature = signature(x = "collunit"),
definition = function(x, name, value) {
slot(x, name) <- value
return(x)
})
#' @title $
#' @param x collunit object
#' @param name name of the slot
#' @description Obtain slots of a collunit without using at-mark
#' @returns null prints element of a slot
#' @export
setMethod(f = "$",
signature = signature(x = "collunit"),
definition = function(x, name) {
slot(x, name)
})
#' @title $ for collunits
#' @param x collunits object
#' @param name name of the slot
#' @description Obtain slots of a collunit without using at-mark
#' @returns null prints element of a slot
#' @export
setMethod(f = "$",
signature = signature(x = "collunits"),
definition = function(x, name) {
x %>%
map(function(y) {
slot(y, name)
}) %>%
unlist()
})
#' @title as.data.frame site
#' @param x site object
#' @description show as dataframe
#' @returns data.frame object with a collection units metadata
#' @export
setMethod(f = "as.data.frame",
signature = signature("collunit"),
definition = function(x) {
data.frame(collectionunitid = x@collectionunitid,
handle = x@handle,
colldate = x@colldate,
location = x@location,
waterdepth = x@waterdepth,
collunittype = x@collunittype,
collectiondevice = x@collectiondevice,
defaultchronology = x@defaultchronology,
collectionunitname = x@collectionunitname,
depositionalenvironment = x@depositionalenvironment)
})
#' @title as.data.frame collunits
#' @param x collunits object
#' @description show as dataframe as prep to save as csv
#' @returns data.frame of multiple collection units metadata.
#' @export
setMethod(f = "as.data.frame",
signature = signature("collunits"),
definition = function(x) {
x@collunits %>% map(as.data.frame) %>% bind_rows()
})
#' @title Length Method collunits
#' @export
#' @param x collunits object
#' @returns length of a `collunits` object
setMethod(f = "length",
signature = signature(x = "collunits"),
definition = function(x) {
length(x@collunits)
})
#' @title c Method - Combine collunits objects
#' @param x collunits object 1
#' @param y collunits object 2
#' @importFrom methods is
#' @returns concatenated collection units without duplicates
#' @export
setMethod(f = "c",
signature = signature(x = "collunits"),
definition = function(x, y) {
if (is(y, "collunits")) {
out <- new("collunits",
collunits = unlist(c(x@collunits,
y@collunits),
recursive = FALSE))
} else if (is(y, "collunit")) {
collunitset <- c(x@collunits, y)
out <- new("collunits", collunits = collunitset)
}
return(out)
})
#' @title write CSV
#' @param x collunits object
#' @param ... Additional parameters associated with the call.
#' @returns null side effect for saving a CSV file.
#' @export
setMethod(f = "write.csv",
signature = "collunits",
definition = function(x, ...) {
df1 <- as.data.frame(x)
write.csv(df1, ...)
})
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