| Version: | 0.3.0 |
| Encoding: | UTF-8 |
| Title: | Handling Taxonomic Lists |
| Depends: | R(≥ 4.3) |
| Imports: | biblio (≥ 0.0.8), foreign, methods, stats, stringdist, stringi, stringr, tools, utils, vegdata |
| Suggests: | ape, knitr, rmarkdown, taxa, testthat |
| LazyData: | true |
| Description: | Handling taxonomic lists through objects of class 'taxlist'. This package provides functions to import species lists from 'Turboveg' (https://www.synbiosys.alterra.nl/turboveg/) and the possibility to create backups from resulting R-objects. Also quick displays are implemented as summary-methods. |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| URL: | https://cran.r-project.org/package=taxlist, https://github.com/ropensci/taxlist, https://docs.ropensci.org/taxlist/ |
| BugReports: | https://github.com/ropensci/taxlist/issues |
| Collate: | 'imports.R' 'internal.R' 'levels.R' 'prune_levels.R' 'deprecated-functions.R' 'id_generator.R' 'replace_x.R' 'insert_rows.R' 'dissect_name.R' 'clean_strings.R' 'taxlist-class.R' 'matched_names-class.R' 'clean.R' 'coerce-methods.R' 'taxon_views.R' 'count_taxa.R' 'taxon_names.R' 'taxon_relations.R' 'add_concept.R' 'taxon_traits.R' 'accepted_name.R' 'get_children.R' 'merge_to_parent.R' 'merge_taxa.R' 'Extract.R' 'subset.R' 'backup_object.R' 'summary.R' 'df2taxlist.R' 'tv2taxlist.R' 'tax2traits.R' 'match_names.R' 'print_name.R' 'indented_list.R' 'Easplist-data.R' 'taxlist-package.R' 'taxlist2df.R' 'parents.R' |
| VignetteBuilder: | knitr |
| RoxygenNote: | 7.3.1 |
| NeedsCompilation: | no |
| Packaged: | 2024-07-03 12:38:37 UTC; miguel |
| Author: | Miguel Alvarez 
[aut, cre],
Zachary Foster
[ctb],
Sam Levin [rev],
Margaret Siple [rev] |
| Maintainer: | Miguel Alvarez <kamapu78@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2024-07-03 13:30:02 UTC |
taxlist: Handling Taxonomic Lists
Description
Handling taxonomic lists through objects of class 'taxlist'. This package provides functions to import species lists from 'Turboveg' (https://www.synbiosys.alterra.nl/turboveg/) and the possibility to create backups from resulting R-objects. Also quick displays are implemented as summary-methods.
Author(s)
Maintainer: Miguel Alvarez kamapu78@gmail.com (ORCID)
Other contributors:
Zachary Foster zacharyfoster1989@gmail.com (ORCID) [contributor]
Sam Levin levisc8@gmail.com [reviewer]
Margaret Siple siplem@uw.edu [reviewer]
See Also
Useful links:
Report bugs at https://github.com/ropensci/taxlist/issues
Deprecated functions
Description
Most of those functions have been replaced by alternative 'update' ones.
Usage
add_parent()
add_trait()
add_level()
replace_view()
taxlist2taxmap()
taxmap2taxlist()
taxmap2taxlist()
tnrs()
List of vascular plants from East Africa
Description
Example of an incomplete taxonomic list including taxa recorded in East Africa.
Usage
Easplist
Format
An object of class taxlist.
Details
This list is a subset of the taxonomic list implemented in the database SWEA-Dataveg. Since this list is being complemented regarding stored vegetation plots, it is an incomplete list.
Source
African Plant Database, SWEA-Dataveg.
Examples
summary(Easplist)
Extract or Replace Parts of taxlist Objects
Description
Quick access to slots taxonTraits and taxonRelations within
taxlist objects.
Usage
## S4 method for signature 'taxlist'
x[i, j, drop = FALSE]
## S4 method for signature 'taxlist'
x$name
Arguments
x |
Object of class taxlist. |
i |
Integer or logical vector used as index for access to taxon concepts, referring to the rows in slot 'taxonRelations'. These indices can be used to produce a object with a subset of taxon concepts. It is not recommended to use character values for this index. |
j |
Integer, logical or character vector used as index for access to variables in slot 'taxonTraits'. These indices can be used to reduce the number of variables in the mentioned slot. |
drop |
A logical value passed to |
name |
A symbol or character value for the method |
Value
The method $ retrieves a vector, while [ retrieves a subset
of the input taxlist object.
Author(s)
Miguel Alvarez kamapu78@gmail.com.
See Also
Examples
## Statistics on life forms
summary(as.factor(Easplist$life_form))
## First concepts in this list
summary(Easplist[1:5, ], "all")
Manage accepted names, synonyms and basionyms
Description
Taxon usage names for a taxon concept can be divided into three categories: accepted names, basionyms and synonyms. Each single taxon concept may at least have an accepted name, while basionym and synonyms are optional.
The function accepted_name() retrieves the accepted names for the indicated
taxon concepts or for the whole taxlist object.
By using show_traits=TRUE, the respective taxon traits will be
displayed as well, providing an overview of taxa included in the object.
The replacement method for this function will set the respective usage name
IDs as accepted names for the respective taxon concept, provided that these
names are already set as synonyms in the respective concepts.
The function synonyms() is working in a similar way as accepted_name(),
but this function does not include taxon traits in the output.
Alternatives for inserting new synonyms into a taxon concept are either
moving synonyms from other taxa by using change_concept<- or
inserting new names in the object by using add_synonym().
The function basionym() is retrieving and setting basionyms in the
respective taxon concepts similarly to accepted_name, but this function
does not retrieve any information on taxon traits, either.
The fucntion change_concept<- replace a taxon usage name (argument
'UsageID') to a different taxonomic concept (argument 'value').
Usage
accepted_name(taxlist, ...)
## S3 method for class 'taxlist'
accepted_name(taxlist, ConceptID, show_traits = FALSE, ...)
accepted_name(taxlist, ...) <- value
## S3 replacement method for class 'taxlist'
accepted_name(taxlist, ConceptID, ...) <- value
synonyms(taxlist, ...)
## S3 method for class 'taxlist'
synonyms(taxlist, ConceptID, ...)
basionym(taxlist, ...)
## S3 method for class 'taxlist'
basionym(taxlist, ConceptID, ...)
basionym(taxlist, ...) <- value
## S3 replacement method for class 'taxlist'
basionym(taxlist, ConceptID, ...) <- value
change_concept(taxlist, ...) <- value
## S3 replacement method for class 'taxlist'
change_concept(taxlist, UsageID, ...) <- value
Arguments
taxlist |
An object of class taxlist. |
... |
Further arguments passed among methods. |
ConceptID |
Integer containing concept IDs where to request or set names for one category. |
show_traits |
Logical value, whether traits should be included in the
output of |
value |
Integer containing usage IDs to be set to the respective category in the respective taxon concept. |
UsageID |
Numeric vector with taxon usage IDs that will be changed to a different taxonomic concept. |
Value
Most of the methods return information in data frames, while replacement methods do it as taxlist objects.
Author(s)
Miguel Alvarez kamapu78@gmail.com
See Also
add_synonym() change_concept<-
Examples
## Set a different accepted name for Cyclosorus interruptus
summary(Easplist, "Cyclosorus interruptus")
accepted_name(Easplist, 50074) <- 53097
summary(Easplist, 50074)
## Inserting a new name first
summary(Easplist, "Basella alba")
Easplist <- add_synonym(taxlist = Easplist, ConceptID = 68,
TaxonName = "Basella cordifolia", AuthorName = "Lam.")
summary(Easplist, 68)
accepted_name(Easplist, 68) <- 56139
summary(Easplist, 68)
## Display synonyms
head(synonyms(taxlist = Easplist))
## Synonyms for an specific concept
synonyms(taxlist = Easplist, ConceptID = 20)
## Basionym for Cyclosrus interruptus
summary(Easplist, 50074)
basionym(Easplist, 50074) <- 53097
summary(Easplist, 50074)
basionym(Easplist, 50074)
## Move the name Typha aethiopica to concept 573 (T. latifolia)
summary(Easplist, c(50105, 573))
change_concept(Easplist, 53130) <- 573
summary(Easplist, c(50105, 573))
Add new taxonomic concepts into taxlist objects
Description
Alternative methods to add new concepts into existing taxlist objects.
Usage
add_concept(taxlist, TaxonName, ...)
## S4 method for signature 'taxlist,data.frame'
add_concept(taxlist, TaxonName, ...)
## S4 method for signature 'taxlist,character'
add_concept(taxlist, TaxonName, ...)
## S4 method for signature 'taxlist,taxlist'
add_concept(taxlist, TaxonName, insert_view = FALSE, ...)
update_concept(taxlist, ConceptID, ...)
Arguments
taxlist |
A taxlist object. |
TaxonName |
Character vector with the accepted name for the new taxon concepts. |
... |
Further arguments passed among methods. |
insert_view |
A numeric (integer) vector, indicating the views to be
inserted in |
ConceptID |
Concept IDs to be updated. |
Filling missed columns with NAs
Description
If columns of y are missed in x, the later gets these columns filled with
NA values.
Usage
add_nacolumn(x, y)
Arguments
x |
( |
y |
( |
Value
A data.frame.
Add a suffix when strings are identical
Description
An integer will be added as suffix in x if an identical value is in y.
If a value with suffix is already in y, the function will search for the
highest suffix to avoid duplicated values.
Usage
add_suffix(x, y, sep = "_")
Arguments
x |
( |
y |
( |
sep |
( |
Value
A character value, either x or x with suffix if already in y.
Coerce taxlist objects to lists.
Description
Coercion of S4 objects to lists can be applied to explore their content, avoiding errors caused by their validation.
Usage
S4_to_list(x)
Arguments
x |
An object of class taxlist or any S4 class. |
Details
Coerce taxlist objects to lists.
Value
An object of class list.
Author(s)
Miguel Alvarez kamapu78@gmail.com
Examples
## Coerce taxlist to list
tax_list <- as(Easplist, "list")
## Coerce data frame to taxlist
Cyperus <- read.csv(file = file.path(path.package("taxlist"), "cyperus",
"names.csv"))
Cyperus$AcceptedName <- !Cyperus$SYNONYM
head(Cyperus)
as(Cyperus, "taxlist")
Make and load backups of R objects
Description
When work with data becomes risky, the best practice is to produce backup
files.
The function of backup_object is a wrapper of save(), adding a
time stamp and a suffix to the name of the resulting file (an R image file
with extension *.rda).
The function load_last is adapted to this style, loading the newest
version to the session.
Usage
backup_object(
...,
objects = character(),
file,
stamp = TRUE,
sep = "_",
date_format = "%Y-%m-%d",
time_format = "%H:%M:%S",
overwrite = FALSE
)
sort_backups(
name,
path = ".",
date_format = "%Y-%m-%d",
fext = ".rda",
sep = "_"
)
load_last(file, path, ..., choice)
Arguments
... |
Names of the objects to be saved (either symbols or character
strings) in |
objects |
A character vector indicating the names of objects to be included in the backup file. |
file |
A character value indicating the name of the backup file, without the extension. |
stamp |
A logical value indicating whether time should be stamped in the backup name or not. |
sep |
A character value used to separate backup's name from stamp and from the suffix. |
date_format |
A character value indicating the format used for the
file stamp. See |
time_format |
A character value indicating the format used for the
the time (not including the date), which will be used for the invisible
report in |
overwrite |
A logical value indicating whether existing files must be overwritten or not. |
name |
A character value indicating the root of the backup's name. |
path |
A character value indicating the path to the folder containing the backup files. |
fext |
A character value indicating the file extension (including the dot symbol). |
choice |
An integer value indicating the backup file to be used for
recovery. This value refers to the row in the output of |
Details
In both functions the argument file may include either the path
relative to the working directory or the absolute path to the file, excluding
stamps and extension.
For overwrite=FALSE (the default), a numeric suffix will be added to
the backup's name, if another backup was produced at the same day.
For overwrite=TRUE no suffix will be included in the file and existing
files will be overwritten.
The function load_last() will load the newest version among backups
stored in the same folder, provided that the backup name includes a time
stamp.
Value
The function backup_object() writes an R-image with extension *.rda
and an invisible vector with the name of the backup, its absolute path and
a time stamp.
The function sort_backups() returns a data frame including the sorted names
of backup files from the oldest to the newest.
Author(s)
Miguel Alvarez kamapu78@gmail.com
See Also
Examples
## A subset with Pseudognaphalium and relatives
Pseudognaphalium <- subset(x = Easplist, subset = grepl("Pseudognaphalium",
TaxonName), slot = "names", keep_parents = TRUE)
## Create a backup with date stamp in tempdir
backup_object(Pseudognaphalium, file = file.path(tempdir(), "Pseudognaphalium"))
## Retrieve paths of backup
info_back <- backup_object(Pseudognaphalium, file = file.path(tempdir(),
"Pseudognaphalium"))
info_back
## Display all backups
sort_backups("Pseudognaphalium", tempdir())
## Delete object
rm(list = "Pseudognaphalium")
## To load the last backup into a session
load_last("Pseudognaphalium", path = tempdir())
## Load pre-installed backup
load_last(file.path(path.package("taxlist"), "extdata", "Podocarpus"))
Delete orphaned records
Description
Manipulation of slots may generate orphaned entries in
taxlist objects.
The function clean deletes such entries and restores the consistency
of the objects.
Usage
clean(object, ...)
## S4 method for signature 'taxlist'
clean(object, times = 2, ...)
Arguments
object |
A taxlist object. |
... |
Further arguments passed from or to other methods. |
times |
An integer indicating how many times the cleaning should be repeated. |
Details
Cleaning of objects will follow the deletion of orphaned names, orphaned taxon trait entries, and orphaned parent entries.
Value
A clean taxlist object.
Author(s)
Miguel Alvarez.
Examples
## Direct manipulation of slot taxonRelations generates an invalid object
Easplist@taxonRelations <- Easplist@taxonRelations[1:5, ]
## Now apply cleaning
Easplist <- clean(Easplist)
summary(Easplist)
One run clean function
Description
One run clean function
Usage
clean_once_taxlist(object)
Cleaning character strings.
Description
Multiple, leading and trailing white spaces as well as wrong encodings may
cause serious problems in information dealing with taxonomic names.
The function clean_strings get rid of them.
Usage
clean_strings(x, ...)
## S4 method for signature 'character'
clean_strings(x, from = "utf8", to = "utf8", ...)
## S4 method for signature 'factor'
clean_strings(x, from = "utf8", to = "utf8", ...)
## S4 method for signature 'data.frame'
clean_strings(x, from = "utf8", to = "utf8", ...)
Arguments
x |
Object to be cleaned. |
... |
Further arguments passed among methods (not yet in use). |
from, to |
Arguments passed to |
Details
This function automatically deletes leading, trailing and multiple white
spaces, either in strings (method character), levels (method
factor or in single columns (method data.frame).
Value
The same as input x.
Author(s)
Miguel Alvarez.
Examples
## Leading, trailing and multiple spaces
clean_strings(" Cyperus papyrus L. ")
Collapse names
Description
Collapse name strings for document contents. It will be used internally when formatting several names and including them in a text body.
Usage
collapse_names(x, collapse)
Arguments
x |
A character vector containing a chain of names. |
collapse |
A character value or vector used to collapse the names and passed to paste0. If its lenght is 2, the second value will be used to connect the two last names. |
Count taxa within a taxlist object.
Description
Counting number of taxa within taxlist objects or character vectors containing taxon names.
Usage
count_taxa(object, data, ...)
## S4 method for signature 'character,missing'
count_taxa(object, na.rm = TRUE, ...)
## S4 method for signature 'factor,missing'
count_taxa(object, na.rm = TRUE, ...)
## S4 method for signature 'taxlist,missing'
count_taxa(object, level, ...)
## S4 method for signature 'formula,taxlist'
count_taxa(object, data, include_na = FALSE, suffix = "_count", ...)
Arguments
object |
An object containing a taxonomic list or a formula. |
data |
An object of class taxlist in the |
... |
further arguments passed among methods. |
na.rm |
Logical value, whether NAs have to be removed from the input vector or not. |
level |
Character value indicating the taxonomic rank of counted taxa. |
include_na |
Logical value indicating whether |
suffix |
Character value used as suffix for the counted rank in the
output data frame (only used in |
Details
This function is written by convenience in order to reduce code for counting
taxa within taxlist objects and it is just a wrapper of length().
Value
An integer with the number of taxa.
Author(s)
Miguel Alvarez kamapu78@gmail.com
Examples
## factor method
count_taxa(iris$Species)
## taxlist method
count_taxa(Easplist)
## count only species
count_taxa(Easplist, level = "species")
## using a formula
count_taxa(~life_form, Easplist, include_na = TRUE)
Convert data frames and strings into taxlist objects
Description
Function converting template data frame into taxlist object. Also character vectors including taxonomic names will be converted but without any information on taxonomic ranks and parental taxa.
Usage
df2taxlist(x, ...)
## S3 method for class 'data.frame'
df2taxlist(x, taxonTraits, taxonViews, levels, clean_strings = TRUE, ...)
## S3 method for class 'character'
df2taxlist(x, ...)
Arguments
x |
A data frame or a character vector with taxonomic names. If x is a data frame, the columns TaxonUsageID (integer with IDs for each name), TaxonConceptID (integer with IDs for the respective taxon concepts), and TaxonName (character) are mandatory. Other optional columns are AuthorName (character with names' authorities), AcceptedName (logical indicating whether the name is an accepted name or a synonym and will be set as TRUE by default), Level (factor sorting taxonomic ranks in the bottom-up direction), Parent (integer, the taxon concept ID of the parental taxon), and ViewID (integer pointing to the ID of taxonomic view, usually a bibliographic reference, and will be used only if 'taxonViews' is provided. Any further column not included in the prototype of taxlist will be considered as names' attributes and inserted in slot taxonNames. |
... |
Further arguments passed among methods. For the
|
taxonTraits |
A data frame with attributes of taxonomic concepts (optional). If provided, the column TaxonConceptID is mandatorial. |
taxonViews |
A data frame or biblio::lib_df with references of taxonomic views (optional). If provided, the column ViewID is mandatorial and have to match the homonymous column at 'x'. |
levels |
A character vector setting the levels or taxonomic ranks from the bottom to the top. This argument is optional and if missing, the column Level will be preserved (if factor) or coerced to factor, except in the case that no column Level is provided. |
clean_strings |
Logical value, whether function |
Value
A taxlist object.
Author(s)
Miguel Alvarez kamapu78@gmail.com.
Examples
Cyperus <- read.csv(file = file.path(path.package("taxlist"), "cyperus",
"names.csv"))
head(Cyperus)
## Convert to 'taxlist' object
Cyperus$AcceptedName <- !Cyperus$SYNONYM
df2taxlist(Cyperus)
## Create a 'taxlist' object from character vectors
Plants <- df2taxlist(c("Triticum aestivum", "Zea mays"), AuthorName = "L.")
summary(Plants, "all")
Dissect Scientific Names into their Elements
Description
Depending the degree of resolution and specific roles of nomenclature, strings containing taxon usage names (scientific names) are constructed with different parts. A string with names can be consequently split into those elements, meanwhile the number of elements may suggest the taxonomic ranks.
This function is a wrapper of strsplit(), while name element can be
re-pasted if indicated in argument repaste.
Usage
dissect_name(x, split = " ", fixed = TRUE, repaste, ...)
Arguments
x |
A character vector containing taxon names. |
split, fixed, ... |
Arguments passed to |
repaste |
An integer vector indicating the elements of the name selected for the output. |
Value
A character matrix with as many rows as names in the input vector.
If repaste is indicated, then the output will be a character vector.
Author(s)
Miguel Alvarez kamapu78@gmail.com
See Also
Examples
# A list of variety names
sp_list <- subset(x = Easplist, subset = Level == "variety", slot = "relations")
sp_list <- accepted_name(sp_list)[c(1:10), "TaxonName"]
# split name
dissect_name(sp_list)
# re-paste the two first words (species name)
dissect_name(sp_list, repaste = c(1:2))
Retrieve children or parents of taxon concepts
Description
Retrieve all children or all parents of a queried taxon concept.
Usage
get_children(taxlist, ...)
## S3 method for class 'taxlist'
get_children(taxlist, ConceptID, ...)
get_parents(taxlist, ...)
## S3 method for class 'taxlist'
get_parents(taxlist, ConceptID, ...)
Arguments
taxlist |
A taxlist object. |
... |
Further arguments passed among methods. |
ConceptID |
Concept IDs for selecting parents or children or a subset of
|
Details
This function produces subsets of taxlist objects
including all children or parents of queried taxon concepts.
Multiple concepts can be queried in these function.
The argument ConceptID can be a vector of concept IDs or a subset of
the input taxlist object.
Value
A taxlist object with a subset including requested concepts with children or parents.
Author(s)
Miguel Alvarez kamapu78@gmail.com
Examples
## Subset with family Ebenaceae and children
Ebenaceae <- subset(x = Easplist, subset = TaxonName == "Ebenaceae")
Ebenaceae
Ebenaceae <- get_children(Easplist, Ebenaceae)
Ebenaceae
## Get parents of Diospyros tricolor
Diostri <- subset(x = Easplist, subset = TaxonConceptID == 52403,
slot = "relations")
Diostri
Diostri <- get_parents(Easplist, Diostri)
Diostri
Generate Identifiers
Description
Creating identifiers for new elements in a database.
The function id_solver() wil compare to set of identifiers and modify the
second to avoid duplicated IDs.
Usage
id_generator(
len,
minvalue = 1,
nchar = 10,
mode = c("numeric", "character"),
...
)
id_solver(insert, to, suffix = c("numeric", "character"), sep = "")
Arguments
len |
Numeric value indicating the length of the retrieved vector with identifiers. |
minvalue |
Numeric value indicating the minimum value in the vector of
identifiers. Used only for |
nchar |
Numeric value indicating the number of characters included in
the retrieved identifiers. Used only for |
mode |
Character value indicating the type of identifier created, which is either numeric (the default) or charcter. |
... |
Further parameters passed to |
insert |
A vector (either numeric or character) containing IDs of elements that will be inserted in a database. |
to |
A vector (either numeric or character) containing IDs of elements thar already exist in target database. |
suffix |
A character vector indicating the mode used for the suffix.
Only 'numeric' or 'character' and partial matchings are accepted here.
This argument is only used for character IDs. If
|
sep |
A character value used as separator between original character ID and the appended suffix. |
Value
A vector with IDs created by id_generator(), either as numeric or
character.
In the case of id_solver(), a vector, which is either identical to
'insert' (if no conflicts) or a vector witht he same properties but with
resolved IDs.
Examples
## Creating numeric IDs
id_generator(len = 10, minvalue = 5)
## Creating character IDs
id_generator(len = 10, mode = "character")
## Solving duplicates in numeric identifiers
id_solver(insert = c(3, 7, 5, 10), to = c(1:5))
## Solving duplicates in bibtexkeys
db_refs <- c("Alvarez2003", "Schmitz1988", "Li2023")
new_refs <- c("Alvarez2003", "Li2023", "Mueller1953", "Alvarez2003a")
any(duplicated(c(db_refs, new_refs)))
solved_refs <- id_solver(insert = new_refs, to = db_refs, suffix = "character")
solved_refs
any(duplicated(c(db_refs, solved_refs)))
Print hierarchical structure in indented lists
Description
Print taxonomic hierarchies (ranks and parent-child relationships) from taxlist objects in an indented list.
Usage
indented_list(object, ...)
## S4 method for signature 'taxlist'
indented_list(
object,
filter,
keep_children = TRUE,
keep_parents = TRUE,
rankless_as,
indent = " ",
lead_br = "",
print = TRUE,
author = TRUE,
level = FALSE,
synonyms = FALSE,
syn_encl = c("= ", ""),
secundum,
alphabetical = FALSE,
...
)
Arguments
object |
A taxlist object containing taxonomic concepts. |
... |
Further arguments (not used yet). |
filter |
A character value (optional) that will be matched with the taxon usage names to produce a subset of 'object'. Note that this filter will be also applied to synonyms, independent of the argument applied in parameter 'synonyms'. |
keep_children |
A logical value indicating whether children of matched concept should be included in the result. |
keep_parents |
A logical value indicating whether parents of matched concept should be included in the result. |
rankless_as |
A character vector indicating a level (taxonomic rank) to which rankless taxa may be set before doing the list. |
indent |
Symbol used for indentation. This symbol will be multiplied by the depth of the taxonomic rank. The default is a blank space. This can be also provided as a named vector, with a different indentation symbol for the respective taxonomic ranks. |
lead_br |
Optional line break symbol leading before the indentation. It may be required for r-markdown documents. |
print |
A logical value indicating whether the indented list should be printed in the console or not (default = TRUE). |
author |
A logical value indicating whether the author should be printed with the name (default = TRUE). |
level |
A logical value indicating whether the name of the level (taxonomic rank) should be included before the name or not (default = FALSE). |
synonyms |
A logical value indicating whether the synonyms should be included after accepted names or not (default = FALSE). |
syn_encl |
A character vector of length 2 including the symbols used to enclose synonyms. First value will be set before the synonyms and second value, after the synonyms. |
secundum |
A character value matching a name in slot 'taxonViews', which will be printed as secundum (taxon view). It is not printed by default. |
alphabetical |
A logical value indicating whether taxa may be sorted by names or by IDs. The default is FALSE, thus taxa are sorted by IDs. Note that argument TRUE may not work properly if the object contains homonymous taxa. |
Value
If 'print = TRUE', the indented list is printed in the console. The result, which is a data frame with the elements used to format the names, can be also assigned to an object.
Author(s)
Miguel Alvarez kamapu78@gmail.com
Examples
## Show taxonomy of papyrus
indented_list(Easplist, "papyrus")
## Include synonyms and taxon views
indented_list(Easplist, "papyrus", level = TRUE, synonyms = TRUE,
secundum = "secundum")
Insert additional rows to a data frame.
Description
Adding new rows from data frame sharing some columns.
Data contained in y is assumed to be additional data and will be
appended.
Columns occurring in only one of the data frames will be added to the output.
Usage
insert_rows(x, y, ...)
## S4 method for signature 'data.frame,data.frame'
insert_rows(x, y, ...)
Arguments
x |
A data frame. |
y |
A data frame including rows (and columns) to be inserted in |
... |
Addicional arguments passed among methods. |
Value
A data frame.
Examples
## Merge data frames including new columns
data(iris)
iris$Species <- paste(iris$Species)
new_iris <- data.frame(Species = rep("humilis", 2), Height = c(15, 20),
stringsAsFactors = FALSE)
insert_rows(iris, new_iris)
Set and retrieves hierarchical levels
Description
Taxonomic hierarchies can be set as levels in taxlist objects, ordered from lower to higher levels.
Add taxonomic levels for specific taxon concepts in a taxlist object. Also changes in concept circumscription may implicate changes in its taxonomic hierarchy.
Usage
levels(x)
## S3 method for class 'taxlist'
levels(x)
levels(x) <- value
## S3 replacement method for class 'taxlist'
levels(x) <- value
Arguments
x |
A taxlist object. |
value |
A character vector with replacement values for levels o |
Details
Taxonomic levels will be handled as factors in the
taxlist objects.
Those levels are useful for creating subsets of related groups (e.g. by
functions get_children() or get_parents()).
Levels in combination to parent-child relationships will be further used for checking consistency of taxonomic lists.
A replacement method of the form levels(x) <- value it is also implemented.
Value
A character vector or a taxlist object with
added or modified taxonomic levels.
Author(s)
Miguel Alvarez kamapu78@gmail.com
See Also
Examples
## Get levels of species list
levels(Easplist)
## Add aggregate as new taxonomic level
levels(Easplist) <- c("form", "variety", "subspecies", "species", "complex",
"aggregate", "genus", "family")
summary(Easplist)
Search matchings between character and taxlist objects
Description
Names provided in a character vector will be compared with names stored in
slot taxonNames within an object of class taxlist by
using the function stringdist::stringsim().
Usage
match_names(x, object, ...)
## S4 method for signature 'character,character'
match_names(
x,
object,
UsageID,
best = 1,
nomatch = TRUE,
method = "lcs",
cutlevel = NULL,
...
)
## S4 method for signature 'character,missing'
match_names(x, best, cutlevel, nomatch = TRUE, ...)
## S4 method for signature 'character,taxlist'
match_names(
x,
object,
show_concepts = FALSE,
accepted_only = FALSE,
include_author = FALSE,
...
)
Arguments
x |
A character vector with names to be compared. |
object |
Either a character vector or a taxlist object containing the taxonomic list for comparison. If missing, the similarity of each name in 'x' will be compared with the rest of the names in the same vector. |
... |
Further arguments passed among methods. |
UsageID |
A vector with IDs for single usage names in the compared list. If the IDs are duplicated or not as much as names in 'object', the function retrieves an error message. If missing, this function will number every name anew (see column 'TaxonUsageID' in the output object). |
best |
Integer value indicating how many matches should be displayed in the output. Matches with the same value of similarity will be considered as one. Note that this argument will be overrode by 'cutlevel'. |
nomatch |
A logical value indicating wheter names without matches should
be included in the output ( |
method |
Further arguments passed to |
cutlevel |
A numeric value indicating a cut level of similarity, considering as match names with similarities equal or bigger than the cut value. This argument overrides 'best'. |
show_concepts |
Logical value indicating whether the respective taxon concepts should be displayed in output or not. |
accepted_only |
Logical value indicating whether only accepted names should be matched or all usage names (including synonyms). |
include_author |
A logical value indicating whether the author name in object (method for taxlist) should be included in the matching list or not. |
Author(s)
Miguel Alvarez kamapu78@gmail.com
See Also
Examples
## Names to be compared
species <- c("Cyperus papyrus", "Typha australis", "Luke Skywalker")
## Comparing character vectors
match_names(c("Cyperus paper", "TIE fighter"), species)
## Retrieve taxon usage names
match_names(species, Easplist)
## Display accepted names in output
match_names(x = species, object = Easplist, show_concepts = TRUE)
# Using cut value for similarity
match_names(x = species, object = Easplist, cutlevel = 0.8)
Names matched with a reference taxonomic list
Description
An S3 class containing results of names compared with a reference list. This class enables further methods applied to these outputs, for instance an interactive selection of multiple choices.
Merge concepts or move names
Description
Merge taxon concepts form a taxlist object into single ones.
Usage
merge_taxa(object, ...)
## S3 method for class 'taxlist'
merge_taxa(
object,
concepts,
level = NULL,
delete_nomatch = FALSE,
print_output = FALSE,
...
)
Arguments
object, taxlist |
Object of class taxlist. |
... |
Further arguments to be passed to or from other methods. |
concepts |
Numeric (integer) vector including taxon concepts to be merged. |
level |
Character vector with queried taxonomic ranks. This setting
works only if |
delete_nomatch |
A logical value indicating whether no matched ranks (i.e. top rank and rankless concepts) should be deleted from the output or not. |
print_output |
Logical value indicating whether the merged concept
should be displayed in the console. Thi works only if a vector is
provided at |
Details
Taxon concepts indicated in argument concepts will be merged into a
single concept.
The new concept inherits the ID and respective attributes from slots
taxonRelations and taxonTraits from the first taxon concept
indicated in argument concepts.
For convenience the resulting concept can be displayed by setting
print_output=TRUE but only when using argument concepts.
An alternative application of this function is implemented through the
argument level, where all lower rank taxa will be merged to the indicated
level or higher (if parent of merged taxa are at a higher rank).
Value
An object of class taxlist.
Author(s)
Miguel Alvarez kamapu78@gmail.com
Examples
## Merge Cyperus papyrus and Cyperus dives
summary(Easplist, c(206, 197))
merged_cyperus <- merge_taxa(object = Easplist, concepts = c(206, 197),
print_output = TRUE)
## Subset with Kyllinga species
ky <- subset(Easplist, TaxonName == "Kyllinga", keep_children = TRUE,
keep_parents = TRUE)
ky
indented_list(ky)
## Merge to species and family
merge_taxa(ky, level = c("species", "family"))
## Merge to variety and genus
merge_taxa(ky, level = c("variety", "genus"))
Merge taxa to their respective parents
Description
Aggregation of taxon concepts to their respective parents. All names of aggregated concepts will become synonyms in the target parent.
Usage
merge_to_parent(object, ...)
## S3 method for class 'taxlist'
merge_to_parent(object, concept_id, ...)
Arguments
object |
An object of class taxlist. |
... |
Further arguments passed among methods. |
concept_id |
A vector of IDs (TaxonConceptID) of taxa that will be aggregated into their respective parents. Note that if one of the IDs is simultaneously the parent of another ID in the vector, this function will retrieve an error message. |
Value
An object of class taxlist with merged taxa.
See Also
Examples
## Subset with Kyllinga species
ky <- subset(Easplist, TaxonName == "Kyllinga", keep_children = TRUE,
keep_parents = TRUE)
ky
indented_list(ky)
## Merge two species with the genus
summary(ky, c(346, 50400))
summary(ky, "Kyllinga", exact = TRUE)
ky <- merge_to_parent(ky, c(346, 50400))
summary(ky, "Kyllinga", exact = TRUE)
Function producing the overview of whole object.
Description
Function producing the overview of whole object.
Usage
overview_taxlist(object, units, check_validity)
Function producing the overview of single taxon concepts.
Description
Function producing the overview of single taxon concepts.
Usage
overview_taxon(object, ConceptID, display, maxsum, secundum = NULL)
Retrieve parents for specific concepts
Description
Retrieve IDs of parents for selected taxa in a taxonomic list.
Usage
parents(taxlist, level, ...)
## S4 method for signature 'taxlist,character'
parents(taxlist, level, concept, ...)
Arguments
taxlist |
An object of class taxlist containing a taxonomic list. |
level |
A character value indicating the level at which the parents will be extracted (upwards in the taxonomic ranks). |
... |
Further arguments passed among methods. |
concept |
A vector containing concept IDs. The taxa for which the parents will be retrieved. If not provided, parents for every single taxon concept in 'taxlist' will be retrieved. |
Examples
# Random selection of 5 taxa
IDs <- sample(Easplist@taxonRelations$TaxonConceptID, 5)
# Print names and names of parents
print_name(Easplist, IDs)
print_name(Easplist, parents(Easplist, "genus", IDs))
print_name(Easplist, parents(Easplist, "family", IDs))
Format usage names for publications
Description
When writing on bio-diversity, usage names could be automatically inserted in
documents including the typical italic format for different elements of a
scientific name.
The function print_name can be applied either in markdown documents or
for graphics.
In Rmarkdown documents use *Cyperus papyrus* L. for
inserting a formatted a species name.
Usage
print_name(object, ...)
## S3 method for class 'character'
print_name(
object,
second_mention = FALSE,
style = "markdown",
isolate = c("var.", "ssp.", "subsp.", "f.", "fma."),
trim = c("spp.", "sp.", "species"),
italics = TRUE,
collapse,
...
)
## S3 method for class 'taxlist'
print_name(
object,
id,
concept = TRUE,
include_author = TRUE,
secundum,
style = "markdown",
italics = TRUE,
collapse,
...
)
Arguments
object |
An object of class taxlist. |
... |
Further arguments passed among methods. |
second_mention |
Logical value, whether the genus name should be abbreviated or not. |
style |
Character value indicating the alternative format for italics.
The available options are |
isolate |
A character vector with words (usually abbreviations) appearing in the middle of scientific names, which are not formatted in italics. |
trim |
A character vectors with words appearing at the end of scientific names that are not formatted in italics, either. |
italics |
A logical value indicating whether the names should be italized or not. |
collapse |
A character value or vector used to collapse the names and
passed to |
id |
Integer containing either a concept or a name ID. |
concept |
Logical value, whether |
include_author |
Logical value, whether authors of the name should be mentioned or not. |
secundum |
Character value indicating the column in slot |
Value
A character value including format to italic font.
Author(s)
Miguel Alvarez kamapu78@gmail.com
See Also
Examples
## Example subspecies
summary(Easplist, 363, secundum = "secundum")
## Empty plot
plot(x = NA, xlim = c(0, 5), ylim = c(7, 1), bty = "n", xaxt = "n", xlab = "",
ylab = "options")
## Accepted name with author
text(x = 0, y = 1, labels = print_name(Easplist, 363, style = "expression"),
pos = 4)
## Including taxon view
text(x = 0, y = 2, labels = print_name(Easplist, 363, style = "expression",
secundum = "secundum"), pos = 4, cex = 0.7)
## Second mention in text
text(x = 0, y = 3, labels = print_name(Easplist, 363, style = "expression",
second_mention = TRUE), pos = 4)
## Using synonym
text(x = 0, y = 4, labels = print_name(Easplist, 50037, style = "expression",
concept = FALSE), pos = 4)
## Markdown style
text(0, 5, labels = print_name(Easplist, 363, style = "markdown"), pos = 4)
## HTML style
text(0, 6, labels = print_name(Easplist, 363, style = "html"), pos = 4,
cex = 0.7)
## LaTeX style for knitr
text(x = 0, y = 7, labels = print_name(Easplist, 363, style = "knitr"), pos = 4,
cex = 0.7)
Prune not used taxonomic ranks
Description
Taxonomic ranks without taxon concepts will be pruned in taxlist objects.
Usage
prune_levels(object, ...)
## S3 method for class 'taxlist'
prune_levels(object, ...)
Arguments
object |
An object of class taxlist. |
... |
Further arguments passed among methods (not yet in use). |
Value
An object of class taxlist with pruned taxonomic ranks.
See Also
Examples
## Subset species belonging to Cyperus
Cyperus <- subset(Easplist, TaxonName == "Cyperus", slot = "taxonNames",
keep_children = TRUE, keep_parents = TRUE)
Cyperus
## Prune not used ranks
prune_levels(Cyperus)
Data manipulation.
Description
This is a series of functions designed for a fast coding of replacements both, as internal functions and in workflows dealing with information stored in vectors. Such functions are especially useful when handling with functional traits stored in taxlist objects.
replace_x() is used to exchange values in vectors.
replace_idx() changes values in vectors by matching indices or conditions.
The function replace_na() works in the same way as replace_idx() but will
only insert values in empty elements (NAs).
Usage
replace_x(x, old, new)
replace_idx(x, idx1 = x, idx2 = idx1, new)
replace_na(x, idx1, idx2 = idx1, new)
Arguments
x |
A vector to be modified. In the case of |
old |
A vector with values to be replaced by |
new |
A vector containing values to be inserted, either comparing values or using indices. |
idx1, idx2 |
Indices applied for value replacements to match |
Value
A vector or data frame with the modified values.
Author(s)
Miguel Alvarez.
Examples
## Replace values in vector
replace_x(x = letters, old = c("b", "p", "f"), new = c("bee", "pork", "fungus"))
## Replace values using indices
replace_idx(x = letters, idx1 = 1:length(letters), idx2 = c(2, 7, 17),
new = c("second", "seventh", "seventeenth"))
## Replace values if they are NAs
letters[2] <- NA
replace_na(x = letters, idx1 = 1:length(letters), idx2 = c(1:3),
new = c("alpha", "beta", "zeta"))
## The same applications but this time for functional traits
summary(as.factor(Easplist$life_form))
# Merge annuals
Easplist@taxonTraits$lifeform <- replace_x(x = Easplist@taxonTraits$life_form,
old = c("obligate_annual", "facultative_annual"), new = c("annual", "annual"))
summary(as.factor(Easplist$lifeform))
# The same effect
Easplist@taxonTraits$lifeform <- replace_idx(x = Easplist@taxonTraits$life_form,
idx1 = grepl("annual", Easplist@taxonTraits$life_form), idx2 = TRUE,
new = "annual")
summary(as.factor(Easplist$lifeform))
Subset method for taxlist objects
Description
Subset of taxlist objects will be done applying either
logical operations or pattern matchings.
Subsets can be referred to information contained either in the slot
taxonNames, taxonRelations or taxonTraits.
Usage
## S4 method for signature 'taxlist'
subset(
x,
subset,
slot = "names",
keep_children = FALSE,
keep_parents = FALSE,
...
)
Arguments
x |
Object of class taxlist. |
subset |
Logical vector or logical operation to apply as subset. |
slot |
Character value indicating the slot to be used for the subset. |
keep_children |
Logical value applied to hierarchical structures. |
keep_parents |
Logical value applied to hierarchical structures. |
... |
Further arguments to be passed to or from other methods. |
Details
The argument subset will be applied to the slot specified in argument
slot.
This argument also allows partial matchings.
Arguments keep_children and keep_parents are applied to objects
including parent-child relationships.
When those arguments are set as FALSE (the default), children or parents
of selected taxon concepts will not be included in the subset.
Be aware that subset() won't work properly inside of function definitions.
Value
An object of class taxlist.
Author(s)
Miguel Alvarez kamapu78@gmail.com
Examples
## Produce a data set with only reed plants
sp_list <- subset(x = Easplist, subset = life_form == "reed_plant",
slot = "taxonTraits", keep_parents = TRUE)
sp_list
summary(as.factor(sp_list$life_form))
Print overviews for taxlist Objects and their content
Description
A method to display either an overview of the content of taxlist objects or an overview of selected taxa.
Usage
## S4 method for signature 'taxlist'
summary(
object,
ConceptID,
units = "Kb",
check_validity = TRUE,
display = "both",
maxsum = 5,
secundum = NULL,
exact = FALSE,
...
)
## S4 method for signature 'taxlist'
show(object)
## S4 method for signature 'taxlist'
print(x, ...)
Arguments
object, x |
A taxlist object. |
ConceptID |
IDs of concepts to be displayed in the summary. |
units |
Character value indicating the units shown in the object's allocated space. |
check_validity |
Logical value indicating whether the validity of
|
display |
Character value indicating the field to be displayed (see details). |
maxsum |
Integer indicating the maximum number of displayed taxa. |
secundum |
A character value indicating the column from slot |
exact |
A logical value indicating whether taxon names should match the exact argument in parameter 'ConceptID'. It works only if 'ConceptID' is provided as character value and is not the keyword 'all'. |
... |
Further arguments passed to or from another methods. |
Details
A general overview indicating number of names, concepts and taxon views
included in taxlist objects.
If argument ConceptID is a vector with concept IDs or names to be matched
by grepl(), then a display of all names included in each concept will be
produced.
Alternative you can use taxon="all" in order to get the listing of names
for all concepts included in the object (truncated to the input number of
maxsum).
For summaries applied to concepts, there are three alternative displays of
names using the argument display.
Use display="name" to show the value TaxonName, display="author" to
show the value AuthorName or display="both" to show both values.
Such values are taken from slot taxonNames.
For big objects it will be recommended to set units="Mb" (see also
object.size() for further alternatives).
Author(s)
Miguel Alvarez kamapu78@gmail.com
See Also
Examples
## summary of the object
summary(Easplist, units = "Mb")
## the same output
summary(Easplist)
show(Easplist)
print(Easplist)
Easplist
## summary for two taxa
summary(Easplist, c(51128, 51140))
## summary by matching a name
summary(Easplist, "Acmella")
## summary for the first 10 taxa
summary(object = Easplist, ConceptID = "all", maxsum = 10)
Set taxonomic information as taxon traits
Description
Taxonomic classification can be included in taxlist
objects within the information provided at slot taxonRelations.
Nevertheless, for statistical analyses it may be more convenient to insert
such information in the slot taxonTraits.
Usage
tax2traits(object, ...)
## S3 method for class 'taxlist'
tax2traits(object, get_names = FALSE, ...)
Arguments
object |
An object of class taxlist. |
... |
Further arguments to be passed among methods. |
get_names |
Logical value indicating whether taxon names should be retrieved instead of taxon IDs. |
Details
This function can only be applied to objects containing parent-child relationships and information on taxonomic levels.
Value
An object of class taxlist with taxonomy added as traits.
Author(s)
Miguel Alvarez kamapu78@gmail.com.
Examples
## Family Acanthaceae with children
Acanthaceae <- subset(x = Easplist, subset = TaxonName == "Acanthaceae",
slot = "names", keep_children = TRUE)
summary(Acanthaceae)
## Insert taxonomy to taxon traits
Acanthaceae <- tax2traits(Acanthaceae, get_names = TRUE)
head(taxon_traits(Acanthaceae))
An S4 class to represent taxonomic lists.
Description
Class for taxonomic lists including synonyms, hierarchical ranks, parent-child relationships, taxon views and taxon traits.
Note that each taxon becomes an identifier, represented by the column
TaxonConceptID in the slot taxonRelations, analogous to a primary key
in a relational database.
This identifier is restricted to an integer in taxlist and is specific for
the object.
In the same way, each taxon usage name has an identifier in the column TaxonUsageID, slot taxonNames. The column ViewID in slot taxonViews is the identifier of the taxon view.
Slots
taxonNames(
data.frame) Table of taxon usage names (accepted names and synonyms).taxonRelations(
data.frame) Relations between concepts, accepted names, basionyms, parents and hierarchical level.taxonTraitsTable of taxon traits.
taxonViewsReferences used to determine the respective concept circumscription.
Author(s)
Miguel Alvarez
References
Alvarez M, Luebert F (2018). The taxlist package: managing plant taxonomic lists in R. Biodiversity Data Journal 6: e23635. doi:10.3897/bdj.6.e23635
Examples
## Class 'taxlist'
showClass("taxlist")
## Create an empty object
sp_list <- new("taxlist")
sp_list
Coerce taxlist objects to data frames
Description
Transform taxlist objects into data frames.
Usage
taxlist2df(x, ...)
## S3 method for class 'taxlist'
taxlist2df(
x,
include_traits = FALSE,
include_views = FALSE,
standard = c("taxlist", "dwc"),
...
)
Arguments
x |
A taxlist object to be coerced. |
... |
Further arguments passed among methods. |
include_traits |
A logical value indicating whether taxon concept attributes have to be included in the output or not. |
include_views |
A logical value indicating whether taxon views have to be included in the output or not. |
standard |
A character value indicating the standard used to name
columns in the output data frame. Per default |
Handle information on taxon usage names.
Description
The slot taxonNames in taxlist objects contains
taxon usage names for the respective taxon.
These functions assist on the access and modification of entries for names.
Usage
taxon_names(taxlist, ...)
## S3 method for class 'taxlist'
taxon_names(taxlist, ...)
taxon_names(taxlist, ...) <- value
## S3 replacement method for class 'taxlist'
taxon_names(taxlist, ...) <- value
add_synonym(taxlist, ...)
## S3 method for class 'taxlist'
add_synonym(taxlist, ConceptID, TaxonName, AuthorName, ...)
update_name(taxlist, ...)
## S3 method for class 'taxlist'
update_name(taxlist, UsageID, ...)
delete_name(taxlist, ...)
## S3 method for class 'taxlist'
delete_name(taxlist, UsageID, ...)
Arguments
taxlist |
A taxlist object to be modified. |
... |
Further arguments passed among methods. In |
value |
A data frame used as new slot |
ConceptID |
Numeric vector indicating the concept ID to which the synonyms will be added. |
TaxonName, AuthorName |
Character values used for the new names (synonyms). |
UsageID |
Numeric vector indicating the taxon usage IDs to be updated. |
Details
The replacement method taxon_names<- is a quick alternative to include
names in empty taxlist objects.
The function add_synonym() works only for adding names to existing
taxon concepts.
For adding new taxon concepts as well you should use add_concept().
Value
A data frame or, in the case of the replacement method, a
taxlist object with modified slot taxonNames.
Author(s)
Miguel Alvarez kamapu78@gmail.com
See Also
Examples
## Display of slot 'taxonNames'
Euclea <- subset(x = Easplist, subset = charmatch("Euclea", TaxonName),
slot = "names", keep_children = TRUE)
Euclea
taxon_names(Euclea)
## Insert a synonym to Diospyros scabra
summary(Easplist, "Diospyros scabra")
sp_list <- add_synonym(taxlist = Easplist, ConceptID = 51793,
TaxonName = "Maba scabra", AuthorName = "Chiov.")
summary(sp_list, "Diospyros scabra")
## Delete a synonym of Launaea cornuta
summary(sp_list, "Launaea cornuta")
sp_list <- delete_name(sp_list, 53821)
summary(sp_list, "Launaea cornuta")
## Hypothetical correction in author name in Launaea cornuta
sp_list <- update_name(taxlist = sp_list, UsageID = 355, AuthorName = "L.")
summary(sp_list, "Launaea cornuta")
Retrieve or replace slot taxonRelations in taxlist objects
Description
Retrieve the content of slot taxonRelations from a
taxlist object or replace it by a new data frame.
Usage
taxon_relations(taxlist, ...)
## S3 method for class 'taxlist'
taxon_relations(taxlist, ...)
taxon_relations(taxlist, ...) <- value
## S3 replacement method for class 'taxlist'
taxon_relations(taxlist, ...) <- value
## S4 method for signature 'taxlist,numeric'
update_concept(taxlist, ConceptID, ...)
Arguments
taxlist |
A taxlist object. |
... |
Further arguments passed among methods. |
value |
A |
ConceptID |
Concept IDs to be updated. |
Details
The replacement method taxon_relations<- should be only used when
constructing taxlist objects from an empty one
(prototype).
New concepts should be first added to a taxlist object
using their respective accepted names.
Synonyms can be further provided using the function add_synonym().
Additional named vectors can be provided to be included in slot taxonNames,
in the cases where those variables already exist, otherwise they will be
ignored.
It is recommended also to provide a concept view as ViewID (see
taxon_views()).
For adding a new view, use add_view().
Value
An object of class taxlist with added names and concepts.
Author(s)
Miguel Alvarez kamapu78@gmail.com
See Also
Examples
## Subset for the genus Euclea and display of slot 'taxonNames'
Euclea <- subset(x = Easplist, subset = charmatch("Euclea", TaxonName),
slot = "names", keep_children = TRUE)
Euclea
taxon_relations(Euclea)
Manipulation of taxon traits in taxlist objects.
Description
The slot taxonTraits in taxlist objects contains
attributes of taxon concepts (e.g. functional traits).
These functions are suitable for replacing, retrieving and appending trait
information in taxonomic lists.
Usage
taxon_traits(taxlist, ...)
## S3 method for class 'taxlist'
taxon_traits(taxlist, ...)
taxon_traits(taxlist, ...) <- value
## S3 replacement method for class 'taxlist'
taxon_traits(taxlist, ...) <- value
update_trait(taxlist, ...)
## S3 method for class 'taxlist'
update_trait(taxlist, taxonTraits, ...)
Arguments
taxlist |
A taxlist object. |
... |
Further arguments to be passed among methods. |
value |
Data frame to be set as slot |
taxonTraits |
a data frame with taxon traits to be inserted in
|
Details
Taxon traits are contained in a data frame at the slot taxonTraits in
taxlist objects.
To optimise space, this data frame contain only entries for those concepts
with information, while taxa with no information are skipped from this table.
Thus appending new variables may also have to include new rows in this slot,
which is automatically carried out by this function.
The replacement method taxon_traits<- should be only used when
constructing taxlist objects from an empty one.
Author(s)
Miguel Alvarez kamapu78@gmail.com
See Also
Examples
## Displaying taxon traits
head(taxon_traits(Easplist))
## Updating traits for Launaea cornuta
summary(Easplist, "Launaea cornuta")
accepted_name(taxlist = Easplist, ConceptID = 355, show_traits = TRUE)
sp_list <- update_trait(taxlist = Easplist, taxonTraits = data.frame(
TaxonConceptID = 355,
life_form = "annual"))
accepted_name(taxlist = sp_list, ConceptID = 355, show_traits = TRUE)
Management of concept views in taxonomic lists.
Description
Retrieve or replace slot taxonViews in an object of class taxlist
Usage
taxon_views(taxlist, ...)
## S3 method for class 'taxlist'
taxon_views(taxlist, ...)
taxon_views(taxlist, ...) <- value
## S3 replacement method for class 'taxlist'
taxon_views(taxlist, ...) <- value
add_view(taxlist, taxonViews, ...)
## S4 method for signature 'taxlist,data.frame'
add_view(taxlist, taxonViews, ...)
Arguments
taxlist |
A taxlist object. |
... |
Further arguments to be passed among methods. |
value |
An object of class data.frame containing the references
used to define the circumscription of taxon concepts included in
|
taxonViews |
A data frame with taxon views to be inserted in
|
Details
Taxon views indicate in taxlist objects the references
determining the circumscription of the respective taxon concepts.
When adding a new concept (see add_concept()), the respective
reference may not yet occur in the input taxlist object.
The term taxon view was introduced by Zhong et al. (1996) and corresponds to the reference used for the definition of a concept.
This function retrieves the slot taxonViews from objects of the class
taxlist.
The replacement method taxon_views<- replaces the whole content of slot
taxonViews and it is only recommended to use when constructing a new
taxlist object from an empty prototype.
Value
An object of class taxlist with added views.
Author(s)
Miguel Alvarez kamapu78@gmail.com
References
Zhong Y, Jung S, Pramanik S, Beaman JH (1996). Data model and comparison and query methods for interacting classifications in a taxonomic database. Taxon 45: 223–241. doi:10.1093/bioinformatics/15.2.149
See Also
Examples
## See existing views
taxon_views(Easplist)
## Add a new view
sp_list <- add_view(taxlist = Easplist, taxonViews = data.frame(
secundum = "Beentje et al. (1952)",
Title = "Flora of Tropical East Africa",
URL = "http://www.kew.org/science/directory/projects/FloraTropEAfrica.html"))
taxon_views(sp_list)
Import species lists from Turboveg databases
Description
Importing species lists from Turboveg 2 databases into a taxlist object.
Internally the funcions foreign::read.dbf() and df2taxlist() are called.
Usage
tv2taxlist(taxlist, tv_home = tv.home(), ...)
Arguments
taxlist |
Character value indicating the name of a species list in Turboveg. |
tv_home |
Character value indicating the path to the main Turboveg
folder. By default the function |
... |
Further arguments passed to |
Value
A taxlist object.
Author(s)
Miguel Alvarez kamapu78@gmail.com
See Also
Examples
## Cyperus data set installed as Turboveg species list
Cyperus <- tv2taxlist(taxlist = "cyperus",
tv_home = file.path(path.package("taxlist"), "tv_data"))
Cyperus
Inserting new rows and columns by merging two data frames
Description
Two data frames sharing partially columns will be merged including the sum of all variables.
Usage
two2one_df(x, y)
Arguments
x, y |
( |