NEWS
taxlist 0.4.0
New Features
- New function
reindex() to reassign identifiers to taxon concepts, taxon
names and taxon views.
taxlist 0.3.0 (2024-07-03)
New Features
- New function
prune_levels() pruning levels that are not used in taxlist
objects.
- New function
merge_to_parent() merging multiple taxa to their respective
parents.
- New function
sort_backups() retrieving a sorted list of backups written by
backup_object().
- New function
taxlist2df() for converting taxlist objects into data
frames.
- New function
parents() retrieving parent taxa at a determined rank for
selected taxon concepts.
Improvements
- Function
merge_taxa() can now be used to query a list of taxonomic ranks.
This is enabled through the argument level.
- A new argument delelte_nomatch in function
merge_taxa() to delete
top ranks and rankless taxa.
- Function
backup_object() retrieves an invisible vector with information
about the written backup.
- Function
load_last() retrieves an invisible data frame with information
about the imported backup. It also include a new argument choice to select
a different backup from the list produced by sort_backups().
- Function
insert_rows() was redefined as a generic function.
- New arguments in function
print_name():
- italics: a logical value that allows to unset italic format of names.
This can be usefull for taxonomic ranks that are not written in italics
(e.g. Family names in plant and animals).
- collapse: a character value (or vector of lengh 2), used to collapse
strings of names, for instance to mention more than one taxa in the text.
taxlist 0.2.4 (2023-03-12)
New Features
- New S3 class
matched_names inheriting data frame properties. This class
will be used for an interactive selection of multiple choices, when a name
matches more than one candidate.
- Character identifiers (primary keys) are enabled.
- New functions
id_generator() to create vectors of identifiers, either as
numeric values (integers) or as character values by using random strings.
- New function
id_solver() to compare vectors of identifiers between a
recipient database and a data set to be inserted into the mentioned database.
This function will propose a modified vector for the new data to avoid
conflicts by duplicated IDs.
- Coercion of
taxlist objects to data.frame objects.
Improvements
- The validation for
taxlist objects is also looking if Parent IDs are
missing in the object.
- Function
match_names() displays multiple matchings per name and also works
comparing a string with itself.
- Simplified coercion in form of
to_class <- as(obj, from_class).
- Function
tnrs() deprecated.
- Simplified coercion in form of
to_class <- as(obj, from_class)
- Function
add_concept() with a method for data.frame objects.
taxlist 0.2.3 (2022-09-12)
New Features
- New arguments
isolate and trim to prevent parts of scientific names to
be formatted in italics.
Improvements
- Function
match_names() allows to sort output data frame in the
'character,taxlist-method'.
- Slot taxonViews allowing class
lib_df from package biblio.
- In function
summary(), when using text as query, a new parameter exact
allow for querying the exact name, which is usefull when querying genera.
- New style of scripts using the package
styler.
- Name of taxon attribute lf_behn_2018 changed to life_form.
- Function
print_name() is now working with more than one name (vectorized)
and reset to an S3 method, including an option for character vectors.
- Function
df2taxlist() redefined to allow import from a single data frame.
taxlist 0.2.2 (2021-07-15)
Bug Fixes
- Functions
taxlist2taxmap() and taxmap2taxlist() temporarily
deprecated due to conflicts with release of taxa v. 0.4.0
taxlist 0.2.1 (2021-03-29)
New Features
- New function
indented_list() to print taxonomic ranks in indented lists.
Improvements
- New argument
repaste in function dissect_name() for re-pasting
dissected names.
- Function
replace_idx() setting by default idx1 = x.
- Functions
replace_idx() and replace_na() setting by default
idx2 = idx1.
- Special characters corrected in data set Cyperus.
- Validation allowing taxa without rank but parents.
taxlist 0.2.0 (2020-10-07)
Improvements
- Several improvements to meet ROpenSci requirements documented here.
taxlist 0.1.9 (2020-05-31)
Bug Fixes
- Problems with encoding of data set
Easplist
taxlist 0.1.8 (2020-04-29)
New Features
- Function
taxlist2taxmap() for the interaction between packages taxlist and taxmap.
- Function
taxmap2taxlist() for the conversion of Taxmap objects into taxlist ones.
Improvements
- Roxygenized version.
- Method
formula for function count_taxa().
- New argument
fext in function backup_object() setting the extension of the backup file.
taxlist 0.1.7 (2020-01-10)
New Features
- Method for character values in function
match_names().
- Set of functions for data manipulation, namely
replace_x(), replace_idx(), replace_na(), and insert_rows().
- Function
clean() with new argument times for repeat cleaning of taxlist objects.
Improvements
- Warning in function
tax2traits() for objects without taxonomic ranks.
- Second argument in function
[ applies only to slot taxonTraits.
- Replacement method for functions
[ and $ deprecated.
- Method for function
$ matches all taxon concepts when retrieving information from slot taxonTraits.
- Missing argument idx2 will be set as idx1 in functions
replace_idx() and replace_na().
- Function
replace_view() deprecated.
- Example data set cleaned (specifically author names)
Bug Fixes
- Function
match_names() was not properly working for the option accepted_only=TRUE.
- Function
merge_taxa() caused orphaned children of replaced taxon concepts.
- Function
clean() not working for deleted names.
taxlist 0.1.6 (2019-01-21)
New Features
- New function
count_taxa()
Improvements
- A new option
style="knitr" for function print_name() (See this issue at Stack Overflow).
- In function
backup_object(), the message will be done after successful saving and not before.
- New argument
accepted_only in function match_names(), for comparing strings only with accepted names.
- Error message for NA's in argument
x at function match_names()
Bugs Fixes
- Function
add_synonym() was not properly working for incomplete entries (missing variables in the replacement values.)
- Function
load_last() was not properly working for values of file without mention of subfolder.
- Function
accepted_name() with option show_traits=TRUE was not displaying taxa with no entries for taxon traits.
- Prototype for object
taxlist wrongly included a slot hierarchy.
taxlist 0.1.5 (2018-06-29)
New Features
- A CITATION file is included in the installation.
- New method
replace_view.
- New method
print_name for formatting taxon names to italic style.
- New method
update_name, for updating information in slot taxonNames.
- New method
synonyms retrieving synonyms for indicated concepts.
- New method
delete_name for deleting synonyms in taxlist objects.
- New method
basionym for handling basionyms.
Improvements
- Function
accepted_name retrieves also information on Level (taxonomic rank) and traits (optional in argument show_traits).
- Function
summary for single taxon is displaying the name of the parent taxon (accepted name) and optional a string for the taxon view.
- Function
backup_object prints a message in the console.
- Related functions will join documentation files.
- Data set
Easplist adapted to new state of database SWEA-Dataveg.
- Function
match_names counts multiple best matchings and includes a new argument show_concepts for displaying the respective accepted names and taxon concept ID.
Bugs Fixes
- Function
load_last was not working for single files with suffix, neither for absolute path or paths with underscores.
- Function
summary for single taxa was not displaying names that are homonyms to the accepted name.
- Re-organized documentation.
taxlist 0.1.4 (2018-05-03)
New Features
- New function
load_last to load last backup in an R-session.
- File inst/ChangeLog replaced by NEWS.md.
- New function
dissect_name for splitting names into their parts.
- New function
match_names matching character vectors with names of a taxlist object.
Improvements
- Function
backup_object is also working with relative paths.
Bugs Fixes
- Function
add_view was not adding new columns in the respective slot.
- Function
tv2taxlist does not modify slot taxonViews in prototype.
- Function
load_last was not working with values of filename having underscores.
taxlist 0.1.3 (2018-01-05)
New Features
- New function:
add_trait.
- New function:
tax2traits.
Improvements
- Argument
level inserted in function merge_taxa.
- Function
clean also set keys to class integer.
- Validation checks for the existence of accepted names in names list.
Bugs Fixes
- Bug in
add_concept: wrong assignment of AcceptedName.
taxlist 0.1.2 (2017-08-06)
New Features
Improvements
- Argument
ConceptID in summary (taxlis-method) can be a character vector matching TaxonName.
taxlist 0.1.1 (2017-07-23)
New Features
- New vignette
taxlist-intro.
Improvements
- Package
vegdata moved from Depends to Imports.
- Function
df2taxlist adapted to species lists with duplicated names.
- Arguments
keep_parents and keep_children implemented in function subset.
taxlist 0.1.0 (2017-06-14)
New Features
- Released to CRAN (https://cran.r-project.org/package=taxlist).