NEWS
taxlist 0.4.0
New Features
- New function
reindex() to reassign identifiers to taxon concepts, taxon
names and taxon views.
- New function
sort_taxa() for sorting taxonomic lists before producing
prints.
Improvements
- Summary provided by
summary() (and print()) produces an indented list
for the hierarchical levels (taxonomic ranks). This list is now inverted
(top to bottom).
The hierarchical display of concepts also lists number of concepts per rank.
- Arrangement of parental chains now is done by an internal fucntion, namely
taxlist:::arrange_taxa().
- Function
indented_list() will follow the order of taxonomic concepts in
slot taxonRelations when alphabetical = FALSE. This function was
formely sorting according to taxonConceptID in the same situation.
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).