- New function
prune_levels()
pruning levels that are not used intaxlist
objects. - New function
merge_to_parent()
merging multiple taxa to their respective parents. - New function
sort_backups()
retrieving a sorted list of backups written bybackup_object()
. - New function
taxlist2df()
for convertingtaxlist
objects into data frames. - New function
parents()
retrieving parent taxa at a determined rank for selected taxon concepts.
- 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 argumentchoice
to select a different backup from the list produced bysort_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.
- 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 todata.frame
objects.
- 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 fordata.frame
objects.
- New arguments
isolate
andtrim
to prevent parts of scientific names to be formatted in italics.
- Function
match_names()
allows to sort output data frame in the'character,taxlist-method'
. - Slot taxonViews allowing class
lib_df
from packagebiblio
. - In function
summary()
, when using text as query, a new parameterexact
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.
- Functions
taxlist2taxmap()
andtaxmap2taxlist()
temporarily deprecated due to conflicts with release of taxa v. 0.4.0
- New function
indented_list()
to print taxonomic ranks in indented lists.
- New argument
repaste
in functiondissect_name()
for re-pasting dissected names. - Function
replace_idx()
setting by defaultidx1 = x
. - Functions
replace_idx()
andreplace_na()
setting by defaultidx2 = idx1
. - Special characters corrected in data set Cyperus.
- Validation allowing taxa without rank but parents.
- Several improvements to meet ROpenSci requirements documented here.
- Problems with encoding of data set
Easplist
- Function
taxlist2taxmap()
for the interaction between packagestaxlist
andtaxmap
. - Function
taxmap2taxlist()
for the conversion ofTaxmap
objects intotaxlist
ones.
- Roxygenized version.
- Method
formula
for functioncount_taxa()
. - New argument
fext
in functionbackup_object()
setting the extension of the backup file.
- Method for character values in function
match_names()
. - Set of functions for data manipulation, namely
replace_x()
,replace_idx()
,replace_na()
, andinsert_rows()
. - Function
clean()
with new argument times for repeat cleaning oftaxlist
objects.
- 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()
andreplace_na()
. - Function
replace_view()
deprecated. - Example data set cleaned (specifically author names)
- Function
match_names()
was not properly working for the optionaccepted_only=TRUE
. - Function
merge_taxa()
caused orphaned children of replaced taxon concepts. - Function
clean()
not working for deleted names.
- New function
count_taxa()
- A new option
style="knitr"
for functionprint_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 functionmatch_names()
, for comparing strings only with accepted names. - Error message for NA's in argument
x
at functionmatch_names()
- 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 offile
without mention of subfolder. - Function
accepted_name()
with optionshow_traits=TRUE
was not displaying taxa with no entries for taxon traits. - Prototype for object
taxlist
wrongly included a slot hierarchy.
- 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 slottaxonNames
. - New method
synonyms
retrieving synonyms for indicated concepts. - New method
delete_name
for deleting synonyms intaxlist
objects. - New method
basionym
for handling basionyms.
- Function
accepted_name
retrieves also information onLevel
(taxonomic rank) and traits (optional in argumentshow_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 argumentshow_concepts
for displaying the respective accepted names and taxon concept ID.
- 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.
- 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 ataxlist
object.
- Function
backup_object
is also working with relative paths.
- Function
add_view
was not adding new columns in the respective slot. - Function
tv2taxlist
does not modify slottaxonViews
in prototype. - Function
load_last
was not working with values offilename
having underscores.
- New function:
add_trait
. - New function:
tax2traits
.
- Argument
level
inserted in functionmerge_taxa
. - Function
clean
also set keys to classinteger
. - Validation checks for the existence of accepted names in names list.
- Bug in
add_concept
: wrong assignment ofAcceptedName
.
- new function
merge_taxa
.
- Argument
ConceptID
insummary
(taxlis-method
) can be a character vector matchingTaxonName
.
- New vignette
taxlist-intro
.
- Package
vegdata
moved from Depends to Imports. - Function
df2taxlist
adapted to species lists with duplicated names. - Arguments
keep_parents
andkeep_children
implemented in functionsubset
.
- Released to CRAN (https://cran.r-project.org/package=taxlist).