NEWS.md

In kamapu/vegtables: Handling Vegetation Data Sets

vegtable 0.1.9

New Features

• New data set veg_layers with information about vegetation layers.
• New function new_layer() to add layer information tables in vegtable objects.

Improvements

• Function count_taxa() also inserts results into slot relations.
• New arguments 'level' and 'include_lower' in function crosstable() They enable selection and/or merging of taxon ranks in cross tables.
• Function cross2db() implemented in two methods, a data.frame-method and a matrix-method.
• New parameter keep_synonyms in function used_concepts(), which can be used to skp synonyms in the output object.

Bug fixes

• Fuction crosstable() was not applying properly the argument use_nas.

vegtable 0.1.8

New Features

• New function veg_diversity() and functions calculating diversity indices: shannon(), evenness(), dominance(), simpson(), and richness().
• New function new_relation() inserting new relations into vegtable objects. This function is internally called by veg_relation().
• New function df2coverconvert() coercing data frames and lists into coverconvert objects.

Improvements

• Slot relations may deal with any element that can be coerced to data.frame.
• All elements in slot syntax have to be of class taxlist
• Parameter in_header defined in several functions is set as in_header = TRUE.
• Former method for 'aggregate()' is now defined in function 'veg_aggregate()'.
• Deprecated functions: match_names(), merge_taxa(). These functions are now exclusive for objects of class taxlist.
• Method names() for vegtable objects will retrieve a list with all names from the respective slots.
• New coercion methods including functions as() and as<-.
• Functions trait_proportion() and trait_stats() are also adding results to the slot relations.

Bug Fixes

• An issue was solved for function taxa2samples() when setting an argument in the parameter 'merge_to', which was not properly working in all cases.

vegtable 0.1.7

New Features

• New function used_concepts() to extract taxon concepts that are occurring in the plot observations.
• New function cover_trans() in replacement of transform()
• New slot syntax in vegtable objects.
• show() and print() methods for objects vegtable, coverconvert, and shaker.

Improvements

• In function make_cocktail(), names of syntaxa are allowed to start with numerical values.
• Function write_juice() includes a messages when working and with some metadata for cross-check when importing in Juice.
• New arguments in function taxa2samples() setting the levels to be included in output object (include_levels) and to remove taxa without levels (na.rm).
• Application of subset() extended to content in slot relations.
• Function vegtable2kml() was deprecated to resolve dependencies on GIS packages associated to package plotKML.
• Validity checks allow plots in slot header without records in samples.
• Function summary() also providing number of plots with records.
• Function transform() deprecated and replaced by cover_trans().

Bug Fixes

• Files written by write_juice() in Linux are now readable in Windows.
• In clean() objects with no entries resulted in invalid objects.
• Bug in count_taxa() for aggregating ranks with missing records for lower taxa.

vegtable 0.1.6

Improvements

• Documentation implemented in roxygen2.
• New argument preserve_ids in function add_releves().

Bug Fixes

• Function count_taxa() adapted to the current package taxlist.

vegtable 0.1.5

New Features

• New function relation2header().
• New functions trait_stats() and trait_proportion().

Improvements

• New argument add_traits in function taxa2samples().
• Output of count_taxa(), formula-method, indicates the counted rank in the output.
• Adjusted settings in function write_juice() for general cases.
• Argument as_matrix in function crosstable() alternating matrix or data.frame as output.
• New arguments suffix and in_header for the function count_taxa().

Bug Fixes

• Function taxa2samples() was not properly working when taxlist had taxon concepts without level information.

vegtable 0.1.4

New Features

• New data set aspect_conv.
• New function taxa2samples() for changing record names by their respective accepted names.
• Function count_taxa() implemented for vegtable objects.

Improvements

• Updated data set Kenya_veg Including hierarchical ranks.

Bugs

• Function cross2db was not working properly for tables with only one column

vegtable 0.1.3

Improvements

• A method for numeric values in function transform().

vegtable 0.1.2

New Features

• File inst/ChangeLog replaced by NEWS.md.
• Method match_names() for vegtable objects.
• New method layers2samples().
• New method add_releves(), adding releves from data frames into vegtable objects.

Improvements

• No column LayerID in prototype for vegtable objects.
• NA values are allowed for layers in slot samples.
• Layers are not any more restricted to single plots.
• Orphaned entries in slot layers will be deleted by function clean().
• Argument match_header included in function veg_relation().
• Validity check is not accepting NA values in TaxonUsageID at slot samples.
• Validity check tests also the values of relations matching header with the respective relation.

vegtable 0.1.1

New Features

• A method for function aggregate.
• Slot layers added to vegtable objects.

Improvements

• Method subset working similarly to taxlist::subset.
• Function clean does not modify slot species.
• Function crosstable access also to taxon traits.
• New argument use_nas for function crosstable.

vegtable 0.1.0

New Features

• First delivery in CRAN.

kamapu/vegtables documentation built on Feb. 17, 2024, 8:29 a.m.