Improved ping_edi() function to gracefully handle network errors and
disabled network-dependent tests to align with CRAN policies and prevent
CRAN check issues. See issue #154.
ecocomDP 1.3.1
Fixes
Resolved rate limiting errors in ping_edi() triggered by recent
updates to the rate limiting mechanism in the EDI data repository and
due to the lack of rate limiting procedures in the ecocomDP R
package.
ecocomDP 1.3.0
Fixes
Fixed and cleaned up NEON data mapping functions to work with latest
NEON data release, return abundance values that are finite and
non-negative.
Added code to resolve duplicate taxon counts within sample/event IDs
for NEON data.
Enhancements
Updated plotting functions.
ecocomDP 1.2.2
Fixes
Fix NEON mosquito mapping error in internal function
map_neon.ecocomdp.10043.001.001 that resulted from an
update to the NEON “Mosquitoes sampled from CO2 traps” (DP1.10043.001)
data model that affects the 2022 data release (and later). The fix is
backwards compatible to older NEON data releases and also fixes a
problem that resulted in pulling duplicate records from the
mos_archivepooling table (archive records are no longer accessed using
ecocomDP).
Fix vulnerability to absence of retiring r-spatial packages. See
issue #147.
Fix plot_sites() to work with version 0.6.0 of the
usmap package. See issue #136.
ecocomDP 1.2.0
Enhancements
Release new plotting functions for taxonomic and geographic
exploration.
Allow multiple input types to the new data parameter of
“use” functions (supercedes dataset), thereby simplifying
and accelerating exploratory manipulation and plotting.
Reformat dataset object returned by read_data().
Generally, this simplifies dataset indexing and usage within iteration
contexts. It removes a layer of nesting and places the dataset id at the
same level as metadata, tables, and validation_issues.
Release new annotation_dictionary() function. This
feature will allow ecocomDP creators to view the semantic annotations
for existing ecocomDP datasets. Annotation dictionary is published as an
EDI data package to apply occasional updates.
Release new validate_mapped_id() function. Ensures
values listed under /variable_mapping/mapped_id resolve without
error
Release new Model Overview vignette. The model overview vignette
consists of the authoritative set of table descriptions, relationships,
and requirements for the ecocomDP model and a visualization of table
contents and relationships.
Release new Shared Practices Vignette. This document delineates the
practices that all creators of ecocomDP formatted datasets should adopt
in order for the community to build a cohesive and interoperable
collection. It contains detailed descriptions of practices, definitions
of concepts, and solutions to many common issues.
Fixes
Prevent L1 EML from inheriting L0 provenance and additional
metadata, these should not be inherited by the L1 in
create_eml()
Deprecation
Discourage use of the observation parameter of plotting
functions and replace it with the more flexible data
parameter (see above). These changes are backwards compatible with
previous releases.
Discourage use of plot_taxa_sample_time() in favor of
plot_sample_space_time(). These changes are backwards
compatible with previous releases.
Discourage use of the previous dataset object returned
by read_data() in favor of a new one. See details above.
These changes are backwards compatible with previous releases.
ecocomDP 1.1.0
Enhancements
Link to ecocomDP article.
Enable full return of L0 location columns in
flatten_data().
Implement a human readable row sorting based on location_id values
in create_location().
Check create_ecocomDP.R for expected function and associated
arguments in create_eml().
Fixes
Fix alignment of categorical variable names and definitions in
create_eml().
Allow only one basisOfRecord in create_eml().
Fix numeric type detection in create_eml().
Fix taxonomic hierarchy expander in create_eml().
Fix empty annotation defaults in create_eml().
Remove all L0 data entities from the L1 EML, these should not be
inherited by the L1 in create_eml().
Handle both present/absent L0 taxonomic coverage in
create_eml().
Fix assignment of self referencing ids in
create_location().
Only return unique locations in create_location().
Fix methods in calc_number_of_years_sampled() and
calc_length_of_survey_years().
Fix handling of datetimes with YYYY format in
read_data().
Include ancillary table datetime in join operations of
flatten_data().
Remove XML attributes to prevent id clashing and schema invalidation
when constructing provenance nodes in create_eml() and
convert_to_dwca().
Fix basisOfRecord reference in convert_to_dwca().
Incorporate L0 methods markdown blocks in
convert_to_dwca().
Prevent namespace clash with the taxonomyCleanr package.