irfcb - v0.5.2

News

• ifcb_download_test_data() gains checksum validation, keep_zip option, and improved retry logic.
• ifcb_extract_biovolumes() and ifcb_summarize_biovolumes() gain a drop_zero_volume option to exclude artifacts with zero biovolume
• ifcb_read_features() and ifcb_extract_biovolumes() now handles single feature_files correctly.
• Tests are now skipped if required resources are unavailable, improving stability in environments with limited access to external dependencies.

What's Changed

• 56 add option to drop feature rows with zero biovolume by @anderstorstensson in https://github.com/EuropeanIFCBGroup/iRfcb/pull/58
• 0.5.2 by @anderstorstensson in https://github.com/EuropeanIFCBGroup/iRfcb/pull/59

Full Changelog: https://github.com/EuropeanIFCBGroup/iRfcb/compare/v0.5.1...v0.5.2

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Published by anderstorstensson 9 months ago

irfcb - v0.5.1

Minor improvements and fixes

• Skipping certain internet-required tests on CRAN servers.
• Corrected help pages for ifcb_download_dashboard_data() and ifcb_download_whoi_plankton().

What's Changed

• patch CRAN issue by @anderstorstensson in https://github.com/EuropeanIFCBGroup/iRfcb/pull/55

Full Changelog: https://github.com/EuropeanIFCBGroup/iRfcb/compare/v0.5.0...v0.5.1

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Published by anderstorstensson about 1 year ago

irfcb - v0.5.0

What's Changed

New features

• Added NEWS.md to track package changes.
• New functions:
  • ifcb_download_dashboard_data() for fetching data from the WHOI IFCB Dashboard.
  • ifcb_download_whoi_plankton() for downloading WHOI-Plankton PNG datasets.
  • ifcb_prepare_whoi_plankton() to process WHOI data for integration.
• New vignette: vignette("whoi-plankton-data-integration").
• Python virtual environments can now be automatically activated by setting the USE_IRFCB_PYTHON environment variable when loading the package.
• Added scale bar support (#42) to:
  • ifcb_extract_pngs()
  • ifcb_extract_classified_images()
  • ifcb_extract_annotated_images()
• Added gamma argument to ifcb_extract_annotated_images () and ifcb_extract_classified_images() for gamma correction.
• ifcb_is_near_land():
  • Now returns a plot if plot = TRUE.
  • Added option to download EEA coastline data using the new argument source.
  • Deprecated the argument utm_zone, which is now determined automatically from longitude.

Minor improvements and fixes

• ifcb_read_hdr_data() now correctly handles files from IFCB Acquire 1.x.x.x (#41).
• ifcb_convert_filenames() is more efficient and now correctly parses filenames like "IFCB1_2010_309_192918" (#40).
• The default location of the venv path in ifcb_py_install() has changed to "~/.virtualenvs/iRfcb".
• Added support for old .adc file format (IFCB1-6) by argument old_adc in:
  • ifcb_extract_pngs()
  • ifcb_extract_classified_images()
  • ifcb_extract_annotated_images()
• ifcb_read_mat() now returns consistent data structures aligned with R.matlab::readMat() (#50).

Deprecations

• ifcb_summarize_png_data() is now defunct (previously deprecated in version 0.3.11).
• Deprecated arguments:
  • adc_folder in ifcb_annotate_batch() (replaced by adc_files).
  • unclassified_id in ifcb_create_empty_manual_file() (replaced by classlist).
  • utm_zone in ifcb_is_near_land() (now determined automatically from longitude).
• ifcb_create_empty_manual_file() now accepts a complete class list via classlist, replacing the older unclassified_id.

Full Changelog

• https://github.com/EuropeanIFCBGroup/iRfcb/compare/v0.4.3...v0.5.0

- R
Published by anderstorstensson about 1 year ago

irfcb - v0.4.3

CRAN release

What's Changed

• 0.4.3 dev by @anderstorstensson in https://github.com/EuropeanIFCBGroup/iRfcb/pull/37

Full Changelog: https://github.com/EuropeanIFCBGroup/iRfcb/compare/v0.4.2...v0.4.3

- R
Published by anderstorstensson about 1 year ago

irfcb - v.0.4.2.

What's Changed

• V.0.4.2 dev by @anderstorstensson in https://github.com/EuropeanIFCBGroup/iRfcb/pull/35
• V.0.4.2 dev by @anderstorstensson in https://github.com/EuropeanIFCBGroup/iRfcb/pull/36

Full Changelog: https://github.com/EuropeanIFCBGroup/iRfcb/compare/v0.4.1...v0.4.2

- R
Published by anderstorstensson about 1 year ago

irfcb - v0.4.1

Improve installation process - Drop imager and base64enc dependency - Add gamma option to image extraction - Update vignettes

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Published by anderstorstensson over 1 year ago

irfcb - v0.4.0

• Reorganize vignettes into multiple tutorials
• Add verbose options to multiple functions
• Move worms helper to main function

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Published by anderstorstensson over 1 year ago

irfcb - v.0.3.15

Patch release - Fix duplicate row output in ifcbgetferrybox_data

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Published by anderstorstensson over 1 year ago

irfcb - v.0.3.14

• update SHARK example

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Published by anderstorstensson over 1 year ago

irfcb - v.0.3.13

Added features to merge manual annotation datasets: - ifcbmergemanual - ifcbadjustclasses - ifcbcreateclass2use

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Published by anderstorstensson over 1 year ago

irfcb - v0.3.12

• add functionality to create new manual mat files
• compress .mat files

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Published by anderstorstensson over 1 year ago

irfcb - v0.3.11

Added compatibility with EcoTaxa - add ecotaxa headers and metadata extractions - possibility to split large zip files

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Published by anderstorstensson over 1 year ago

irfcb - v0.3.10

• update docs
• remove deprecated code

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Published by anderstorstensson over 1 year ago

irfcb - v0.3.9

Buggfix - fix issue if nrow(taxalist) == 0 in ifcbcountmatannotations - add recursive search option to ifcbcountmatannotations, ifcbextractannotatedimages and ifcbzipmatlab

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Published by anderstorstensson over 1 year ago

irfcb - v0.3.8

Minor update - parameterize marineonly and recursive file listing - break out useful helper function from ifcbis_diatom

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Published by anderstorstensson over 1 year ago

irfcb - v0.3.7

Minor patch: - add classifer name to mat extraction

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Published by anderstorstensson over 1 year ago

irfcb - v0.3.6

• remove Öresund from baltic shape file
• update shark column names

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Published by anderstorstensson over 1 year ago

irfcb - v0.3.5

• replace ifcbgetsveaposition() with ifcbgetferryboxdata()
• add multiple attemps to worms api call
• update title

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Published by anderstorstensson almost 2 years ago

irfcb - v0.3.4

• Add option to summarize biovolume data from manual files
• Add sleep time parameter for ifcbdownloadtest_data

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Published by anderstorstensson almost 2 years ago

irfcb - v.0.3.3

• Manual MAT count fix
• Download using curl
• Parameterize PSD micron factor
• Minor bug fixes

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Published by anderstorstensson almost 2 years ago

irfcb - v0.3.2

Minor update - Use a smaller test dataset - Improve coverage

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Published by anderstorstensson almost 2 years ago

irfcb - v0.3.1

Minor documentation updates

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Published by anderstorstensson almost 2 years ago

irfcb - v0.3.0

Move to stable version

• Include tests
• Improve functionality

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Published by anderstorstensson almost 2 years ago

irfcb - v.0.2.6

Minor update of documentation

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Published by anderstorstensson almost 2 years ago

irfcb - v0.2.5

• Improve webpage
• Improve tutorial
• Code cleanup

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Published by anderstorstensson almost 2 years ago

irfcb - v.0.2.4

Move documentation to vignette and provide verbose option to functions

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Published by anderstorstensson almost 2 years ago

irfcb - v.0.2.3

Improve NA handling, and make examples runable

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Published by anderstorstensson almost 2 years ago

irfcb - v.0.2.2

Fix issue when NAs are passed to ifcbisnear_land

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Published by anderstorstensson almost 2 years ago

irfcb - v0.2.1

Minor update

• Update SHARK column names in ifcbgetshark_colnames
• Add new function: ifcbgettrophic_type

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Published by anderstorstensson almost 2 years ago

irfcb - v0.2.0

Update documentation and added new functions:

• extractaphiaid: Extract the AphiaID from the first row of each worms_records tibble
• extractclass: Extract the class from the first row of each wormsrecords tibble
• handlemissingpositions: Handle Missing Positions by Rounding Timestamps
• ifcbextractbiovolumes: Extract biovolumes from IFCB data and compute carbon content
• ifcbgetshark_colnames: Get Shark Column Names
• ifcbgetsvea_position: Get GPS coordinates from ferrybox data based on timestamps
• ifcbisdiatom: Identify Diatoms in Taxa List
• ifcbisin_basin: Check if Points are in a Specific Sea Basin
• ifcbpsdplot: Generate PSD Plot for a Given Sample
• ifcbreadfeatures: Read feature files from a specified folder
• ifcbsummarizebiovolumes: Summarize biovolumes and carbon content from IFCB data
• ifcbsummarizeclass_counts: Count Cells from TreeBagger Classifier Output
• ifcbwhichbasin: Determine if Points are in a Specified Sea Basin
• summarize_TBclass: Summarize TreeBagger Classifier Results
• vol2C_lgdiatom: Convert Biovolume to Carbon for Large Diatoms
• vol2C_nondiatom: Convert Biovolume to Carbon for Non-Diatom Protists

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Published by anderstorstensson almost 2 years ago

irfcb - v0.1.2

Fix error in ifcbvolumeanalyzed when inhibition time = 0

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Published by anderstorstensson almost 2 years ago

irfcb - v0.1.1

• update documentation
• fix warning for ifcbisnear_land

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Published by anderstorstensson almost 2 years ago

irfcb - v.0.1.0

First release of iRfcb

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Published by anderstorstensson almost 2 years ago