Changelog

Source: NEWS.md

DATRASextra 0.4.0

This release focuses on API consistency. Several arguments and function names have been renamed so that naming conventions are uniform across the package (e.g. verbose instead of warn_missing, legend instead of do_legend, write_datras instead of write_exchange). Two new arguments have been added: plus_group in add_total_weight_by_haul() and lw_pars in the weight functions for supplying custom length-weight parameters. The default bin width in add_numbers_at_length() now matches the survey’s native recording resolution instead of always using 1 cm. All renaming changes are breaking; see the detailed entries below.

Breaking changes (API consistency)

• prune_datras(): arguments remove_hl and remove_ca renamed to drop_hl and drop_ca to match the verb used by drop_hl() and drop_ca(). Argument warn_missing renamed to verbose for consistency with all other functions.

• plot_length_distribution() and plot_species_composition(): argument do_legend renamed to legend for consistency with plot_datras_overview(), plot_stratified_index(), and plot_spatial_indicators(). legend_ncol default changed from 1L to 1.

• get_aphia(): first argument renamed from x to species.

• get_latin(): first argument renamed from x to aphia.

• write_exchange() renamed to write_datras() for consistency with read_datras().

• add_swept_area_simple() is no longer exported. Use add_swept_area() (with default method = "simple") instead.

• add_swept_area() output column SweptArea.median renamed to SweptArea_median, for consistency with the underscore naming convention used elsewhere (e.g. SweptArea_imputed).

Breaking changes

• check_lengths() and check_weights() now return the input datras_raw object invisibly (consistent with check_outliers()), instead of a plain list. Results are attached as attributes: attr(x, "length_check") and attr(x, "weight_check"), respectively. Code that assigned the return value to a separate variable (e.g. res <- check_lengths(x)) and then accessed res$lPars should be updated to x <- check_lengths(x) and attr(x, "length_check")$lPars.

• The default for impute_missing_depth in clean_datras() has changed from TRUE to FALSE. Enable explicitly with impute_missing_depth = TRUE if needed (requires the mgcv package).

Minor changes

• add_total_weight_by_haul() gains a plus_group argument (default FALSE), passed through to add_weight_at_length(). Argument order changed: per_minute moved to the last position so shared filtering arguments (max_length, max_weight) align with add_weight_at_length().

• add_numbers_at_length(): default for by changed from 1 to get_accuracy_cm(x), consistent with check_lengths() and add_total_numbers_by_haul(). Surveys recorded at 0.5 cm resolution now use 0.5 cm bins by default.

• add_weight_at_length() and add_total_weight_by_haul() gain a lw_pars argument for supplying custom length-weight parameters a and b directly, without modifying the internal species_info table. Accepts a named vector (c(a = 0.01, b = 3.0)), a named list, or a data frame with columns a and b. For multi-species objects, a data frame with a Valid_Aphia (or aphia) column can be used to supply per-species parameters; species not covered fall back to lw_source.

• mgcv and icesDatras are no longer hard dependencies. Both have been removed from Imports; mgcv is now listed under Suggests. The DATRAS API calls previously handled by icesDatras are now made directly in base R.

• add_swept_area() (simple method) now reports swept-area missingness and imputation. It adds a per-haul logical column SweptArea_imputed to HH, attaches a survey-by-gear summary as attr(x, "swept_area_summary"), and prints it unless verbose = FALSE. The summary reports n_imputed / prop_imputed and n_NA / prop_NA, the hauls whose swept area is still NA after imputation (e.g. gears that cannot be imputed). A new full_report argument (default FALSE) additionally reports per-column missingness counts (na_DoorSpread, na_WingSpread, na_Distance, na_HaulDur) of the original input columns.

• Added the article Matching EMODnet seabed habitats to hauls, showing how to download EUSeaMap polygons from the EMODnet Seabed Habitats WFS and attach a seabed habitat class to each haul in HH with a spatial join.

• Replaced the article Constructing a prediction grid within a survey domain with Building a spatiotemporal prediction grid, which uses the new make_survey_grid() function to build the grid and add a year dimension.

DATRASextra 0.1.1

New features

• New make_survey_grid() function creates a regular prediction grid from coordinate vectors. Supports any coordinate system, optional pruning of grid nodes by maximum distance to observations (via RANN), and optional crossing with a time vector.

• New spawning_info dataset: a lookup table of spawning months by species and ICES area, including the WoRMS AphiaID for each species.

• read_datras() gains a ncores argument (default 1) for parallel reading of zip files using parallel::mclapply(). Effective on non-Windows systems; falls back silently to sequential on Windows.

Minor changes

• Added vignette Working with datras_raw objects introducing the datras_raw / DATRASraw class structure and common workflows.

• Added the Getting started article The datras_raw object, describing the object structure, indexing, ICES vocabulary lookups, and the numbers- and weight-at-length matrices.

• download_datras() gains a timeout argument (default 10 seconds). When the ICES DATRAS server does not respond within the given time (e.g. due to firewall restrictions), the function now falls back to cached survey/year information instead of hanging indefinitely. The timeout also applies to the internal survey-list lookup.

Bug fixes

• Fixed $ and $<- dispatch on datras_raw objects (#38). The DATRAS package defines $.DATRASraw to look inside x[[2]], which was written for an older internal structure and caused x$HH to return NULL instead of the HH data frame. New $.datras_raw and $<-.datras_raw methods intercept dispatch before the broken method is reached: if the name matches a top-level table (CA, HH, or HL) the table is returned or replaced; otherwise the call is routed to the HH data frame, preserving the existing column-shortcut convention used internally (e.g. x$SweptArea <- ...).

DATRASextra 0.1.0

Initial beta release

This is the first beta release of DATRASextra, an R package extending the ICES DATRAS workflow with tools for downloading, processing, cleaning, standardising, and analysing bottom-trawl survey data.

Main features

• Download and import ICES DATRAS survey data
• Read, write, clean, and subset datras_raw objects
• Reproduce key components of the FishGlob data-processing workflow
• Estimate swept area and standardise haul metrics
• Calculate numbers- and weight-at-length distributions
• Aggregate total numbers and biomass by haul and length group
• Support species harmonisation and WoRMS-based taxonomic information
• Visualise survey structure, catch composition, and length distributions
• Convert DATRAS data into FishGlob-like formats for downstream analyses

Notes

• This is an early beta release and the API may still change.
• Additional documentation, vignettes, and workflow examples are under development.