                 Changes in version 0.2.4 (2026-07-23)                  

  - Fixed a bug in check_weight_tot_nb() that caused a crash ("missing
    value where TRUE/FALSE needed") when processing records with an
    empty or NA FAUNISTIC_CATEGORY. The function now gracefully handles
    these cases and emits a specific warning.
  - System-wide standardization of validation checks to explicitly
    prefix log messages with "Error: " or "Warning: " for clearer
    parsing and debugging of data inconsistencies.

                 Changes in version 0.2.3 (2026-04-23)                  

  - CRAN submission compliance updates:
      - Refactored DESCRIPTION: Updated Authors@R format, added Language
        field, and moved shinyjs and svDialogs to Suggests.
      - Updated .Rd documentation: Fixed unclosed \references{}
        brackets, resolved 'Invalid URL' checks, corrected syntax
        errors, and removed typos across all manual files.
      - Replaced packageVersion() with meta$Version in inst/CITATION for
        compatibility when the package is not yet installed.
      - Ensured strict adherence to CRAN repository policies regarding
        files written outside of tempdir().
  - Bug fixes and robustness improvements:
      - Fixed a critical crash in check_individual_weightTE() caused by
        missing LENGTH_CLASSES_CODE values (handled NA and added safety
        checks).
      - Resolved a logic error in the plotting routine of
        check_individual_weightTE() where incorrect length-weight
        parameters were applied due to an index bug.
      - Added robustness to plotting functions to skip species/sex
        combinations with no valid data points.

                        Changes in version 0.2.2                        

  - Improved check_spawning_period(): TA and TC records are now matched
    on both HAUL_NUMBER and COUNTRY, avoiding incorrect month
    assignments when haul numbers are shared across countries.
  - Added run_RoME_app(): launches an embedded Shiny graphical user
    interface for running RoME analyses directly from the package
    environment.

                        Changes in version 0.2.1                        

  - Included the stratification schema table used in the Black Sea
    (Romania and Bulgaria) for the rapana whelk beam trawl survey:
    stratification_scheme_rapana.

                        Changes in version 0.2.0                        

  - RDBFIS III revision. Major improvements to check_weight(),
    check_length(), check_individual_weightTC(),
    check_smallest_mature(), check_species_TBTC(),
    check_spawning_period(), check_dictionary(), and check_raising().
    New functions: check_swept_area() and plot_abundance(). Updated
    check_distance() to use geosphere::distGeo().

                         Changes in version 0.1                         

Fixes 0.1.2

1.  Each example has been reduced to less than 5 seconds of time to run.

Fixes 0.1.3

1.  Eliminated Namespace with empty importFrom: 'grDevices'
2.  Corrected the wrong pintsize in function check_position.
3.  Eliminated the folders created in all the RoME functions from the
    tempdir.

Fixes 0.1.4

1.  Corrected the wrong pintsize in function check_temperature.
2.  Revised again for eliminating the folders created in all the RoME
    functions from the tempdir.

Fixes 0.1.5

1.  Corrected the wrong pointsize in function check_weight.

Fixes 0.1.6

1.  Eliminated detritus from the temporary directories.

Fixes 0.1.7

1.  Changed the reference version of R indicated in the file
    DESCRIPTION.

Fixes 0.1.8

1.  Solved the error in check_dm for saving the Logfile.

Fixes 0.1.9

1.  Space removed from filenames of the files stored in the temporary
    directory.

Fixes 0.1.10

1.  Addressed the problem of nested temporary directories in Linux.

Fixes 0.1.11

1.  Error solved in check_dm.Rd example

Fixes 0.1.12

1.  Solved the problems of nested temporary directories in Linux.

Fixes 0.1.13

1.  Solved other problems of nested temporary directories in Linux.

Fixes 0.1.14

1.  Fixed problems of recursive directories creation in Debian with
    check_dm() function.

Fixes 0.1.15

1.  Revision of Documentation Rd files following the .
2.  Revision of contributors description in Documentation file

Fixes 0.1.16

1.  Inclusion of length-weight dataframe into RoME() parameters

Fixes 0.1.17

1.  Modification of RoME function to allow estimation of R sufi files
    from both TC and TE tables

Fixes 0.1.18

1.  Improvement of output plots using functions of ggplot2 package

Fixes 0.1.19

1.  issue in check_area function corrected

Fixes 0.1.20

1.  inclusion of new functions (e.g. RoMEcc) to adapt the package to
    work with the RDBFID database

Fixes 0.1.21

1.  inclusion of new function to convert RDBFIS headers to MEDITS format

Fixes 0.1.23

1.  check dictionary function allows also NA values

Fixes 0.1.24

1.  included country in filtering TB and TC data in check_raising

Fixes 0.1.26

1.  improvement of check_raising outputs

Fixes 0.1.27

1.  bugs fixed

Fixes 0.1.28

1.  included the zip parameter in RoMEcc
2.  replaced the zip function with the "zip" library one

Fixes 0.1.29

1.  check_haul_species_TCTB function modified to produce Critical_Error
    file
2.  checkHeader function modified to produce Critical_Error file
3.  check_class function modified to produce Critical_Error file
4.  check_consistencyTA_duration: identify errors if SHOOTING_TIME or
    HAULING_TIME fields are not integer
5.  inclusion of the function RoMEBScc specifically working on Black Sea
    MEDITS-like data

Fixes 0.1.30

1.  New stratification_ _scheme table

Fixes 0.1.31

1.  generalization of check_stratum
2.  optimization of check_weight

Fixes 0.1.34

1.  optimization of zip saving
2.  optimization of temporary directory use

Fixes 0.1.35

1.  improved management of errors in check_length function

Fixes 0.1.36

1.  quasi-identical records' check output changed in warning message
    instead of error

Fixes 0.1.37

1.  warning messages modified in check_bridles_length function

Fixes 0.1.38

1.  header.conversion function modified for the
    measuring_system_salinity field in input file (TA)

Fixes 0.1.39

1.  improvement of check_individual_weightTE function

Fixes 0.2.0

0.  RDBFIS III Fixes

1.  check_weight() now logs detailed records of species with mean
    weights outside reference ranges into a CSV file instead of writing
    extensive messages in the .dat log, ensuring clearer logs and easier
    downstream analysis. Plots are now saved exclusively to files and
    are no longer displayed interactively, and species plots are limited
    to those with at least 5 observations to reduce unnecessary graph
    generation. The function was adapted to work with the updated
    DataTargetSpecies table

2.  check_length() now saves all detailed inconsistencies into a CSV
    file instead of writing verbose messages in the .dat log, improving
    clarity and data traceability, using the new updated
    DataTargetSpecies table.

3.  check_individual_weightTC changed to save the table for the
    comparison between the estimated vs observed weights in TC.

4.  the check_smallest_mature function was adapted to work with the
    updated DataTargetSpecies table

5.  check_smallest_mature: Improved handling of non-numeric values in
    Maturity_parameters and introduced a 10% buffer when checking
    lengths. Added a CSV output listing all records where mature
    individuals are smaller than reference sizes, including the
    threshold size and bibliographic references. The function has also
    been adapted to the new format of DataTargetSpecies.

6.  check_species_TBTC function improved with more robust data filtering
    checks and streamlined log file content to reduce verbosity. The
    function has also been adapted to the new format of
    DataTargetSpecies.

7.  check_spawning_period now logs all maturity-stage consistency
    warnings into a dedicated CSV file rather than filling the .dat log
    with verbose messages, improving traceability and downstream
    analyses. The function robustly handles missing (NA) values in both
    maturity parameters and survey data to avoid false positives. It now
    separates warnings for immature individuals observed within the
    spawning period but above size thresholds, and for mature
    individuals found outside the spawning period, distinguishing
    whether they fall below bibliographic size limits. CSV outputs
    include comprehensive details such as spawning months, size
    thresholds, and the type of inconsistency detected. The function has
    been adapted to work with the updated DataTargetSpecies table.

8.  check_dictionary() now reports the actual invalid value in every log
    entry. Previously it said "value not allowed for X"; now each line
    includes the offending string or NA (e.g., "Haul 109: value 'XYZ'
    not allowed for COURSE in TA"), and messages are batched into a
    single writeLines() call to eliminate hundreds of small I/O
    operations. The function was dramatically rebuilt to optimize
    computational time, achieving a runtime reduction of >90% for this
    routine (e.g., from 12.91 s down to 0.07 s).

9.  check_length(): the internal per-row loop has been replaced with
    vectorized index computations (which() + match()), and all I/O is
    consolidated into single write.table() and write() calls. These
    changes preserve the original logic and output formats (including
    handling of missing, negative, and out-of-range classes with the
    updated DataTargetSpecies), while delivering a around 66% reduction
    in the routine's execution time (e.g., from 2.77 s down to 0.93 s).

10. Replaced all class(...) == checks with inherits(...) to improve code
    robustness and avoid R CMD check notes. Fixed documentation
    mismatches, ensuring consistency between code default arguments and
    Rd files. Corrected a misplaced brace in the Rd documentation of
    check_position_in_Med(), resolving a note from R CMD check.

11. NEW function: check_swept_area the function checks the key
    swept-area field used later to standardise abundance indices. It
    scans the TA file for the chosen year, flags and removes any haul
    whose wing opening, distance or depth is missing, non-numeric or
    would lead to an impossible swept-area value, and logs each problem
    haul in detail. By doing this before abundance calculations begin,
    the function ensures that every density estimate rests on a solid,
    verifiable swept-area input.

12. updated function: check_raising check_raising() has been rewritten
    to use native dplyr operations, which removes the old explicit loops
    and makes the code markedly faster. The routine now calculates the
    raising factor molt for every TC subsample and records, one line at
    a time, any situation in which that ratio falls below one. It also
    adds a new consistency test that compares the grand total raised
    from TC with both the sex-specific counts and the overall total
    reported in TB, logging every discrepancy with haul and species
    identifiers so that problematic records are easy to trace. Rows that
    lack swept-area information or contain invalid totals are discarded
    but never cause the function to stop; they are simply listed in the
    log file. In line with the behaviour of plot_abundance(), the
    function now returns TRUE when no inconsistencies are found and
    FALSE otherwise, while continuing execution to the end in all cases.

13. NEW function: plot_abundance() Introduces an automated routine that
    reads TA and TB tables, computes swept-area-standardised abundance
    indices (n/km^2) per haul and species, applies quality-control
    filters (swept area missing/zero, invalid totals, minimum number of
    hauls), and produces box-plots in chunks of maximum 36 species each.
    All images are saved to Graphs/Abundance and a detailed logfile is
    written to Logfiles/.

14. updated function: check_distance() Replaced the custom distance
    calculation with the function geosphere::distGeo() for computing
    geodesic distances between shooting and hauling coordinates. This
    modification avoids the issue of estimating zero distances when the
    same value is reported for both shooting and hauling longitude or
    latitude in a given haul. Computational efficiency was improved by
    vectorizing the distance computation using mapply() instead of a
    row-wise loop.

Fixes 0.2.1

0.  RDBFIS III Fixes
1.  Included the stratification schema table used in the Black Sea, by
    Romania and Bulgaria, in the rana whelk beam trawl survey:
    stratification_scheme_rapana.

Fixes 0.2.2 (26/03/2026)

Improved check_spawning_period() by matching TA and TC records on both
HAUL_NUMBER and COUNTRY, avoiding incorrect month assignments when haul
numbers are shared across countries.

Added an embedded Shiny application to the package: run_RoME_app(). It
provides a graphical user interface for running RoME analyses directly
from the package environment.
