Generate the AlgAware Word report — generate

Creates a Word document with overview maps, heatmaps, stacked bar charts, station sections, and image mosaics. Optionally includes a front page with logo, diary number placeholder, a phytoplankton pie map, and two summary mosaics.

Usage

generate_report(
  output_path,
  station_summary,
  baltic_wide,
  westcoast_wide,
  baltic_mosaics = list(),
  westcoast_mosaics = list(),
  taxa_lookup = NULL,
  cruise_info = "",
  classifier_name = NULL,
  use_llm = FALSE,
  annotator = "",
  image_counts = NULL,
  total_bio_images = NULL,
  llm_model = NULL,
  n_station_samples = NULL,
  llm_provider = NULL,
  on_llm_progress = NULL,
  frontpage_baltic_mosaic = NULL,
  frontpage_westcoast_mosaic = NULL,
  unclassified_fractions = NULL,
  frontpage_baltic_taxa = NULL,
  frontpage_westcoast_taxa = NULL,
  report_number = NULL,
  report_dnr = NULL,
  ctd_data = NULL,
  ctd_data_full = NULL,
  lims_data = NULL,
  lims_data_full = NULL,
  chl_stats = NULL,
  chl_map_source = "ferrybox",
  phyto_groups = NULL
)

Arguments

output_path: Path for the output .docx file.
station_summary: Aggregated station data.
baltic_wide: Wide-format Baltic summary.
westcoast_wide: Wide-format West Coast summary.
baltic_mosaics: Named list of mosaic images (Baltic).
westcoast_mosaics: Named list of mosaic images (West Coast).
taxa_lookup: Optional taxa lookup table with HAB column.
cruise_info: Character string with cruise/date information for title.
classifier_name: Optional character string with the classifier model name used for automated classification.
use_llm: Logical; if TRUE and an LLM API key is configured (OPENAI_API_KEY or GEMINI_API_KEY), generate report text using an LLM. Default FALSE uses placeholder text.
annotator: Character string with the analyst name for the introduction statement.
image_counts: Optional data frame from fetch_image_counts() with cruise-wide image counts and coordinates for the track map.
total_bio_images: Optional integer; total number of biological images used in the report (excluding non-biological classes).
llm_model: Optional character string; name of the LLM model used for text generation (e.g. "gpt-4.1").
n_station_samples: Optional integer; total number of IFCB samples matched to AlgAware stations.
llm_provider: Optional character string; LLM provider to use ("openai" or "gemini"). NULL auto-detects.
on_llm_progress: Optional callback function called before each LLM request with arguments (step, total, detail) for progress reporting.
frontpage_baltic_mosaic: Optional magick image for the front page Baltic Sea mosaic. If NULL (together with West Coast), no front page is generated.
frontpage_westcoast_mosaic: Optional magick image for the front page West Coast mosaic.
unclassified_fractions: Optional named list or data frame of unclassified proportion estimates passed to the LLM prompts for context.
frontpage_baltic_taxa: Optional character vector of taxa names matching the numbered images in the Baltic mosaic (for captions).
frontpage_westcoast_taxa: Optional character vector of taxa names matching the numbered images in the West Coast mosaic.
report_number: Optional report issue number (e.g. "1").
report_dnr: Optional diarienummer string for the front page (e.g. "2026-1234").
ctd_data: Optional CTD profile data from read_cnv_folder() (AlgAware-matched, used for the chlorophyll map).
ctd_data_full: Optional full CTD profile data from read_cnv_folder_all() (all standard stations, used for the CTD section with regional fluorescence profiles and time series).
lims_data: Optional LIMS discrete Chl-a data from read_lims_data() (AlgAware-matched, used for the chlorophyll map).
lims_data_full: Optional LIMS data from read_lims_data_all() (all standard stations, used for the CTD section time series).
chl_stats: Optional historical statistics from load_chl_statistics().
chl_map_source: Character; active chlorophyll map source: "ferrybox", "ctd", "lims" (bottle, 0-20 m), or "lims_hose" (hose integrated, 0-10 m).
phyto_groups: Optional data frame with columns name, AphiaID, and phyto_group (typically from SHARK4R::assign_phytoplankton_group()). Used to render the per-station phytoplankton group composition pie map. If NULL, the assignments are computed on demand via SHARK4R when available.

Value

Invisible path to the created document.