Package index • macroibi

User-facing functions

Primary functions for running the app and generating reports.

run_macroibi(): Launch the MacroIBI Shiny application
generate_reports(): Generate reports from autosave files
refresh_taxonomy(): Refresh Taxonomy Data

Internal

Internal functions not intended for direct use.

add_ordinal_suffix(): Add ordinal suffix to a date
assemble_download_data(): Assemble download data from selected genera
autosave_module_server(): Autosave module server
autosave_module_ui(): Autosave module UI
build_autosave_df(): Flatten selected genera into an autosave-friendly data.frame
build_group_defs(): Build group definitions from a list of group names
build_section_data_list(): Convert a per-section data.frame into the section data list
build_sections_from_autosave(): Rebuild section data from an autosave data.frame
build_summarized_metrics(): Build summarized metric table for autosave
build_taxon_choices(): Build choices for the main taxon selectize input
build_tree_nodes(): Build taxonomic tree nodes for selected TSNs
calculate_corixid_ratio_static(): Calculate corixid ratio without reactives
calculate_corixids_ratio(): Calculate the Corixids ratio metric
calculate_metric_score(): Calculate a metric score
calculate_metrics_from_sections(): Calculate metrics from section data without reactives
collect_lineage(): Collect lineage for a TSN
compute_unique_taxa(): Compute count of unique taxa given hierarchical taxonomy
copy_demo_autosaves(): Copy demo autosaves from given directories
download_module_server(): Download module server
download_module_ui(): Download module UI
draw_tree_base(): Draw a taxonomic tree using base graphics
escape_latex(): Escape LaTeX characters
format_date_for_filename(): Format a date for safe use in filenames
generate_pdf_report(): Generate a PDF report from template
generate_single_output(): Generate a single output file
get_app_path(): Retrieve a stored path
ibi_quality_class(): Classify an IBI total score into a RAM quality class
init_app_state(): Initialize application paths
is_latex_available(): Check whether a LaTeX distribution is available
layout_tree(): Layout a taxonomic tree for plotting
load_taxonomy(): Load bundled taxonomy data
macroibi macroibi-package: macroibi: Wetland Macroinvertebrate IBI Dashboard
macroibi_server(): Internal server
macroibi_ui(): Internal UI builder
metric_calibration_df(): Canonical IBI metric calibration table
normalize_in_region_flag(): Normalize in_region to a logical flag
normalize_uploaded_taxa(): Normalize uploaded taxa into per-section row lists
`%||%`: Null-coalescing operator
parse_flexible_date(): Parse a date string flexibly
`%>%`: Pipe operator
prepare_results_data(): Prepare results data for reports
process_autosave_file(): Process a single autosave file and generate outputs
rank_levels: Default taxonomic rank levels used for tree layout
reactive_handler(): Evaluate a reactive or numeric value safely
report_deps: Internal: packages used in report templates
require_latex(): Require LaTeX or stop / notify
resolve_selected_taxon(): Resolve selected taxon to section + IDs
results_download_server(): Results download server
results_download_ui(): Results download UI
safe_reactive_value(): Safely retrieve a reactive value
sanitize_group_id(): Sanitize group ID for stable use in file names/IDs
seed_demo_autosaves_from_inst(): Seed demo autosaves from inst/
server_metrics(): Metric scores server
server_taxon_section(): Taxon section server
split_uploaded_results(): Extract metadata and taxa rows from uploaded CSV
sum_group_totals(): Sum group totals with a minimum length requirement
summarize_metric_scores(): Append IBI summary row to metric scores
taxonomic_tree_server(): Taxonomic tree server
taxonomic_tree_ui(): Taxonomic tree UI
ui_metric_scores(): Metric scores UI
ui_taxon_section(): Taxon section UI
upload_module_server(): Upload module server
upload_module_ui(): Upload module UI