Package 'EthnoBotaPhyWR'

Ethnobota fever

Description

Collects and plots ethnobotanical and phytochemical data for a given taxon. This function performs data retrieval, merging, and logging, and produces summary statistics and outputs for downstream analysis and visualization.

Usage

ethnobotafever_tree(
  taxon_name,
  n_multiple_genera,
  n_ethnobotanical_count_min,
  n_compounds_count_min,
  example_family_names,
  path_molecules,
  path_classes,
  path_ethnobotanical,
  export_tree_full,
  export_tree_phyto,
  export_tree_phyto_sub,
  export_table_classified,
  export_table_counts,
  export_table_counts_sub,
  local_cache,
  log_dir
)

Arguments

taxon_name	Character. Name of the taxon of interest.
n_multiple_genera	Integer. Minimum number of genera for filtering.
n_ethnobotanical_count_min	Integer. Minimum ethnobotanical count for filtering.
n_compounds_count_min	Integer. Minimum compound count for filtering.
example_family_names	Character vector. Example family names for comparison.
path_molecules	Character, data.frame, or NULL. Local molecules file or table.
path_classes	Character, data.frame, or NULL. Local classes file or seed data.
path_ethnobotanical	Character, data.frame, or NULL. Local ethnobotanical file or table.
export_tree_full	Character. Path for the main full-tree PDF figure.
export_tree_phyto	Character. Path for the phytochemical overview PDF figure.
export_tree_phyto_sub	Character. Path for the species-level phytochemical PDF figure.
export_table_classified	Character. Path for the classified compounds export.
export_table_counts	Character. Path for the genus-level summary table export.
export_table_counts_sub	Character or NULL. Path for the filtered species-level counts export.
local_cache	Character. Directory containing .rda tree cache datasets (for example data-raw).
log_dir	Character. Directory for log files.

Details

This function is a pipeline for data collection, merging, and reporting. It logs progress and statistics throughout. All side effects (file writes, logs) are documented inline.

Value

A list containing the rendered plots, exported tables, and the log-file path.

Examples

NULL

---

Orchids Compound Classifications

Description

NPClassifier taxonomy results for SMILES strings found in Orchidaceae. Maps each unique SMILES to its pathway, superclass, class, and glycoside status.

Usage

orchids_compound_classes

Format

A data.frame with 1574 rows and 5 columns:

query

Canonical SMILES string

pathway

NPClassifier pathway classification

superclass

NPClassifier superclass classification

class

NPClassifier class classification

glycoside

Logical: whether compound is a glycoside

Details

This dataset is a deduplicated lookup table for compound classifications. Use it to quickly retrieve NPClassifier results for a given SMILES string without querying the live API.

Source

NPClassifier Web Service (https://npclassifier.gnps2.org/)

Examples

data(orchids_compound_classes)
head(orchids_compound_classes)
nrow(orchids_compound_classes)

---

Orchids Compound Data

Description

A dataset containing phytochemical information from Orchidaceae species. This is a curated subset linking taxonomic data, chemical structures (SMILES), and NPClassifier taxonomy.

Usage

orchids_compounds

Format

A data.frame with 3055 rows and 10 columns:

taxon

Wikidata QID (Q-identifier) for the species

taxon_name

Scientific name of the species

compound

Wikidata QID for the chemical compound

compound_smiles_canonical

Canonical SMILES representation

compound_inchikey

InChIKey chemical identifier

connectivity_layer

First block of InChIKey (connectivity skeleton)

pathway

NPClassifier pathway classification

superclass

NPClassifier superclass classification

class

NPClassifier class classification

glycoside

Logical: whether compound is a glycoside

Source

Curated from:

• Wikidata (https://www.wikidata.org/)

• LOTUS database (https://lotus.naturalproducts.net/)

• NPClassifier (https://npclassifier.gnps2.org/)

Examples

data(orchids_compounds)
head(orchids_compounds)
table(orchids_compounds$superclass)

---

Orchids Ethnobotanical Uses

Description

A dataset of ethnobotanical uses reported for Orchidaceae species, linked to their Open Tree of Life (OTT) taxonomy identifiers.

Usage

orchids_ethnobotanical

Format

A data.frame with 419 rows and 3 columns:

taxon_name

Scientific name of the species

taxon

Wikidata QID (Q-identifier) for the species

taxon_id_ott

Open Tree of Life taxonomy identifier

Details

Each row represents a species with documented ethnobotanical uses. The taxon_id_ott field enables integration with phylogenetic analyses via the Open Tree of Life API.

Source

Wikidata (https://www.wikidata.org/) and Open Tree of Life (https://tree.opentreeoflife.org/)

Examples

data(orchids_ethnobotanical)
head(orchids_ethnobotanical)
nrow(orchids_ethnobotanical)

---

Cached Tree Result for Orchidaceae

Description

Precomputed tree cache generated by get_trees_cached() for the Orchidaceae pipeline. The .rda file contains a single object named trees_5141741f198446414395a45383e3a7ec.

Usage

trees_5141741f198446414395a45383e3a7ec

Format

An .rda file containing a list with:

taxa_not_in_tree

A tidytable/data.frame of taxa that were not found in the tree

tree_taxa_full

A phylo object for the full induced tree

tree_taxa_phyto

A phylo object for the phytochemical subset tree

Source

Generated by get_trees_cached() from Open Tree of Life queries.

---

Cached Tree Result for Orchidaceae

Description

Precomputed tree cache generated by get_trees_cached() for the Orchidaceae pipeline. The .rda file contains a single object named trees_886f2bbc1ee37e9433e35b78f5db91ef.

Usage

trees_886f2bbc1ee37e9433e35b78f5db91ef

Format

An .rda file containing a list with:

taxa_not_in_tree

A tidytable/data.frame of taxa that were not found in the tree

tree_taxa_full

A phylo object for the full induced tree

tree_taxa_phyto

A phylo object for the phytochemical subset tree

Source

Generated by get_trees_cached() from Open Tree of Life queries.

---

Cached Tree Result for Orchidaceae

Description

Precomputed tree cache generated by get_trees_cached() for the Orchidaceae pipeline. The .rda file contains a single object named trees_8cca7de252bc0994398aec413cebdbbc.

Usage

trees_8cca7de252bc0994398aec413cebdbbc

Format

An .rda file containing a list with:

taxa_not_in_tree

A tidytable/data.frame of taxa that were not found in the tree

tree_taxa_full

A phylo object for the full induced tree

tree_taxa_phyto

A phylo object for the phytochemical subset tree

Source

Generated by get_trees_cached() from Open Tree of Life queries.

---

Cached Tree Result for Orchidaceae

Description

Precomputed tree cache generated by get_trees_cached() for the Orchidaceae pipeline. The .rda file contains a single object named trees_9a06c9c148110e62a4e1d2ff8094e462.

Usage

trees_9a06c9c148110e62a4e1d2ff8094e462

Format

An .rda file containing a list with:

taxa_not_in_tree

A tidytable/data.frame of taxa that were not found in the tree

tree_taxa_full

A phylo object for the full induced tree

tree_taxa_phyto

A phylo object for the phytochemical subset tree

Source

Generated by get_trees_cached() from Open Tree of Life queries.

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