barroso_write_specimens

Write lists of examined specimens in the format of a journal

barRoso::barroso_write_specimens()

Description

Writes the lists of examined specimens of one, several or all species of a database of herbarium records in Darwin Core format, as standardized by barroso_std(), into a Word (.docx) file, in the format of a botanical journal, e.g. Systematic Botany, Taxon, Kew Bulletin or Phytotaxa.

Details

The records are formatted with barroso_dwc(), so the columns may also come from other sources, e.g. speciesLink. The columns used are species, country, stateProvince, municipality, locality, decimalLatitude, decimalLongitude, minimumElevationInMeters, maximumElevationInMeters, day, month, year, reproductiveCondition, recordedBy, addCollector, recordNumber, collectionCode and catalogNumber; and, when present, the columns of barroso_flag_duplicates() with all herbaria of each specimen (duplicateCollectionCodes, duplicateCatalogNumbers). The author of each species comes from scientificNameAuthorship, acceptedScientificName or scientificName.

Duplicates of the same collection (same collector and number, or same collector, date and locality when there is no number) are written once, with all their herbaria. The specimens are ordered by country, state, municipality and date.

Examples of the format of each journal:

Systematic Botany: Representative Specimens Examined—Brazil. —Bahia: Abaíra, Catolés, 13°23′S, 41°48′W, 1200 m, 8 May 1994 (fl), D.B.O.S. Cardoso et al. 2066 (HUEFS, RB). (header and states in small capitals, countries in bold, collectors and numbers in italics, as also in Taxon and Acta Botanica Brasilica) Taxon: Additional specimens examined. – BRAZIL. BAHIA: Abaíra, Catolés, 13°23′S, 41°48′W, 1200 m a.s.l., 8 May 1994 (fl.), D.B.O.S. Cardoso & al. 2066 (HUEFS, RB). Kew Bulletin: SPECIMENS EXAMINED. BRAZIL. Bahia: Abaíra, Catolés, 13°23’S, 41°48’W, 1200 m, 8 May 1994 (fl.), D. B. O. S. Cardoso et al. 2066 (HUEFS, RB). Phytotaxa: Additional specimens examined:―BRAZIL. Bahia: Abaíra: Catolés, …, 8 May 1994 (fl), D.B.O.S. Cardoso et al. 2066 (HUEFS, RB). Brittonia: Additional specimens examined.—BRAZIL. Bahia: …, 8 May 1994 [fl], D. B. O. S. Cardoso et al. 2066 (HUEFS, RB). Candollea: Additional specimens examined. – Brazil. Bahia: …, 13°23’S 41°48’W, 1200 m, 8.V.1994, fl., Cardoso et al. 2066 (HUEFS, RB). Edinburgh Journal of Botany: Additional specimens examined. BRAZIL. Bahia: …, 8 v 1994 (fl), Cardoso et al. 2066 (HUEFS, RB). Systematics and Biodiversity: Additional specimens examined. BRAZIL. Bahia: …, 8 May 1994 (fl), D. B. O. S. Cardoso et al. 2066 (HUEFS, RB). Acta Botanica Brasilica: Additional specimens examined: BRAZIL. Bahia: …, 13°23’ S, 41°48’ W, 8 May 1994, (fl.), D.B.O.S. Cardoso et al. 2066 (HUEFS!, RB!). Plant Ecology and Evolution: Additional material examined. BRAZIL • Bahia, Abaíra, Catolés; 13°23′S, 41°48′W; 1200 m; 8 May 1994 (fl); Cardoso et al. 2066; HUEFS, RB. PhytoKeys: Additional specimens examined. Brazil. Bahia: Mun. Abaíra, Catolés, 13°23’S, 41°48’W, 1200 m alt., 8 May 1994 (fl), D.B.O.S. Cardoso et al. 2066 (HUEFS, RB). Willdenowia: Brazil: Bahia: Municipality Abaíra, Catolés, 13°23’S, 41°48’W, 1200 m, 8 May 1994 (fl), D. B. O. S. Cardoso & al. 2066 (HUEFS, RB); Serra do Barbado, … Municipality Mucugê, … . — Minas Gerais: … (header once, before all species) Annals of the Missouri Botanical Garden: Additional specimens examined. BRAZIL. Bahia: Abaíra, Catolés, 13°23′S, 41°48′W, 1200 m, 8 May 1994 (fl./fr.), D. B. O. S. Cardoso et al. 2066 (HUEFS, RB). Botanical Journal of the Linnean Society: Representative specimens examined: BRAZIL. Bahia: Abaíra, Catolés, 13°23′S, 41°48′W, 1200 m, 8.v.1994 (fl), D.B.O.S. Cardoso et al. 2066 (HUEFS, RB); Serra do Barbado, … Brazilian Journal of Botany: Selected additional specimens—BRAZIL. Bahia: …, 08 May 1994 (fl and fr), Cardoso et al. 2066 (HUEFS, RB). Nordic Journal of Botany: Ormosia arborea – Brazil, Bahia, Abaíra, Catolés, …, 8 May 1994, (fl. fr.), Cardoso et al. 2066 (HUEFS, RB). Mucugê, … Rodriguésia: Additional material examined: BRAZIL. BAHIA: Abaíra, Catolés, …, 8.V.1994, fl., D.B.O.S. Cardoso et al. 2066 (HUEFS, RB). Mucugê, …, A. Fernandes (EAC 11356). Acta Amazonica: Additional specimens examined: BRAZIL. Bahia: Abaíra, Catolés. 13º23’S, 41º48’W. Elev. 1200m. Fl. 8 May 1994, D.B.O.S. Cardoso et al. 2066 (HUEFS, RB). Acta Botanica Mexicana: Specimens examined: BRAZIL. Bahia, municipio Abaíra, Catolés, 1200 m, 13°23’S, 41°48’W, 8.V.1994 (fl), D. B. O. S. Cardoso et al. 2066 (HUEFS, RB); loc. cit., 9.V.1994 (fr), … Botany Letters: Representative specimens examined: BRAZIL. — BAHIA: Abaíra, Catolés, 13°23′S, 41°48′W, 1200 m, 8 May 1994 (fl.), D.B.O.S. Cardoso et al. 2066 (HUEFS, RB). — MINAS GERAIS: … Darwiniana: Material examinado: BRASIL. Bahia, Abaíra, Catolés, 13º23’ S, 41º48’ O, 1200 m s. m., 8-V-1994 (fl), D.B.O.S. Cardoso et al. 2066 (HUEFS, RB); ídem, … (with language = “es”) Feddes Repertorium: Additional specimens: BRAZIL. Bahia: Abaíra, Catolés, …, 8 May 1994 (fl), Cardoso et al. 2066 (HUEFS, RB). Hoehnea: Material examinado: BRASIL. BAHIA: Abaíra, Catolés, 13°23’S, 41°48’W, 1200 m, 8-V-1994 (fl.), D.B.O.S. Cardoso et al. 2066 (HUEFS, RB); l.c., Serra do Barbado, … (state in small capitals, with language = “pt”) Plant Systematics and Evolution: Additional specimens examined: BRAZIL. Bahia. Abaíra, Catolés, 1200 m a. s. l., 13° 23′ S, 41° 48′ W, 8 May 1994 (fl.), D.B.O.S. Cardoso et al. 2066 (HUEFS!, RB!). Serra do Barbado, …; Mucugê, …

Arguments

Argument	Description
df	A data frame of herbarium records in Darwin Core format, e.g. the output of `barroso_std()` or `barroso_dwc()`. Not needed when `path` is given.
path	Path to an .xlsx, .xls or .csv file with the herbarium records, used when `df` is `NULL`.
sheet	Sheet name or index of the .xlsx file. Default 1.
species	Character vector of species names, with or without authors (e.g. `"Ormosia arborea"`), to write the specimens of just these species. If `NULL` (default), the specimens of all species are written.
journal	Name of the journal whose format is followed, as in recent papers of the journal: `"Systematic Botany"` (default), `"Acta Botanica Brasilica"`, `"Annals of the Missouri Botanical Garden"`, `"Botanical Journal of the Linnean Society"`, `"Brazilian Journal of Botany"`, `"Brittonia"`, `"Candollea"`, `"Edinburgh Journal of Botany"`, `"Kew Bulletin"`, `"Nordic Journal of Botany"`, `"Phytotaxa"`, `"PhytoKeys"`, `"Plant Ecology and Evolution"`, `"Rodriguesia"`, `"Systematics and Biodiversity"`, `"Taxon"` or `"Willdenowia"`. The name can be written in any case, with or without accents, and abbreviated (e.g. `"systematic botany"`, `"Kew"`, `"Edinburgh"`, `"Rodriguésia"`).
header	Text of the header before the specimens, e.g. `"Additional specimens examined"`, `"Paratypes"` or `"Selected specimens"`, written with the format and punctuation of the journal. If `NULL` (default), the header of the journal, e.g. `"Representative Specimens Examined"` in Systematic Botany. Use `""` to write no header.
language	Language of the section header, months and countries: `"en"` (default) or `"pt"`.
catalog_numbers	Logical. If `TRUE`, the catalog number is written after each herbarium, e.g. `"(IAC no. 14754, NY no. 1162464)"` in Brittonia. Default `FALSE`.
dir	Folder where the .docx file is saved. By default, the folder of `path`, or `"results_specimens"` when the records are given in `df`.
filename	Name of the .docx file. By default, the name of `path` (or `"specimens"`) followed by the journal, e.g. `"Ormosia_herbarium_records_Systematic_Botany.docx"`.
font_family	Font of the document. Default `"Times New Roman"`.
font_size	Font size in points. Default 12.
verbose	Logical. Print progress messages. Default `TRUE`.

Value

Invisibly, a data frame with the species (species_name) and their examined specimens (specimens_text, one specimen per line). The .docx file is written as a side effect.

Examples

# All species of a database standardized by barRoso
barroso_write_specimens(path = "results/Ormosia_herbarium_records.xlsx",
                        journal = "Systematic Botany")

# Two species, in the format of Kew Bulletin
barroso_write_specimens(df = data_all_clean,
                        species = c("Ormosia arborea", "Ormosia fastigiata"),
                        journal = "Kew Bulletin",
                        dir = "results")

--- title: 'barroso_write_specimens' description: 'Write lists of examined specimens in the format of a journal' toc: true toc-depth: 3 --- ```{r} #| eval: false barRoso::barroso_write_specimens() ``` ### Description Writes the lists of examined specimens of one, several or all species of a database of herbarium records in Darwin Core format, as standardized by `barroso_std()`, into a Word (.docx) file, in the format of a botanical journal, e.g. Systematic Botany, Taxon, Kew Bulletin or Phytotaxa. ### Details The records are formatted with `barroso_dwc()`, so the columns may also come from other sources, e.g. speciesLink. The columns used are `species`, `country`, `stateProvince`, `municipality`, `locality`, `decimalLatitude`, `decimalLongitude`, `minimumElevationInMeters`, `maximumElevationInMeters`, `day`, `month`, `year`, `reproductiveCondition`, `recordedBy`, `addCollector`, `recordNumber`, `collectionCode` and `catalogNumber`; and, when present, the columns of `barroso_flag_duplicates()` with all herbaria of each specimen (`duplicateCollectionCodes`, `duplicateCatalogNumbers`). The author of each species comes from `scientificNameAuthorship`, `acceptedScientificName` or `scientificName`. Duplicates of the same collection (same collector and number, or same collector, date and locality when there is no number) are written once, with all their herbaria. The specimens are ordered by country, state, municipality and date. Examples of the format of each journal: Systematic Botany: Representative Specimens Examined—Brazil. —Bahia: Abaíra, Catolés, 13°23′S, 41°48′W, 1200 m, 8 May 1994 (fl), D.B.O.S. Cardoso et al. 2066 (HUEFS, RB). (header and states in small capitals, countries in bold, collectors and numbers in italics, as also in Taxon and Acta Botanica Brasilica) Taxon: Additional specimens examined. – BRAZIL. BAHIA: Abaíra, Catolés, 13°23′S, 41°48′W, 1200 m a.s.l., 8 May 1994 (fl.), D.B.O.S. Cardoso & al. 2066 (HUEFS, RB). Kew Bulletin: SPECIMENS EXAMINED. BRAZIL. Bahia: Abaíra, Catolés, 13°23'S, 41°48'W, 1200 m, 8 May 1994 (fl.), D. B. O. S. Cardoso et al. 2066 (HUEFS, RB). Phytotaxa: Additional specimens examined:―BRAZIL. Bahia: Abaíra: Catolés, ..., 8 May 1994 (fl), D.B.O.S. Cardoso et al. 2066 (HUEFS, RB). Brittonia: Additional specimens examined.—BRAZIL. Bahia: ..., 8 May 1994 [fl], D. B. O. S. Cardoso et al. 2066 (HUEFS, RB). Candollea: Additional specimens examined. – Brazil. Bahia: ..., 13°23'S 41°48'W, 1200 m, 8.V.1994, fl., Cardoso et al. 2066 (HUEFS, RB). Edinburgh Journal of Botany: Additional specimens examined. BRAZIL. Bahia: ..., 8 v 1994 (fl), Cardoso et al. 2066 (HUEFS, RB). Systematics and Biodiversity: Additional specimens examined. BRAZIL. Bahia: ..., 8 May 1994 (fl), D. B. O. S. Cardoso et al. 2066 (HUEFS, RB). Acta Botanica Brasilica: Additional specimens examined: BRAZIL. Bahia: ..., 13°23’ S, 41°48’ W, 8 May 1994, (fl.), D.B.O.S. Cardoso et al. 2066 (HUEFS!, RB!). Plant Ecology and Evolution: Additional material examined. BRAZIL • Bahia, Abaíra, Catolés; 13°23′S, 41°48′W; 1200 m; 8 May 1994 (fl); Cardoso et al. 2066; HUEFS, RB. PhytoKeys: Additional specimens examined. Brazil. Bahia: Mun. Abaíra, Catolés, 13°23'S, 41°48'W, 1200 m alt., 8 May 1994 (fl), D.B.O.S. Cardoso et al. 2066 (HUEFS, RB). Willdenowia: Brazil: Bahia: Municipality Abaíra, Catolés, 13°23'S, 41°48'W, 1200 m, 8 May 1994 (fl), D. B. O. S. Cardoso & al. 2066 (HUEFS, RB); Serra do Barbado, ... Municipality Mucugê, ... . — Minas Gerais: ... (header once, before all species) Annals of the Missouri Botanical Garden: Additional specimens examined. BRAZIL. Bahia: Abaíra, Catolés, 13°23′S, 41°48′W, 1200 m, 8 May 1994 (fl./fr.), D. B. O. S. Cardoso et al. 2066 (HUEFS, RB). Botanical Journal of the Linnean Society: Representative specimens examined: BRAZIL. Bahia: Abaíra, Catolés, 13°23′S, 41°48′W, 1200 m, 8.v.1994 (fl), D.B.O.S. Cardoso et al. 2066 (HUEFS, RB); Serra do Barbado, ... Brazilian Journal of Botany: Selected additional specimens—BRAZIL. Bahia: ..., 08 May 1994 (fl and fr), Cardoso et al. 2066 (HUEFS, RB). Nordic Journal of Botany: Ormosia arborea – Brazil, Bahia, Abaíra, Catolés, ..., 8 May 1994, (fl. fr.), Cardoso et al. 2066 (HUEFS, RB). Mucugê, ... Rodriguésia: Additional material examined: BRAZIL. BAHIA: Abaíra, Catolés, ..., 8.V.1994, fl., D.B.O.S. Cardoso et al. 2066 (HUEFS, RB). Mucugê, ..., A. Fernandes (EAC 11356). Acta Amazonica: Additional specimens examined: BRAZIL. Bahia: Abaíra, Catolés. 13º23’S, 41º48’W. Elev. 1200m. Fl. 8 May 1994, D.B.O.S. Cardoso et al. 2066 (HUEFS, RB). Acta Botanica Mexicana: Specimens examined: BRAZIL. Bahia, municipio Abaíra, Catolés, 1200 m, 13°23'S, 41°48'W, 8.V.1994 (fl), D. B. O. S. Cardoso et al. 2066 (HUEFS, RB); loc. cit., 9.V.1994 (fr), ... Botany Letters: Representative specimens examined: BRAZIL. — BAHIA: Abaíra, Catolés, 13°23′S, 41°48′W, 1200 m, 8 May 1994 (fl.), D.B.O.S. Cardoso et al. 2066 (HUEFS, RB). — MINAS GERAIS: ... Darwiniana: Material examinado: BRASIL. Bahia, Abaíra, Catolés, 13º23’ S, 41º48’ O, 1200 m s. m., 8-V-1994 (fl), D.B.O.S. Cardoso et al. 2066 (HUEFS, RB); ídem, ... (with language = "es") Feddes Repertorium: Additional specimens: BRAZIL. Bahia: Abaíra, Catolés, ..., 8 May 1994 (fl), Cardoso et al. 2066 (HUEFS, RB). Hoehnea: Material examinado: BRASIL. BAHIA: Abaíra, Catolés, 13°23’S, 41°48’W, 1200 m, 8-V-1994 (fl.), D.B.O.S. Cardoso et al. 2066 (HUEFS, RB); l.c., Serra do Barbado, ... (state in small capitals, with language = "pt") Plant Systematics and Evolution: Additional specimens examined: BRAZIL. Bahia. Abaíra, Catolés, 1200 m a. s. l., 13° 23′ S, 41° 48′ W, 8 May 1994 (fl.), D.B.O.S. Cardoso et al. 2066 (HUEFS!, RB!). Serra do Barbado, ...; Mucugê, ... ### Arguments | Argument | Description | |---|---| | df | A data frame of herbarium records in Darwin Core format, e.g. the output of `barroso_std()` or `barroso_dwc()`. Not needed when `path` is given. | | path | Path to an .xlsx, .xls or .csv file with the herbarium records, used when `df` is `NULL`. | | sheet | Sheet name or index of the .xlsx file. Default 1. | | species | Character vector of species names, with or without authors (e.g. `"Ormosia arborea"`), to write the specimens of just these species. If `NULL` (default), the specimens of all species are written. | | journal | Name of the journal whose format is followed, as in recent papers of the journal: `"Systematic Botany"` (default), `"Acta Botanica Brasilica"`, `"Annals of the Missouri Botanical Garden"`, `"Botanical Journal of the Linnean Society"`, `"Brazilian Journal of Botany"`, `"Brittonia"`, `"Candollea"`, `"Edinburgh Journal of Botany"`, `"Kew Bulletin"`, `"Nordic Journal of Botany"`, `"Phytotaxa"`, `"PhytoKeys"`, `"Plant Ecology and Evolution"`, `"Rodriguesia"`, `"Systematics and Biodiversity"`, `"Taxon"` or `"Willdenowia"`. The name can be written in any case, with or without accents, and abbreviated (e.g. `"systematic botany"`, `"Kew"`, `"Edinburgh"`, `"Rodriguésia"`). | | header | Text of the header before the specimens, e.g. `"Additional specimens examined"`, `"Paratypes"` or `"Selected specimens"`, written with the format and punctuation of the journal. If `NULL` (default), the header of the journal, e.g. `"Representative Specimens Examined"` in Systematic Botany. Use `""` to write no header. | | language | Language of the section header, months and countries: `"en"` (default) or `"pt"`. | | catalog_numbers | Logical. If `TRUE`, the catalog number is written after each herbarium, e.g. `"(IAC no. 14754, NY no. 1162464)"` in Brittonia. Default `FALSE`. | | dir | Folder where the .docx file is saved. By default, the folder of `path`, or `"results_specimens"` when the records are given in `df`. | | filename | Name of the .docx file. By default, the name of `path` (or `"specimens"`) followed by the journal, e.g. `"Ormosia_herbarium_records_Systematic_Botany.docx"`. | | font_family | Font of the document. Default `"Times New Roman"`. | | font_size | Font size in points. Default 12. | | verbose | Logical. Print progress messages. Default `TRUE`. | ### Value Invisibly, a data frame with the species (`species_name`) and their examined specimens (`specimens_text`, one specimen per line). The .docx file is written as a side effect. ### Examples ```r # All species of a database standardized by barRoso barroso_write_specimens(path = "results/Ormosia_herbarium_records.xlsx", journal = "Systematic Botany") # Two species, in the format of Kew Bulletin barroso_write_specimens(df = data_all_clean, species = c("Ormosia arborea", "Ormosia fastigiata"), journal = "Kew Bulletin", dir = "results") ```