Write Lists of Examined Specimens

Overview

Taxonomic revisions and descriptions of new species cite the specimens examined for each species, in a format that differs from journal to journal: the header, the case and format (bold, italics, small capitals) of countries, states and collectors, how dates and coordinates are written, and how herbaria are listed.

The function barroso_write_specimens() writes these lists for one, several or all species of a database of herbarium records into a Word (.docx) file, in the format of a chosen journal. This article goes through the whole workflow with two R scripts, using the herbarium records of Luetzelburgia (Leguminosae), a genus of 15 species of South American trees:

01_get_standardized_records_script.R downloads the records from GBIF, REFLORA and JABOT, combines and standardizes them, and saves a spreadsheet;
02_write_examined_specimens_script.R writes the lists of examined specimens from this spreadsheet, in the format of several journals.

Both scripts are run from an RStudio project, e.g. build_herbarium_records_database, with the scripts in a folder scripts and the results saved in a folder results.

Script 1: get standardized records

The records are downloaded with plantR (GBIF), refloraR (REFLORA Virtual Herbarium) and jabotR (JABOT, Rio de Janeiro Botanical Garden). The list of accepted species comes from Kew’s WCVP, with the package rWCVPdata.

# 01_get_standardized_records_script.R

library(barRoso)
library(refloraR)
library(jabotR)
library(plantR)
library(dplyr)
library(openxlsx)
library(rWCVPdata)

# Create a folder for the results of today
dir <- "results"
folder_name <- paste0(dir, "/", format(Sys.time(), "%d%b%Y"))
if (!dir.exists(folder_name)) dir.create(folder_name, recursive = TRUE)

# All accepted species of Luetzelburgia in WCVP
wcvp_names <- rWCVPdata::wcvp_names
luetz_wcvp <- subset(wcvp_names,
                     genus == "Luetzelburgia" &
                       taxon_rank == "Species" &
                       taxon_status == "Accepted")
luetz_list <- sort(luetz_wcvp$taxon_name)

# GBIF: one search for each species, skipping species without records
data_gbif <- lapply(luetz_list, function(x) {
  gbif <- tryCatch(plantR::rgbif2(species = x, n.records = 5000, force = TRUE,
                                  remove_na = FALSE, save = FALSE, compress = FALSE),
                   error = function(e) NULL)
  if (!is.data.frame(gbif) || nrow(gbif) == 0) return(NULL)
  gbif
})
names(data_gbif) <- luetz_list
data_gbif <- dplyr::bind_rows(data_gbif, .id = "original_search")

# REFLORA Virtual Herbarium
data_reflora <- refloraR::reflora_records(repatriated = TRUE, taxon = "Luetzelburgia",
                                          indets = TRUE, updates = TRUE,
                                          verbose = TRUE, save = FALSE)
unlink("reflora_download/", recursive = TRUE, force = TRUE)

# JABOT
data_jabot <- jabotR::jabot_records(taxon = "Luetzelburgia", indets = TRUE,
                                    updates = TRUE, verbose = TRUE, save = FALSE)
unlink("jabot_download/", recursive = TRUE, force = TRUE)

# Combine the sources, keeping GBIF for the herbaria present in more than one
records_list <- list(GBIF = data_gbif,
                     REFLORA = data_reflora,
                     JABOT = data_jabot)
data_all <- barRoso::barroso_cat(list_sources = records_list,
                                 keep_source = "GBIF")

# Standardize collectors, herbaria, places and taxa, and remove duplicates
data_all_clean <- barRoso::barroso_std(data_all,
                                       unvouchered = TRUE,
                                       delunkcoll = TRUE,
                                       flag_duplicates = TRUE,
                                       rm_duplicates = TRUE)

# Fix and flag coordinates
data_all_clean <- barRoso::std_coordinates(data_all_clean)

# Save the database
openxlsx::write.xlsx(data_all_clean,
                     paste0(folder_name, "/Luetzelburgia_herbarium_records.xlsx"))

In November 2026, this script found 3,215 records in GBIF, 1,093 in REFLORA and 351 in JABOT:

#> barroso_cat: removing 1089 records of 39 herbaria from REFLORA also present in GBIF
#> barroso_cat: removing 337 records of 10 herbaria from JABOT also present in GBIF

After the standardization, without duplicates, unvouchered records and records of unknown collectors, the database has 1,202 records of 15 species, from Brazil (1,155), Bolivia (35), Colombia (3) and Guyana (3).

Script 2: write the examined specimens

The second script reads the spreadsheet saved by the first one, and writes one .docx file for each journal, in the same folder:

# 02_write_examined_specimens_script.R

library(barRoso)
library(openxlsx)

# The most recent spreadsheet within the results folder
dir <- "results"
records_files <- list.files(dir,
                            pattern = "^Luetzelburgia_herbarium_records[.]xlsx$",
                            recursive = TRUE,
                            full.names = TRUE)
records_file <- records_files[which.max(file.mtime(records_files))]
folder_name <- dirname(records_file)

# Read the records once, so the spreadsheet is not read again for each journal
data_records <- openxlsx::read.xlsx(records_file)

# One Word (.docx) file for each journal. To write just some species, use the
# argument species, e.g. species = c("Luetzelburgia andina", "Luetzelburgia harleyi")
journals <- c("Annals of the Missouri Botanical Garden",
              "Systematic Botany",
              "Kew Bulletin",
              "Rodriguesia")

for (journal in journals) {
  barRoso::barroso_write_specimens(
    df = data_records,
    species = NULL,
    journal = journal,
    dir = folder_name,
    filename = paste0("Luetzelburgia_examined_specimens_", gsub("\\s+", "_", journal))
  )
}
#> Skipping 5 records not identified to species
#> Examined specimens of 15 species (1131 specimens) written in the format of
#> Annals of the Missouri Botanical Garden to:
#> results/01Nov2026/Luetzelburgia_examined_specimens_Annals_of_the_Missouri_Botanical_Garden.docx
#> ...

For each species, the file has the species name and its author, followed by a paragraph with its specimens, e.g. in the format of Systematic Botany:

Luetzelburgia auriculata (Allemão) Ducke

Representative Specimens Examined—Brazil. —Bahia: Barreiras, Prainha, margem do Rio das Ondas, 12°08′48″S, 45°00′55″W, 1 May 2009, D. Cardoso 2628 (HUEFS). —Ceará: Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21 Jan 2009, D. Cardoso et al. 2379 (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas, 5°09′44″S, 40°53′18″W, 15 Jun 2014, F.H.F. Nascimento 1402 (HUEFS).

Arguments

Argument	Description
`df` or `path`	The records, as a data frame or an .xlsx/.csv file, in Darwin Core format (e.g. the output of `barroso_std()` or `barroso_dwc()`)
`species`	Species to write, with or without authors (e.g. `"Luetzelburgia andina"`); `NULL` for all species
`journal`	The journal whose format is followed, one of the 24 journals below
`header`	Text of the header, e.g. `"Paratypes"` or `"Additional specimens examined"`; `NULL` for the header of the journal, `""` for no header
`language`	Language of the paper: `"en"` (English), `"pt"` (Portuguese) or `"es"` (Spanish), for the header (e.g. `"Material examinado"`), months, countries (`"BRASIL"`), phenology (`"fl. e fr."`, `"est."`) and the west hemisphere in Spanish (`"O"`)
`catalog_numbers`	If `TRUE`, the catalog number is written after each herbarium, e.g. `"IAC no. 14754"` in Brittonia
`dir`, `filename`	Folder and name of the .docx file
`font_family`, `font_size`	Font of the document

Journal formats

The journal argument lists all available formats, each checked against recent papers of the journal, including the bold, italics and small capitals used. The journal can be written in any case, with or without accents, and abbreviated, e.g. "systematic botany", "Kew", "Edinburgh" or "Rodriguesia". The examples below show the same records of Luetzelburgia auriculata in each format, as written in the .docx file. The records of D. Cardoso et al. 2379 and D. Machado Cardoso 2379 are duplicates of the same collection, and are cited once, with all their herbaria.

Systematic Botany

With header in bold italics, countries in bold, states in small capitals after an em dash, and collectors with numbers in italics:

Representative Specimens Examined—Brazil. —Bahia: Barreiras, Prainha, margem do Rio das Ondas, 12°08′48″S, 45°00′55″W, 1 May 2009, D. Cardoso 2628 (HUEFS). —Ceará: Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21 Jan 2009, D. Cardoso et al. 2379 (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas, 5°09′44″S, 40°53′18″W, 15 Jun 2014, F.H.F. Nascimento 1402 (HUEFS).

Acta Amazonica

With header in bold, fields separated by periods, elevation like “Elev. 140m”, phenology as a field before the date (e.g. “Fl. 15 April 1987”), and collectors not in italics:

Additional specimens examined: BRAZIL. Bahia: Barreiras, Prainha, margem do Rio das Ondas. 12º08’48”S, 45º00’55”W. 1 May 2009, D. Cardoso 2628 (HUEFS). Ceará: Caucaia, Lagoa dos Caetanos. 3ºS, 38ºW. 21 January 2009, D. Cardoso et al. 2379 (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas. 5º09’44”S, 40º53’18”W. 15 June 2014, F.H.F. Nascimento 1402 (HUEFS).

Acta Botanica Brasilica

With header, countries and states in bold, collectors in italics, herbaria marked as seen, and municipalities separated by periods:

Additional specimens examined: BRAZIL. Bahia: Barreiras, Prainha, margem do Rio das Ondas, 12°08’48” S, 45°00’55” W, 1 May 2009, D. Cardoso 2628 (HUEFS!). Ceará: Caucaia, Lagoa dos Caetanos, 3° S, 38° W, 21 January 2009, D. Cardoso et al. 2379 (ASE!, BOTU!, CNMT!, HDJF!, HEPH!, HUCS!, HUEFS!, HUESB!, SORO!, UB!, UESC!, VIC!). Crateús, RPPN Serra das Almas, 5°09’44” S, 40°53’18” W, 15 June 2014, F.H.F. Nascimento 1402 (HUEFS!).

Acta Botanica Mexicana

With states followed by a comma, municipalities after “municipio”, elevation before the coordinates, dates with Roman numerals, two collectors joined by “and”, and “loc. cit.” for the same place as the previous specimen:

Specimens examined: BRAZIL. Bahia, municipio Barreiras, Prainha, margem do Rio das Ondas, 12°08’48’‘S, 45°00’55’‘W, 1.V.2009, D. Cardoso 2628 (HUEFS). Ceará, municipio Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21.I.2009, D. Cardoso et al. 2379 (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); municipio Crateús, RPPN Serra das Almas, 5°09’44’‘S, 40°53’18’’W, 15.VI.2014, F. H. F. Nascimento 1402 (HUEFS).

Annals of the Missouri Botanical Garden

With states in bold, and collectors with spaced initials in italics:

Additional specimens examined. BRAZIL. Bahia: Barreiras, Prainha, margem do Rio das Ondas, 12°08′48″S, 45°00′55″W, 1 May 2009, D. Cardoso 2628 (HUEFS). Ceará: Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21 Jan. 2009, D. Cardoso et al. 2379 (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas, 5°09′44″S, 40°53′18″W, 15 June 2014, F. H. F. Nascimento 1402 (HUEFS).

Botanical Journal of the Linnean Society

With header in italics, states in bold, dates like “16.vi.2007”, and each municipality cited once:

Representative specimens examined: BRAZIL. Bahia: Barreiras, Prainha, margem do Rio das Ondas, 12°08′48″S, 45°00′55″W, 1.v.2009, D. Cardoso 2628 (HUEFS). Ceará: Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21.i.2009, D. Cardoso et al. 2379 (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas, 5°09′44″S, 40°53′18″W, 15.vi.2014, F.H.F. Nascimento 1402 (HUEFS).

Botany Letters

With header and countries in bold, states in uppercase after an em dash, full months, and collectors in italics followed by numbers in roman:

Representative specimens examined: BRAZIL. — BAHIA: Barreiras, Prainha, margem do Rio das Ondas, 12°08′48″S, 45°00′55″W, 1 May 2009, D. Cardoso 2628 (HUEFS). — CEARÁ: Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21 January 2009, D. Cardoso et al. 2379 (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas, 5°09′44″S, 40°53′18″W, 15 June 2014, F.H.F. Nascimento 1402 (HUEFS).

Brazilian Journal of Botany

With collectors cited by surname, and days with two digits:

Selected additional specimens—BRAZIL. Bahia: Barreiras, Prainha, margem do Rio das Ondas, 12°08′48″S, 45°00′55″W, 01 May 2009, Cardoso 2628 (HUEFS). Ceará: Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21 Jan 2009, Cardoso et al. 2379 (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas, 5°09′44″S, 40°53′18″W, 15 Jun 2014, Nascimento 1402 (HUEFS).

Brittonia

With countries and states in bold, phenology between square brackets, and “et al.” not in italics:

Additional specimens examined.—BRAZIL. Bahia: Barreiras, Prainha, margem do Rio das Ondas, 12°08′48″S, 45°00′55″W, 1 May 2009, D. Cardoso 2628 (HUEFS). Ceará: Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21 Jan 2009, D. Cardoso et al. 2379 (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas, 5°09′44″S, 40°53′18″W, 15 Jun 2014, F. H. F. Nascimento 1402 (HUEFS).

Candollea

With countries in bold small capitals, states in bold, and dates with Roman numerals:

Additional specimens examined. – Brazil. Bahia: Barreiras, Prainha, margem do Rio das Ondas, 12°08’48”S 45°00’55”W, 1.V.2009, Cardoso 2628 (HUEFS). Ceará: Caucaia, Lagoa dos Caetanos, 3°S 38°W, 21.I.2009, Cardoso et al. 2379 (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas, 5°09’44”S 40°53’18”W, 15.VI.2014, Nascimento 1402 (HUEFS).

Darwiniana

In Spanish (language = "es"), with header in a sans-serif font, states in bold followed by a comma, “O” (oeste) for west, elevation in “m s. m.”, dates like “11-XII-1993”, and “ídem” for the same place as the previous specimen:

Material examinado: BRASIL. Bahia, Barreiras, Prainha, margem do Rio das Ondas, 12º08’48” S, 45º00’55” O, 1-V-2009, D. Cardoso 2628 (HUEFS). Ceará, Caucaia, Lagoa dos Caetanos, 3º S, 38º O, 21-I-2009, D. Cardoso et al. 2379 (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas, 5º09’44” S, 40º53’18” O, 15-VI-2014, F.H.F. Nascimento 1402 (HUEFS).

Edinburgh Journal of Botany

With states in bold, just the surname of collectors in italics, and municipalities separated by periods:

Additional specimens examined. BRAZIL. Bahia: Barreiras, Prainha, margem do Rio das Ondas, 12°08′48″S, 45°00′55″W, 1 v 2009, Cardoso 2628 (HUEFS). Ceará: Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21 i 2009, Cardoso et al. 2379 (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC). Crateús, RPPN Serra das Almas, 5°09′44″S, 40°53′18″W, 15 vi 2014, Nascimento 1402 (HUEFS).

Feddes Repertorium

With header, countries and states in bold, just the surname of collectors in italics, and catalog numbers between square brackets (with catalog_numbers = TRUE, e.g. “K [K002885503]”):

Additional specimens: BRAZIL. Bahia: Barreiras, Prainha, margem do Rio das Ondas, 12°08′48″S, 45°00′55″W, 1 May 2009, Cardoso 2628 (HUEFS). Ceará: Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21 Jan. 2009, Cardoso et al. 2379 (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas, 5°09′44″S, 40°53′18″W, 15 June 2014, Nascimento 1402 (HUEFS).

Hoehnea

In Portuguese (language = "pt"), with states in small capitals, dates like “6-VI-1984”, collectors with numbers in italics, and “l.c.” for the municipality of the previous specimen:

Material examinado: BRASIL. Bahia: Barreiras, Prainha, margem do Rio das Ondas, 12°08’48”S, 45°00’55”W, 1-V-2009, D. Cardoso 2628 (HUEFS). Ceará: Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21-I-2009, D. Cardoso et al. 2379 (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas, 5°09’44”S, 40°53’18”W, 15-VI-2014, F.H.F. Nascimento 1402 (HUEFS).

Kew Bulletin

With header and countries in bold uppercase Arial, and numbers not in italics:

SPECIMENS EXAMINED. BRAZIL. Bahia: Barreiras, Prainha, margem do Rio das Ondas, 12°08’48”S, 45°00’55”W, 1 May 2009, D. Cardoso 2628 (HUEFS). Ceará: Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21 Jan. 2009, D. Cardoso et al. 2379 (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas, 5°09’44”S, 40°53’18”W, 15 June 2014, F. H. F. Nascimento 1402 (HUEFS).

Nordic Journal of Botany

With the species cited in the paragraph of its specimens, under a single header:

Additional specimen examined

Luetzelburgia auriculata – Brazil, Bahia, Barreiras, Prainha, margem do Rio das Ondas, 12°08′48″S, 45°00′55″W, 1 May 2009, Cardoso 2628 (HUEFS). Ceará, Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21 Jan. 2009, Cardoso et al. 2379 (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC). Crateús, RPPN Serra das Almas, 5°09′44″S, 40°53′18″W, 15 June 2014, Nascimento 1402 (HUEFS).

Phytotaxa

With municipalities followed by a colon:

Additional specimens examined:―BRAZIL. Bahia: Barreiras: Prainha, margem do Rio das Ondas, 12°08’48”S, 45°00’55”W, 1 May 2009, D. Cardoso 2628 (HUEFS). Ceará: Caucaia: Lagoa dos Caetanos, 3°S, 38°W, 21 January 2009, D. Cardoso et al. 2379 (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús: RPPN Serra das Almas, 5°09’44”S, 40°53’18”W, 15 June 2014, F.H.F. Nascimento 1402 (HUEFS).

PhytoKeys

With countries in bold small capitals, states in bold, and municipalities after “Mun.”:

Additional specimens examined. Brazil. Bahia: Mun. Barreiras, Prainha, margem do Rio das Ondas, 12°08’48”S, 45°00’55”W, 1 May 2009, D. Cardoso 2628 (HUEFS). Ceará: Mun. Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21 Jan. 2009, D. Cardoso et al. 2379 (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Mun. Crateús, RPPN Serra das Almas, 5°09’44”S, 40°53’18”W, 15 June 2014, F.H.F. Nascimento 1402 (HUEFS).

Plant Ecology and Evolution

With specimens separated by bullets, fields by semicolons, and herbaria without parentheses:

Additional material examined. BRAZIL • Bahia, Barreiras, Prainha, margem do Rio das Ondas; 12°08’48”S, 45°00’55”W; 1 May 2009; Cardoso 2628; HUEFS • Ceará, Caucaia, Lagoa dos Caetanos; 3°S, 38°W; 21 Jan. 2009; Cardoso et al. 2379; ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC • Crateús, RPPN Serra das Almas; 5°09’44”S, 40°53’18”W; 15 June 2014; Nascimento 1402; HUEFS.

Plant Systematics and Evolution

With header in italics, countries and states in bold, elevation in “m a. s. l.” before the coordinates, coordinates with spaces (e.g. “8° 09′ 04″ S”), herbaria marked as seen, “et al.” not in italics, and specimens of the same municipality separated by periods:

Additional specimens examined: BRAZIL. Bahia. Barreiras, Prainha, margem do Rio das Ondas, 12° 08′ 48″ S, 45° 00′ 55″ W, 1 May 2009, D. Cardoso 2628 (HUEFS!). Ceará. Caucaia, Lagoa dos Caetanos, 3° S, 38° W, 21 Jan 2009, D. Cardoso et al. 2379 (ASE!, BOTU!, CNMT!, HDJF!, HEPH!, HUCS!, HUEFS!, HUESB!, SORO!, UB!, UESC!, VIC!); Crateús, RPPN Serra das Almas, 5° 09′ 44″ S, 40° 53′ 18″ W, 15 Jun 2014, F.H.F. Nascimento 1402 (HUEFS!).

Rodriguésia

With specimens separated by periods, and collections without number cited with the catalog number instead of “s.n.”:

Additional material examined: BRAZIL. BAHIA: Barreiras, Prainha, margem do Rio das Ondas, 12º08’48”S, 45º00’55”W, 1.V.2009, D. Cardoso 2628 (HUEFS). CEARÁ: Caucaia, Lagoa dos Caetanos, 3ºS, 38ºW, 21.I.2009, D. Cardoso et al. 2379 (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC). Crateús, RPPN Serra das Almas, 5º09’44”S, 40º53’18”W, 15.VI.2014, F.H.F. Nascimento 1402 (HUEFS).

Systematics and Biodiversity

With header in bold:

Additional specimens analysed. BRAZIL. Bahia: Barreiras, Prainha, margem do Rio das Ondas, 12°08’48”S, 45°00’55”W, 1 May 2009, D. Cardoso 2628 (HUEFS). Ceará: Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21 January 2009, D. Cardoso et al. 2379 (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas, 5°09’44”S, 40°53’18”W, 15 June 2014, F. H. F. Nascimento 1402 (HUEFS).

Taxon

With states in uppercase, “& al.”, and elevation in “m a.s.l.”:

Additional specimens examined. – BRAZIL. BAHIA: Barreiras, Prainha, margem do Rio das Ondas, 12°08′48″S, 45°00′55″W, 1 May 2009, D. Cardoso 2628 (HUEFS); CEARÁ: Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21 Jan 2009, D. Cardoso & al. 2379 (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas, 5°09′44″S, 40°53′18″W, 15 Jun 2014, F.H.F. Nascimento 1402 (HUEFS).

Willdenowia

With a single header before all species, countries and states in small capitals, and each municipality cited once, after “Municipality”:

Additional specimens examined.

Brazil: Bahia: Municipality Barreiras, Prainha, margem do Rio das Ondas, 12°08’48”S, 45°00’55”W, 1 May 2009, D. Cardoso 2628 (HUEFS). — Ceará: Municipality Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21 Jan 2009, D. Cardoso & al. 2379 (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC). Municipality Crateús, RPPN Serra das Almas, 5°09’44”S, 40°53’18”W, 15 Jun 2014, F. H. F. Nascimento 1402 (HUEFS).

How the specimens are written

Columns. The function uses the Darwin Core columns species, country, stateProvince, municipality (or county, where GBIF keeps the municipalities of Brazil), locality, decimalLatitude, decimalLongitude, minimumElevationInMeters, maximumElevationInMeters, day, month, year, phenology (or reproductiveCondition), recordedBy, addCollector, recordNumber, collectionCode, catalogNumber. Missing columns are just skipped.
Collectors. The names standardized by barroso_std() (e.g. D. B. O. S. Cardoso) are written as each journal cites them. The additional collector (addCollector) is written as et al. (& al. in Taxon) or as the name of the second collector, e.g. R.M. Harley & A.M. Giulietti.

Phenology. The phenology in the column phenology (as in records from REFLORA and JABOT) or reproductiveCondition, e.g. fl, fl, fr, flower, fruit or st, is written as in each journal:

Format	Journals
`(fl, fr)`	Systematic Botany, Phytotaxa, Edinburgh Journal of Botany, Acta Botanica Mexicana, Darwiniana (`(veg, fl)`), and journals whose papers show no phenology (Botanical Journal of the Linnean Society, Feddes Repertorium, PhytoKeys, Plant Ecology and Evolution, Systematics and Biodiversity, Willdenowia)
`(fl., fr.)`	Taxon, Kew Bulletin, Acta Botanica Brasilica (after a comma), Botany Letters, Hoehnea, Plant Systematics and Evolution
`(fl./fr.)`	Annals of the Missouri Botanical Garden
`(fl. fr.)`	Nordic Journal of Botany
`(fl and fr)`	Brazilian Journal of Botany
`[fl, fr]`	Brittonia
`fl. and fr.`	Rodriguésia, and `fl., fr.` in Candollea, without brackets
`Fl., fr.`	Acta Amazonica, before the date

In Portuguese and Spanish, and becomes e or y, and sterile (st) becomes est.

Repeated places. Some journals do not repeat the place of the previous specimen: l.c. for the same municipality in Hoehnea, and loc. cit. or ídem for the same locality in Acta Botanica Mexicana and Darwiniana.
Duplicates. Duplicates of the same collection (same species, collector surname and number, or same collector, date and locality when there is no number) are written once, with all their herbaria in alphabetical order, including those found by barroso_flag_duplicates() (duplicateCollectionCodes).
Types. The type status is not written, as types are cited apart from the examined specimens.
Collections without number. The catalog number of the first herbarium is written, e.g. R. Spruce s.n. (K000892474, LD), so that the specimen can be found. Use catalog_numbers = TRUE to write the catalog numbers of all herbaria.
Order. Specimens are ordered by country, state, municipality and date. Records not identified to species are skipped.
Species. For each species, a heading with the species name in italics and its author (from scientificNameAuthorship, acceptedScientificName or scientificName) is followed by the paragraph of its specimens.

The function returns, invisibly, a data frame with the species and their specimens, one per line, which can be checked in R:

res <- barroso_write_specimens(path = "results/01Nov2026/Luetzelburgia_herbarium_records.xlsx",
                               species = "Luetzelburgia andina", verbose = FALSE)
cat(res$specimens_text)

Tips

Standardize the database first with barroso_std(), so that collectors, herbarium acronyms and places are written consistently, and duplicates are removed.
Check the countries and states of the database before writing: the specimens are cited as they are in the data.
For the paratypes of a new species, use species and header = "Paratypes".

--- title: "Write Lists of Examined Specimens" format: html: toc: true toc-depth: 2 --- ## Overview Taxonomic revisions and descriptions of new species cite the specimens examined for each species, in a format that differs from journal to journal: the header, the case and format (bold, italics, small capitals) of countries, states and collectors, how dates and coordinates are written, and how herbaria are listed. The function `barroso_write_specimens()` writes these lists for one, several or all species of a database of herbarium records into a Word (.docx) file, in the format of a chosen journal. This article goes through the whole workflow with two R scripts, using the herbarium records of *Luetzelburgia* (Leguminosae), a genus of 15 species of South American trees: 1. `01_get_standardized_records_script.R` downloads the records from GBIF, REFLORA and JABOT, combines and standardizes them, and saves a spreadsheet; 2. `02_write_examined_specimens_script.R` writes the lists of examined specimens from this spreadsheet, in the format of several journals. Both scripts are run from an RStudio project, e.g. `build_herbarium_records_database`, with the scripts in a folder `scripts` and the results saved in a folder `results`. ## Script 1: get standardized records The records are downloaded with [plantR](https://github.com/LimaRAF/plantR) (GBIF), [refloraR](https://dboslab.github.io/refloraR-website/) (REFLORA Virtual Herbarium) and [jabotR](https://dboslab.github.io/jabotR-website/) (JABOT, Rio de Janeiro Botanical Garden). The list of accepted species comes from Kew's [WCVP](https://powo.science.kew.org/), with the package `rWCVPdata`. ```r # 01_get_standardized_records_script.R library(barRoso) library(refloraR) library(jabotR) library(plantR) library(dplyr) library(openxlsx) library(rWCVPdata) # Create a folder for the results of today dir <- "results" folder_name <- paste0(dir, "/", format(Sys.time(), "%d%b%Y")) if (!dir.exists(folder_name)) dir.create(folder_name, recursive = TRUE) # All accepted species of Luetzelburgia in WCVP wcvp_names <- rWCVPdata::wcvp_names luetz_wcvp <- subset(wcvp_names, genus == "Luetzelburgia" & taxon_rank == "Species" & taxon_status == "Accepted") luetz_list <- sort(luetz_wcvp$taxon_name) # GBIF: one search for each species, skipping species without records data_gbif <- lapply(luetz_list, function(x) { gbif <- tryCatch(plantR::rgbif2(species = x, n.records = 5000, force = TRUE, remove_na = FALSE, save = FALSE, compress = FALSE), error = function(e) NULL) if (!is.data.frame(gbif) || nrow(gbif) == 0) return(NULL) gbif }) names(data_gbif) <- luetz_list data_gbif <- dplyr::bind_rows(data_gbif, .id = "original_search") # REFLORA Virtual Herbarium data_reflora <- refloraR::reflora_records(repatriated = TRUE, taxon = "Luetzelburgia", indets = TRUE, updates = TRUE, verbose = TRUE, save = FALSE) unlink("reflora_download/", recursive = TRUE, force = TRUE) # JABOT data_jabot <- jabotR::jabot_records(taxon = "Luetzelburgia", indets = TRUE, updates = TRUE, verbose = TRUE, save = FALSE) unlink("jabot_download/", recursive = TRUE, force = TRUE) # Combine the sources, keeping GBIF for the herbaria present in more than one records_list <- list(GBIF = data_gbif, REFLORA = data_reflora, JABOT = data_jabot) data_all <- barRoso::barroso_cat(list_sources = records_list, keep_source = "GBIF") # Standardize collectors, herbaria, places and taxa, and remove duplicates data_all_clean <- barRoso::barroso_std(data_all, unvouchered = TRUE, delunkcoll = TRUE, flag_duplicates = TRUE, rm_duplicates = TRUE) # Fix and flag coordinates data_all_clean <- barRoso::std_coordinates(data_all_clean) # Save the database openxlsx::write.xlsx(data_all_clean, paste0(folder_name, "/Luetzelburgia_herbarium_records.xlsx")) ``` In November 2026, this script found 3,215 records in GBIF, 1,093 in REFLORA and 351 in JABOT: ``` #> barroso_cat: removing 1089 records of 39 herbaria from REFLORA also present in GBIF #> barroso_cat: removing 337 records of 10 herbaria from JABOT also present in GBIF ``` After the standardization, without duplicates, unvouchered records and records of unknown collectors, the database has 1,202 records of 15 species, from Brazil (1,155), Bolivia (35), Colombia (3) and Guyana (3). ## Script 2: write the examined specimens The second script reads the spreadsheet saved by the first one, and writes one .docx file for each journal, in the same folder: ```r # 02_write_examined_specimens_script.R library(barRoso) library(openxlsx) # The most recent spreadsheet within the results folder dir <- "results" records_files <- list.files(dir, pattern = "^Luetzelburgia_herbarium_records[.]xlsx$", recursive = TRUE, full.names = TRUE) records_file <- records_files[which.max(file.mtime(records_files))] folder_name <- dirname(records_file) # Read the records once, so the spreadsheet is not read again for each journal data_records <- openxlsx::read.xlsx(records_file) # One Word (.docx) file for each journal. To write just some species, use the # argument species, e.g. species = c("Luetzelburgia andina", "Luetzelburgia harleyi") journals <- c("Annals of the Missouri Botanical Garden", "Systematic Botany", "Kew Bulletin", "Rodriguesia") for (journal in journals) { barRoso::barroso_write_specimens( df = data_records, species = NULL, journal = journal, dir = folder_name, filename = paste0("Luetzelburgia_examined_specimens_", gsub("\\s+", "_", journal)) ) } #> Skipping 5 records not identified to species #> Examined specimens of 15 species (1131 specimens) written in the format of #> Annals of the Missouri Botanical Garden to: #> results/01Nov2026/Luetzelburgia_examined_specimens_Annals_of_the_Missouri_Botanical_Garden.docx #> ... ``` For each species, the file has the species name and its author, followed by a paragraph with its specimens, e.g. in the format of Systematic Botany: > ***Luetzelburgia auriculata*** **(Allemão) Ducke** > > ***Representative Specimens Examined***—**Brazil.** —Bahia: Barreiras, Prainha, margem do Rio das Ondas, 12°08′48″S, 45°00′55″W, 1 May 2009, *D. Cardoso 2628* (HUEFS). —Ceará: Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21 Jan 2009, *D. Cardoso et al. 2379* (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas, 5°09′44″S, 40°53′18″W, 15 Jun 2014, *F.H.F. Nascimento 1402* (HUEFS). ## Arguments | Argument | Description | |---|---| | `df` or `path` | The records, as a data frame or an .xlsx/.csv file, in Darwin Core format (e.g. the output of `barroso_std()` or `barroso_dwc()`) | | `species` | Species to write, with or without authors (e.g. `"Luetzelburgia andina"`); `NULL` for all species | | `journal` | The journal whose format is followed, one of the 24 journals below | | `header` | Text of the header, e.g. `"Paratypes"` or `"Additional specimens examined"`; `NULL` for the header of the journal, `""` for no header | | `language` | Language of the paper: `"en"` (English), `"pt"` (Portuguese) or `"es"` (Spanish), for the header (e.g. `"Material examinado"`), months, countries (`"BRASIL"`), phenology (`"fl. e fr."`, `"est."`) and the west hemisphere in Spanish (`"O"`) | | `catalog_numbers` | If `TRUE`, the catalog number is written after each herbarium, e.g. `"IAC no. 14754"` in Brittonia | | `dir`, `filename` | Folder and name of the .docx file | | `font_family`, `font_size` | Font of the document | ## Journal formats The `journal` argument lists all available formats, each checked against recent papers of the journal, including the bold, italics and small capitals used. The journal can be written in any case, with or without accents, and abbreviated, e.g. `"systematic botany"`, `"Kew"`, `"Edinburgh"` or `"Rodriguesia"`. The examples below show the same records of *Luetzelburgia auriculata* in each format, as written in the .docx file. The records of *D. Cardoso et al. 2379* and *D. Machado Cardoso 2379* are duplicates of the same collection, and are cited once, with all their herbaria. ### Systematic Botany With header in bold italics, countries in bold, states in small capitals after an em dash, and collectors with numbers in italics: > ***Representative Specimens Examined***—**Brazil.** —Bahia: Barreiras, Prainha, margem do Rio das Ondas, 12°08′48″S, 45°00′55″W, 1 May 2009, *D. Cardoso 2628* (HUEFS). —Ceará: Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21 Jan 2009, *D. Cardoso et al. 2379* (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas, 5°09′44″S, 40°53′18″W, 15 Jun 2014, *F.H.F. Nascimento 1402* (HUEFS). ### Acta Amazonica With header in bold, fields separated by periods, elevation like "Elev. 140m", phenology as a field before the date (e.g. "Fl. 15 April 1987"), and collectors not in italics: > **Additional specimens examined:** BRAZIL. Bahia: Barreiras, Prainha, margem do Rio das Ondas. 12º08’48”S, 45º00’55”W. 1 May 2009, D. Cardoso 2628 (HUEFS). Ceará: Caucaia, Lagoa dos Caetanos. 3ºS, 38ºW. 21 January 2009, D. Cardoso et al. 2379 (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas. 5º09’44”S, 40º53’18”W. 15 June 2014, F.H.F. Nascimento 1402 (HUEFS). ### Acta Botanica Brasilica With header, countries and states in bold, collectors in italics, herbaria marked as seen, and municipalities separated by periods: > **Additional specimens examined: BRAZIL. Bahia:** Barreiras, Prainha, margem do Rio das Ondas, 12°08’48” S, 45°00’55” W, 1 May 2009, *D. Cardoso 2628* (HUEFS!). **Ceará:** Caucaia, Lagoa dos Caetanos, 3° S, 38° W, 21 January 2009, *D. Cardoso et al. 2379* (ASE!, BOTU!, CNMT!, HDJF!, HEPH!, HUCS!, HUEFS!, HUESB!, SORO!, UB!, UESC!, VIC!). Crateús, RPPN Serra das Almas, 5°09’44” S, 40°53’18” W, 15 June 2014, *F.H.F. Nascimento 1402* (HUEFS!). ### Acta Botanica Mexicana With states followed by a comma, municipalities after "municipio", elevation before the coordinates, dates with Roman numerals, two collectors joined by "and", and "loc. cit." for the same place as the previous specimen: > Specimens examined: BRAZIL. Bahia, municipio Barreiras, Prainha, margem do Rio das Ondas, 12°08'48''S, 45°00'55''W, 1.V.2009, *D. Cardoso 2628* (HUEFS). Ceará, municipio Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21.I.2009, *D. Cardoso et al. 2379* (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); municipio Crateús, RPPN Serra das Almas, 5°09'44''S, 40°53'18''W, 15.VI.2014, *F. H. F. Nascimento 1402* (HUEFS). ### Annals of the Missouri Botanical Garden With states in bold, and collectors with spaced initials in italics: > *Additional specimens examined.* BRAZIL. **Bahia:** Barreiras, Prainha, margem do Rio das Ondas, 12°08′48″S, 45°00′55″W, 1 May 2009, *D. Cardoso 2628* (HUEFS). **Ceará:** Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21 Jan. 2009, *D. Cardoso et al. 2379* (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas, 5°09′44″S, 40°53′18″W, 15 June 2014, *F. H. F. Nascimento 1402* (HUEFS). ### Botanical Journal of the Linnean Society With header in italics, states in bold, dates like "16.vi.2007", and each municipality cited once: > *Representative specimens examined:* BRAZIL. **Bahia**: Barreiras, Prainha, margem do Rio das Ondas, 12°08′48″S, 45°00′55″W, 1.v.2009, *D. Cardoso 2628* (HUEFS). **Ceará**: Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21.i.2009, *D. Cardoso et al. 2379* (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas, 5°09′44″S, 40°53′18″W, 15.vi.2014, *F.H.F. Nascimento 1402* (HUEFS). ### Botany Letters With header and countries in bold, states in uppercase after an em dash, full months, and collectors in italics followed by numbers in roman: > **Representative specimens examined: BRAZIL.** — BAHIA: Barreiras, Prainha, margem do Rio das Ondas, 12°08′48″S, 45°00′55″W, 1 May 2009, *D. Cardoso* 2628 (HUEFS). — CEARÁ: Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21 January 2009, *D. Cardoso et al.* 2379 (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas, 5°09′44″S, 40°53′18″W, 15 June 2014, *F.H.F. Nascimento* 1402 (HUEFS). ### Brazilian Journal of Botany With collectors cited by surname, and days with two digits: > *Selected additional specimens*—BRAZIL. Bahia: Barreiras, Prainha, margem do Rio das Ondas, 12°08′48″S, 45°00′55″W, 01 May 2009, *Cardoso 2628* (HUEFS). Ceará: Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21 Jan 2009, *Cardoso et al. 2379* (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas, 5°09′44″S, 40°53′18″W, 15 Jun 2014, *Nascimento 1402* (HUEFS). ### Brittonia With countries and states in bold, phenology between square brackets, and "et al." not in italics: > ***Additional specimens examined***.—**BRAZIL. Bahia:** Barreiras, Prainha, margem do Rio das Ondas, 12°08′48″S, 45°00′55″W, 1 May 2009, *D. Cardoso 2628* (HUEFS). **Ceará:** Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21 Jan 2009, *D. Cardoso* et al. *2379* (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas, 5°09′44″S, 40°53′18″W, 15 Jun 2014, *F. H. F. Nascimento 1402* (HUEFS). ### Candollea With countries in bold small capitals, states in bold, and dates with Roman numerals: > *Additional specimens examined.* – **Brazil.** **Bahia:** Barreiras, Prainha, margem do Rio das Ondas, 12°08'48"S 45°00'55"W, 1.V.2009, *Cardoso 2628* (HUEFS). **Ceará:** Caucaia, Lagoa dos Caetanos, 3°S 38°W, 21.I.2009, *Cardoso et al. 2379* (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas, 5°09'44"S 40°53'18"W, 15.VI.2014, *Nascimento 1402* (HUEFS). ### Darwiniana In Spanish (`language = "es"`), with header in a sans-serif font, states in bold followed by a comma, "O" (oeste) for west, elevation in "m s. m.", dates like "11-XII-1993", and "ídem" for the same place as the previous specimen: > Material examinado: BRASIL. **Bahia**, Barreiras, Prainha, margem do Rio das Ondas, 12º08’48” S, 45º00’55” O, 1-V-2009, *D. Cardoso 2628* (HUEFS). **Ceará**, Caucaia, Lagoa dos Caetanos, 3º S, 38º O, 21-I-2009, *D. Cardoso et al. 2379* (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas, 5º09’44” S, 40º53’18” O, 15-VI-2014, *F.H.F. Nascimento 1402* (HUEFS). ### Edinburgh Journal of Botany With states in bold, just the surname of collectors in italics, and municipalities separated by periods: > *Additional specimens examined.* **BRAZIL. Bahia**: Barreiras, Prainha, margem do Rio das Ondas, 12°08′48″S, 45°00′55″W, 1 v 2009, *Cardoso* 2628 (HUEFS). **Ceará**: Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21 i 2009, *Cardoso* et al. 2379 (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC). Crateús, RPPN Serra das Almas, 5°09′44″S, 40°53′18″W, 15 vi 2014, *Nascimento* 1402 (HUEFS). ### Feddes Repertorium With header, countries and states in bold, just the surname of collectors in italics, and catalog numbers between square brackets (with `catalog_numbers = TRUE`, e.g. "K [K002885503]"): > **Additional specimens: BRAZIL. Bahia:** Barreiras, Prainha, margem do Rio das Ondas, 12°08′48″S, 45°00′55″W, 1 May 2009, *Cardoso* 2628 (HUEFS). **Ceará:** Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21 Jan. 2009, *Cardoso et al.* 2379 (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas, 5°09′44″S, 40°53′18″W, 15 June 2014, *Nascimento* 1402 (HUEFS). ### Hoehnea In Portuguese (`language = "pt"`), with states in small capitals, dates like "6-VI-1984", collectors with numbers in italics, and "l.c." for the municipality of the previous specimen: > Material examinado: BRASIL. Bahia: Barreiras, Prainha, margem do Rio das Ondas, 12°08’48”S, 45°00’55”W, 1-V-2009, *D. Cardoso 2628* (HUEFS). Ceará: Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21-I-2009, *D. Cardoso et al. 2379* (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas, 5°09’44”S, 40°53’18”W, 15-VI-2014, *F.H.F. Nascimento 1402* (HUEFS). ### Kew Bulletin With header and countries in bold uppercase Arial, and numbers not in italics: > **SPECIMENS EXAMINED. BRAZIL.** Bahia: Barreiras, Prainha, margem do Rio das Ondas, 12°08'48"S, 45°00'55"W, 1 May 2009, *D. Cardoso* 2628 (HUEFS). Ceará: Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21 Jan. 2009, *D. Cardoso et al.* 2379 (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas, 5°09'44"S, 40°53'18"W, 15 June 2014, *F. H. F. Nascimento* 1402 (HUEFS). ### Nordic Journal of Botany With the species cited in the paragraph of its specimens, under a single header: > **Additional specimen examined** > > *Luetzelburgia auriculata* – Brazil, Bahia, Barreiras, Prainha, margem do Rio das Ondas, 12°08′48″S, 45°00′55″W, 1 May 2009, Cardoso 2628 (HUEFS). Ceará, Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21 Jan. 2009, Cardoso et al. 2379 (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC). Crateús, RPPN Serra das Almas, 5°09′44″S, 40°53′18″W, 15 June 2014, Nascimento 1402 (HUEFS). ### Phytotaxa With municipalities followed by a colon: > **Additional specimens examined:―**BRAZIL. Bahia: Barreiras: Prainha, margem do Rio das Ondas, 12°08’48”S, 45°00’55”W, 1 May 2009, *D. Cardoso 2628* (HUEFS). Ceará: Caucaia: Lagoa dos Caetanos, 3°S, 38°W, 21 January 2009, *D. Cardoso et al. 2379* (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús: RPPN Serra das Almas, 5°09’44”S, 40°53’18”W, 15 June 2014, *F.H.F. Nascimento 1402* (HUEFS). ### PhytoKeys With countries in bold small capitals, states in bold, and municipalities after "Mun.": > **Additional specimens examined.** **Brazil.** **Bahia:** Mun. Barreiras, Prainha, margem do Rio das Ondas, 12°08'48"S, 45°00'55"W, 1 May 2009, *D. Cardoso 2628* (HUEFS). **Ceará:** Mun. Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21 Jan. 2009, *D. Cardoso et al. 2379* (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Mun. Crateús, RPPN Serra das Almas, 5°09'44"S, 40°53'18"W, 15 June 2014, *F.H.F. Nascimento 1402* (HUEFS). ### Plant Ecology and Evolution With specimens separated by bullets, fields by semicolons, and herbaria without parentheses: > **Additional material examined.** BRAZIL • Bahia, Barreiras, Prainha, margem do Rio das Ondas; 12°08’48”S, 45°00’55”W; 1 May 2009; *Cardoso 2628*; HUEFS • Ceará, Caucaia, Lagoa dos Caetanos; 3°S, 38°W; 21 Jan. 2009; *Cardoso et al. 2379*; ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC • Crateús, RPPN Serra das Almas; 5°09’44”S, 40°53’18”W; 15 June 2014; *Nascimento 1402*; HUEFS. ### Plant Systematics and Evolution With header in italics, countries and states in bold, elevation in "m a. s. l." before the coordinates, coordinates with spaces (e.g. "8° 09′ 04″ S"), herbaria marked as seen, "et al." not in italics, and specimens of the same municipality separated by periods: > *Additional specimens examined*: **BRAZIL. Bahia**. Barreiras, Prainha, margem do Rio das Ondas, 12° 08′ 48″ S, 45° 00′ 55″ W, 1 May 2009, *D. Cardoso 2628* (HUEFS!). **Ceará**. Caucaia, Lagoa dos Caetanos, 3° S, 38° W, 21 Jan 2009, *D. Cardoso* et al. *2379* (ASE!, BOTU!, CNMT!, HDJF!, HEPH!, HUCS!, HUEFS!, HUESB!, SORO!, UB!, UESC!, VIC!); Crateús, RPPN Serra das Almas, 5° 09′ 44″ S, 40° 53′ 18″ W, 15 Jun 2014, *F.H.F. Nascimento 1402* (HUEFS!). ### Rodriguésia With specimens separated by periods, and collections without number cited with the catalog number instead of "s.n.": > **Additional material examined:** BRAZIL. BAHIA: Barreiras, Prainha, margem do Rio das Ondas, 12º08’48”S, 45º00’55”W, 1.V.2009, *D. Cardoso 2628* (HUEFS). CEARÁ: Caucaia, Lagoa dos Caetanos, 3ºS, 38ºW, 21.I.2009, *D. Cardoso et al. 2379* (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC). Crateús, RPPN Serra das Almas, 5º09’44”S, 40º53’18”W, 15.VI.2014, *F.H.F. Nascimento 1402* (HUEFS). ### Systematics and Biodiversity With header in bold: > **Additional specimens analysed.** BRAZIL. Bahia: Barreiras, Prainha, margem do Rio das Ondas, 12°08'48"S, 45°00'55"W, 1 May 2009, *D. Cardoso 2628* (HUEFS). Ceará: Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21 January 2009, *D. Cardoso et al. 2379* (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas, 5°09'44"S, 40°53'18"W, 15 June 2014, *F. H. F. Nascimento 1402* (HUEFS). ### Taxon With states in uppercase, "& al.", and elevation in "m a.s.l.": > *Additional specimens examined.* – BRAZIL. BAHIA: Barreiras, Prainha, margem do Rio das Ondas, 12°08′48″S, 45°00′55″W, 1 May 2009, *D. Cardoso 2628* (HUEFS); CEARÁ: Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21 Jan 2009, *D. Cardoso & al. 2379* (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC); Crateús, RPPN Serra das Almas, 5°09′44″S, 40°53′18″W, 15 Jun 2014, *F.H.F. Nascimento 1402* (HUEFS). ### Willdenowia With a single header before all species, countries and states in small capitals, and each municipality cited once, after "Municipality": > **Additional specimens examined.** > > Brazil: Bahia: Municipality Barreiras, Prainha, margem do Rio das Ondas, 12°08'48"S, 45°00'55"W, 1 May 2009, *D. Cardoso 2628* (HUEFS). — Ceará: Municipality Caucaia, Lagoa dos Caetanos, 3°S, 38°W, 21 Jan 2009, *D. Cardoso & al. 2379* (ASE, BOTU, CNMT, HDJF, HEPH, HUCS, HUEFS, HUESB, SORO, UB, UESC, VIC). Municipality Crateús, RPPN Serra das Almas, 5°09'44"S, 40°53'18"W, 15 Jun 2014, *F. H. F. Nascimento 1402* (HUEFS). ## How the specimens are written - **Columns.** The function uses the Darwin Core columns `species`, `country`, `stateProvince`, `municipality` (or `county`, where GBIF keeps the municipalities of Brazil), `locality`, `decimalLatitude`, `decimalLongitude`, `minimumElevationInMeters`, `maximumElevationInMeters`, `day`, `month`, `year`, `phenology` (or `reproductiveCondition`), `recordedBy`, `addCollector`, `recordNumber`, `collectionCode`, `catalogNumber`. Missing columns are just skipped. - **Collectors.** The names standardized by `barroso_std()` (e.g. `D. B. O. S. Cardoso`) are written as each journal cites them. The additional collector (`addCollector`) is written as `et al.` (`& al.` in Taxon) or as the name of the second collector, e.g. `R.M. Harley & A.M. Giulietti`. - **Phenology.** The phenology in the column `phenology` (as in records from REFLORA and JABOT) or `reproductiveCondition`, e.g. `fl`, `fl, fr`, `flower, fruit` or `st`, is written as in each journal: | Format | Journals | |---|---| | `(fl, fr)` | Systematic Botany, Phytotaxa, Edinburgh Journal of Botany, Acta Botanica Mexicana, Darwiniana (`(veg, fl)`), and journals whose papers show no phenology (Botanical Journal of the Linnean Society, Feddes Repertorium, PhytoKeys, Plant Ecology and Evolution, Systematics and Biodiversity, Willdenowia) | | `(fl., fr.)` | Taxon, Kew Bulletin, Acta Botanica Brasilica (after a comma), Botany Letters, Hoehnea, Plant Systematics and Evolution | | `(fl./fr.)` | Annals of the Missouri Botanical Garden | | `(fl. fr.)` | Nordic Journal of Botany | | `(fl and fr)` | Brazilian Journal of Botany | | `[fl, fr]` | Brittonia | | `fl. and fr.` | Rodriguésia, and `fl., fr.` in Candollea, without brackets | | `Fl., fr.` | Acta Amazonica, before the date | In Portuguese and Spanish, `and` becomes `e` or `y`, and sterile (`st`) becomes `est`. - **Repeated places.** Some journals do not repeat the place of the previous specimen: `l.c.` for the same municipality in Hoehnea, and `loc. cit.` or `ídem` for the same locality in Acta Botanica Mexicana and Darwiniana. - **Duplicates.** Duplicates of the same collection (same species, collector surname and number, or same collector, date and locality when there is no number) are written once, with all their herbaria in alphabetical order, including those found by [`barroso_flag_duplicates()`](/articles/detect_duplicates.qmd) (`duplicateCollectionCodes`). - **Types.** The type status is not written, as types are cited apart from the examined specimens. - **Collections without number.** The catalog number of the first herbarium is written, e.g. `R. Spruce s.n. (K000892474, LD)`, so that the specimen can be found. Use `catalog_numbers = TRUE` to write the catalog numbers of all herbaria. - **Order.** Specimens are ordered by country, state, municipality and date. Records not identified to species are skipped. - **Species.** For each species, a heading with the species name in italics and its author (from `scientificNameAuthorship`, `acceptedScientificName` or `scientificName`) is followed by the paragraph of its specimens. The function returns, invisibly, a data frame with the species and their specimens, one per line, which can be checked in R: ```r res <- barroso_write_specimens(path = "results/01Nov2026/Luetzelburgia_herbarium_records.xlsx", species = "Luetzelburgia andina", verbose = FALSE) cat(res$specimens_text) ``` ## Tips - Standardize the database first with [`barroso_std()`](/articles/standardize_specimens.qmd), so that collectors, herbarium acronyms and places are written consistently, and duplicates are removed. - Check the countries and states of the database before writing: the specimens are cited as they are in the data. - For the paratypes of a new species, use `species` and `header = "Paratypes"`. ## See Also - [`barroso_write_specimens()` reference](/reference/barroso_write_specimens.qmd) - [Standardize Specimen Records](/articles/standardize_specimens.qmd) - [Compare Herbarium Sources](/articles/compare_herbarium_sources.qmd) - [Write Taxonomic Descriptions](/articles/write_taxonomic_descriptions.qmd)