reflora_parse

Parse Darwin Core Archive files

refloraR::reflora_parse()

Description

Read Darwin Core Archive (DwC-A) files from any downloaded dwca folder at REFLORA Virtual Herbarium hosted by the Rio de Janeiro Botanical Garden.

Arguments

Argument	Description
path	Pathway to the computer’s directory, where the REFLORA-downloaded dwca folders are.
herbarium	A vector of specific herbarium acronyms (collection code) in uppercase letters or leave it as `NULL` to parse specimen records for all herbarim dcwa folders in the defined path directory.
repatriated	Logical. If `FALSE`, skips downloading records from REFLORA-associated herbaria that have been repatriated. Default is `TRUE`. Use `reflora_summary()` to check which collections are repatriated.
verbose	Logical, if `FALSE`, a message showing steps when summarizing specimen records will not be printed in the console in full.

Value

A list of dwca files, including data and associated metada.

Examples

reflora_download(herbarium = c("ALCB", "HUEFS", "K", "RB"),
                 verbose = TRUE,
                 dir = "reflora_download")

dwca <- reflora_parse(path = "reflora_download",
                      verbose = TRUE)

---
title: 'reflora_parse'
description: 'Parse Darwin Core Archive files'
toc: true
toc-depth: 3
---


```{r}
#| eval: false
refloraR::reflora_parse()
```

### Description

Read Darwin Core Archive (DwC-A) files from any downloaded dwca
folder at [REFLORA Virtual Herbarium](https://ipt.jbrj.gov.br/reflora/)
hosted by the [Rio de Janeiro Botanical Garden](https://www.gov.br/jbrj/pt-br).

### Arguments

| Argument | Description |
|---|---|
| path | Pathway to the computer's directory, where the REFLORA-downloaded dwca folders are. |
| herbarium | A vector of specific herbarium acronyms (collection code) in uppercase letters or leave it as `NULL` to parse specimen records for all herbarim dcwa folders in the defined path directory. |
| repatriated | Logical. If `FALSE`, skips downloading records from REFLORA-associated herbaria that have been repatriated. Default is `TRUE`. Use `reflora_summary()` to check which collections are repatriated. |
| verbose | Logical, if `FALSE`, a message showing steps when summarizing specimen records will not be printed in the console in full. |

### Value

A list of dwca files, including data and associated metada.

### Examples

```r
reflora_download(herbarium = c("ALCB", "HUEFS", "K", "RB"),
                 verbose = TRUE,
                 dir = "reflora_download")

dwca <- reflora_parse(path = "reflora_download",
                      verbose = TRUE)
```