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README.Rmd
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README.Rmd
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finch
=====
```{r echo=FALSE}
hook_output <- knitr::knit_hooks$get("output")
knitr::knit_hooks$set(output = function(x, options) {
lines <- options$output.lines
if (is.null(lines)) {
return(hook_output(x, options)) # pass to default hook
}
x <- unlist(strsplit(x, "\n"))
more <- "..."
if (length(lines) == 1) { # first n lines
if (length(x) > lines) {
# truncate the output, but add ....
x <- c(head(x, lines), more)
}
} else {
x <- c(if (abs(lines[1])>1) more else NULL,
x[lines],
if (length(x)>lines[abs(length(lines))]) more else NULL
)
}
# paste these lines together
x <- paste(c(x, ""), collapse = "\n")
hook_output(x, options)
})
knitr::opts_chunk$set(
warning = FALSE,
message = FALSE,
collapse = TRUE,
comment = "#>"
)
```
[](https://github.com/ropensci/finch/actions?query=workflow%3AR-check)
[](https://cranchecks.info/pkgs/finch)
[](https://codecov.io/gh/ropensci/finch)
[](https://cran.r-project.org/package=finch)
`finch` parses Darwin Core simple and archive files
Docs: <https://docs.ropensci.org/finch/>
* Darwin Core description at Biodiversity Information Standards site <http://rs.tdwg.org/dwc.htm>
* Darwin Core at Wikipedia <https://en.wikipedia.org/wiki/Darwin_Core>
## Install
Stable version
```{r eval=FALSE}
install.packages("finch")
```
Development version, from GitHub
```{r eval=FALSE}
remotes::install_github("ropensci/finch")
```
```{r}
library("finch")
```
## Parse
To parse a simple darwin core file like
```
<?xml version="1.0" encoding="UTF-8"?>
<SimpleDarwinRecordSet
xmlns="http://rs.tdwg.org/dwc/xsd/simpledarwincore/"
xmlns:dc="http://purl.org/dc/terms/"
xmlns:dwc="http://rs.tdwg.org/dwc/terms/"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://rs.tdwg.org/dwc/xsd/simpledarwincore/ ../../xsd/tdwg_dwc_simple.xsd">
<SimpleDarwinRecord>
<dwc:occurrenceID>urn:catalog:YPM:VP.057488</dwc:occurrenceID>
<dc:type>PhysicalObject</dc:type>
<dc:modified>2009-02-12T12:43:31</dc:modified>
<dc:language>en</dc:language>
<dwc:basisOfRecord>FossilSpecimen</dwc:basisOfRecord>
<dwc:institutionCode>YPM</dwc:institutionCode>
<dwc:collectionCode>VP</dwc:collectionCode>
<dwc:catalogNumber>VP.057488</dwc:catalogNumber>
<dwc:individualCount>1</dwc:individualCount>
<dwc:locationID xsi:nil="true"/>
<dwc:continent>North America</dwc:continent>
<dwc:country>United States</dwc:country>
<dwc:countryCode>US</dwc:countryCode>
<dwc:stateProvince>Montana</dwc:stateProvince>
<dwc:county>Garfield</dwc:county>
<dwc:scientificName>Tyrannosourus rex</dwc:scientificName>
<dwc:genus>Tyrannosourus</dwc:genus>
<dwc:specificEpithet>rex</dwc:specificEpithet>
<dwc:earliestPeriodOrHighestSystem>Creataceous</dwc:earliestPeriodOrHighestSystem>
<dwc:latestPeriodOrHighestSystem>Creataceous</dwc:latestPeriodOrHighestSystem>
<dwc:earliestEonOrHighestEonothem>Late Cretaceous</dwc:earliestEonOrHighestEonothem>
<dwc:latestEonOrHighestEonothem>Late Cretaceous</dwc:latestEonOrHighestEonothem>
</SimpleDarwinRecord>
</SimpleDarwinRecordSet>
```
This file is in this package as an example file, get the file, then `simple()`
```{r}
file <- system.file("examples", "example_simple_fossil.xml", package = "finch")
out <- simple_read(file)
```
Index to `meta`, `dc` or `dwc`
```{r}
out$dc
```
## Parse Darwin Core Archive
To parse a Darwin Core Archive like can be gotten from GBIF use `dwca_read()`
There's an example Darwin Core Archive:
```{r}
file <- system.file("examples", "0000154-150116162929234.zip", package = "finch")
(out <- dwca_read(file, read = TRUE))
```
List files in the archive
```{r output.lines=1:10}
out$files
```
High level metadata for the whole archive
```{r output.lines=1:20}
out$emlmeta
```
High level metadata for each data file, there's many files, but we'll just look at one
```{r}
hm <- out$highmeta
head( hm$occurrence.txt )
```
You can get the same metadata as above for each dataset that went into the tabular dataset downloaded
```{r eval=FALSE}
out$dataset_meta[[1]]
```
View one of the datasets, brief overview.
```{r}
head( out$data[[1]][,c(1:5)] )
```
You can also give `dwca()` a local directory, or url that contains a Darwin Core Archive.
## Meta
* Please [report any issues or bugs](https://github.com/ropensci/finch/issues).
* License: MIT
* Get citation information for `finch` in R doing `citation(package = 'finch')`
* Please note that this package is released with a [Contributor Code of Conduct](https://ropensci.org/code-of-conduct/). By contributing to this project, you agree to abide by its terms.
[](https://ropensci.org)