minimal-edi-package.Rmd

---
title: "Minimal EDI package generated using EMLassemblyline and ediutilities"
author: "Joe Futrelle"
date: "2022-01-24"
output: html_notebook
---

Libraries used

```{r}
# two of the required packages are installed from GitHub
# library(remotes)
# remotes::install_github("EDIorg/EMLassemblyline")
# remotes::install_github("WHOIGit/ediutilities")

library(EMLassemblyline)
library(ediutilities)
library(here)
library(lubridate)
library(pander)
```

Read example data table

```{r}
data_table <- read.csv(here('nes-lter-minimal.csv'))
data_table$date = ymd_hms(data_table$date)
```

Generate basic summary of data table

```{r}
# Just for inspecting the summary: change all character columns to factor
DF <- data_table
DF[sapply(DF, is.character)] <- lapply(DF[sapply(DF, is.character)], as.factor)
pander::pander(summary(DF))

```

Read the Excel metadata template and generate text templates used by
EMLassemblyline

```{r}
excel_to_template(here('nes-lter-minimal-info'), 'nes-lter-minimal', rights='CC0')
```
Generate the package and insert the parent project node into the resulting EML

```{r}
# use a dummy package ID
pkg_id <- 'knb-lter-nes.999.1'

make_eml(here(),
         dataset.title='Demonstration of minimal EDI package',
         data.table='nes-lter-minimal.csv',
         data.table.description='Example NES-LTER data',
         data.table.name = 'Subset of NES-LTER nutrient data',
         temporal.coverage = temporal_coverage(data_table$date),
         geographic.description = "NES-LTER Transect",
         geographic.coordinates = geographic_coordinates(data_table$latitude, data_table$longitude),
         maintenance.description = "ongoing",
         user.id = "NES",
         user.domain = "LTER",
         package.id = pkg_id)

project_insert(pkg_id)
```