https://github.com/annakrystalli/dataspice-tutorial

Tutorial in practical research data management: creating simple metadata files using dataspice

https://github.com/annakrystalli/dataspice-tutorial

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Tutorial in practical research data management: creating simple metadata files using dataspice

README.Rmd

---
output: github_document
---





```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

```{r, echo=FALSE, message=FALSE}
library(tidyverse)
```

# dataspice-tutorial


[![DOI](https://zenodo.org/badge/136082880.svg)](https://zenodo.org/badge/latestdoi/136082880)

The goal of dataspice-tutorial is a practical exercise in creating metadata for an example field collected data product using package `dataspice`. 

- Understand basic metadata and why it is important
- Understand where and how to store them
- Understand how they can feed into more complex metadata objects.





- ### [Tutorial](http://annakrystalli.me/dataspice-tutorial/)
- ### [Introductory slides](http://annakrystalli.me/dataspice-tutorial/slides.html)

***




## `dataspice` 

Package [`dataspice`](https://github.com/ropenscilabs/dataspice) makes it easier for researchers to create basic, lightweight and concise metadata files for their datasets. Metadata fields are based on [schema.org](http://schema.org/Dataset)




## Data source : NEON data portal 

![](http://data.neonscience.org/neon-data-theme/images/logo--blue-neon-data.png)


### *Woody plant vegetation structure*

 This data product contains the quality-controlled, native sampling resolution data from in-situ measurements of live and standing dead woody individuals and shrub groups, from all terrestrial NEON sites with qualifying woody vegetation. The **exact measurements collected per individual depend on growth form**, and these measurements are focused on:  
 
- enabling biomass and productivity estimation,  
- estimation of shrub volume and biomass   
- calibration / validation of multiple NEON airborne remote-sensing data products. 

  In general, comparatively large individuals that are visible to remote-sensing instruments are mapped, tagged and measured, and other smaller individuals are tagged and measured but not mapped. Smaller individuals may be subsampled according to a nested subplot approach in order to standardize the per plot sampling effort.

Structure and mapping data are reported **per individual per plot**; sampling metadata, such as _per growth form sampling area (m2)_ or National Land Cover Database Vegetation Type Name (NLCD class) are reported **per plot**. 

For additional details, see protocols:

- **[NEON.DP1.10098/NEON.DP1.10045](https://github.com/annakrystalli/dataspice-tutorial/blob/master/assets/methods/NEON_vegStructure_userGuide_vA.pdf): NEON User Guide to Woody Plant Vegetation Structure (NEON.DP1.10098) and Non- herbaceous Perennial Vegetation Structure (NEON.DP1.10045)**

- **[NEON.DOC.000987vG](https://github.com/annakrystalli/dataspice-tutorial/blob/master/assets/methods/NEON.DOC.000987vF.pdf): TOS Protocol and Procedure: Measurement of Vegetation Structure, and Science Design**

- **[NEON.DOC.000914](https://github.com/annakrystalli/dataspice-tutorial/blob/master/assets/methods/NEON.DOC.000914vA.pdf): TOS Science Design for Plant Biomass, Productivity and Leaf Area Index.**

***

### `dataspice` exercise data

The data are a trimmed subset of data downladed from the [**NEON data portal**](http://data.neonscience.org/browse-data) after filtering for:

- time periods between **`2015-06` - `2016-06`**

- locations within NEON Domain area **`D01: Northeast`**

Filter returned data from **2 sites** from **`2015-6`** to **`2015-11`**.




### vst_perplotperyear.csv

Plot level data

```{r, echo=FALSE, message=FALSE}
readr::read_csv(here::here("data", "vst_perplotperyear.csv")) %>% head(6) %>% knitr::kable()
```




### vst_mappingandtagging.csv

Individual level data

```{r, echo=FALSE, message=FALSE}
readr::read_csv(here::here("data", "vst_mappingandtagging.csv")) %>% head(6) %>% knitr::kable()
```




***




> ##### Citation
National Ecological Observatory Network. 2018. Data Products: DP1.10098.001.  Provisional data downloaded from http://data.neonscience.org on 2018-05-04. Battelle, Boulder, CO, USA

***


dataspice tutorial is licensed under a Creative Commons Attribution 4.0 International License.

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