README.Rmd

---
title: "OISST Mainstays"
output: github_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(gmRi)
use_gmri_style_rmd(css_file = "gmri_rmarkdown.css")
```

# About

This repository maintains core workflows for accessing, processing, and mapping OISST data. For many of the global extent netcdf files processing will be done using python and xarray.

The processing and manipulation of tabular data and other files will be done using R and Rmarkdown for consistent reporting (and becauseI am much better with these tools)

## Working with Docker and Local Paths

### `make up` & `make down`

These commands provide a quick way to spin up notebooks and rstudio server.

Enter `make up` into the terminal for a quick start.
Watch for the notebook service to give you a URL with a login token. Toss that link into the browser to start the notebook.

Once the environment is running Rstudio server can be found at `localhost:8787` which can be entered into any browser.

### docker-compose.override.yaml

For colleagues wishing to access shared resources a `docker-compose.override.yaml` file will need to be placed in the main directory of this repository to link shared paths to shared resources.


### Operating locally for `BASE` steps

The workflow steps that make up the core foundation of the workflow are often too large to run succesfully in docker. To get around this a suitable conda environment may be needed to run the notebooks. In my case I need to navigate to this repo in the terminal and type `conda activate py36`.

Most of the notebooks will have a "workspace" parameter to be set which determines the path structures for the rest of the notebooks accordingly.


## Data Access

[OISSTv2](https://www.ncdc.noaa.gov/oisst/optimum-interpolation-sea-surface-temperature-oisst-v21) data products used for this project have been accessed directly from the [NOAA Physical Sciences Laboratory](https://psl.noaa.gov/data/gridded/data.noaa.oisst.v2.highres.html). The focus of theese workflows is on sea surface temperature products, with gridded datasets containing daily mean sea surface temperature downloaded individually prior to any re-working or processing steps.


## Notebooks

The notebooks in this repo form the core workflow for processing climatology products from the global OISSTv2 products. The notebooks are numbered to suggest a step-wise workflow that will take the original files containing sea surface temperature observations and step the user through calculating a climatology, and for getting timeseries for particular regions of interest. Ongoing development is being done now to create an automatic updating procedure.

## Rstudio Products

.Rmd files are then used to produce consistent reports for the processed sea surface temperature products. 

As reports are completed the will be made available [here using github pages](https://github.com/adamkemberling/oisst_mainstays/blob/master/index.md)