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introduction.Rmd
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introduction.Rmd
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# Introduction {#intro}
## Overview
The single biggest motivation of the Ocean Health Index is to use science to inform marine management. And not just any science, the best available science, data, methods, and tools.
OHI assessments are highly collaboratative, and include information and perspectives from different dicisplines and stakeholders. For OHI assessments to be most efficient and transparent, we emphasize reproducibility and [collaborative open data science tools](http://ohi-science.org/news/ohi-and-open-data-science).
You are in the [Conduct Phase](http://ohi-science.org/projects/ohi-process/) of an OHI assessment, what is involved?
In the Conduct Phase, you will tailor the conceptual **OHI framework** for your assessment area, and then tailor the **OHI Toolbox** to calculate OHI scores for your assessment area (see figure below).
The core OHI features for the Framework and the Toolbox to help guide you as you tailor your assessment. This means you're not starting from scratch; you will build directly off of previous work by the OHI team's [global assessments](http://ohi-science.org/ohi-global/) and by the growing number of independently-led [OHI+ assessments](http://ohi-science.org/projects/ohi-assessments/).
## What to expect
We have developed conceptual guidance and computer software and workflows to streamline your assessment as much as possible. This will let you focus on tailoring the OHI for your assessment. This means that you can focus on **goal models and data for goals, pressures, and resilience**. You do not need to focus on how scores are calculated: our Toolbox software will use your data and your goal models and calculate OHI scores for you.
There is a lot of bookkeeping involved and we strongly advocate transparency and repeatability throughout your assessment, so that you can remember what you did and communicate it to others in the future. This is why we emphasize collaborative documentation about all decisions made, and coding using open data science tools.
### Tailor the Conceptual Framework
First, you should focus on developing goal status models and gathering appropriate data. This will take ~1/3 of the total time for your assessment, and will involve the whole team. There are a lot of decisions to make about what data to use and how to set reference points. Documenting these decisions are critical.
**Here's what you will do:**
1. Understand how goal status models work, and what has been done in the past
- [ohi-science.org/goals](http://ohi-science.org/goals/)
- [global assessments supplemental information](http://htmlpreview.github.io/?https://github.com/OHI-Science/ohi-global/published/documents/methods/Supplement.html)
2. Tailor the OHI Framework to your assessment area. This means exploring available data and defining the spatial boundaries of your assessment. You will gather data and think about reference points as you develop goal status models.
- Gather data with the Data Planner: Chapters \@ref(gathering-data) and \@ref(planner-guide)
### Tailor the OHI Toolbox
Next, you'll use the OHI Toolbox, which means your technical team will be coding in R, RStudio, Git, and GitHub. **It's important that you have already tailored the conceptual framework and have gathered the data you need before you begin using the Toolbox.**
#### Learn the OHI workflow
To learn the open data science workflow we use and describe in [Lowndes et al. 2017, *Nature Ecology & Evolution*](https://www.nature.com/articles/s41559-017-0160), use our OHI [data science training](http://ohi-science.org/data-science-training/).
#### Prepare your data layers
This will take another ~1/3 of the total time for your assessment.
1. Prepare Data: Chapter \@ref(prep-data)
#### Understand how the OHI Toolbox works
1. [Create your repo from the OHI+ template](https://github.com/OHI-Science/ohi-plus-template)
1. [Learn about your repo](http://ohi-science.org/manual/#full-repository)
1. Learn how the Toolbox works (hands-on): Chapters \@ref(toolbox-ecosystem), \@ref(calcs-basic), \@ref(calcs-advanced)
#### Tailor the OHI Toolbox's goal status models for your assessment.
This will take the final ~1/3 of the total time for your assessment. The `ohicore` R package will calculate OHI scores using the information you tailor (status models, and your data for status, trend, pressures, and resilience) and calculate the final scores.
1. [Modify goal models](http://ohi-science.org/manual/#modifying-goal-models)
1. [Modify pressures/resilience](http://ohi-science.org/manual/#modifying-pressures-and-resilience)
## Tools and Resources
During your OHI assessment you will mainly use:
- **Google Drive** (or similar, recommended) to collaborate with your whole team, and document thoughts and decisions about data and status goal models and reference points, etc
- **The OHI Toolbox** (required) to organize and prepare data, and tailor goal status models
### Google Drive folder
This is a place you can organize presentations, meeting agendas, notes, and the OHI+ Planner (see Chapter \@ref(data-planner).
_Why Google Drive?_ OHI is a long-term, highly collaborative process. To make working together with multiple team members effecient, you will use many open-science tools, including Google Drive, Rstudio, and Github. Lets start with collaborating in Google Drive, where all participants can view and edit the same materials, and take notes. The advantage of using a shared Google Drive folder is that all your decision-making and insights are collected here in one place, rather than in disparate emails or notes, or lost without even being recorded.
### OHI Toolbox
The **OHI Toolbox** is made to organize and process data, document decision making, calculate scores, and share results within or outside your team. It was created to facilitate score calculations as well as the organization of information and transparency of the entire workflow. The Toolbox is built with **open-source, freely available software**, particularly **_Github_** and **_RStudio_**.
**Treat the Toolbox as your notebook, calculator, and presentation of your work.** No more endless email chains or passing spreadsheets back and forth! If someone wants to see where your data comes from, how you have processed the data, the rationale for including or excluding certain data, and how the scores are calculated, they can find the answers from your work. It increases the credibility and reproducibility of your assessment.
It also makes your technical team more stable.
**The Toolbox will also preserve team memory.** If there are personnel changes, it is easy for any new member to pick up where it was left when your data preparation has been documented clearly and kept in one place. It will also help your "future self": months or years later you can revisit your work and understand what you have done.
Your Toolbox is organized into **a GitHub repository** where you will store all your work. They will be tailor-made for your OHI+ assessment upon request.