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FINAL_PROJECTS.Rmd
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---
title: "Final projects!"
author: "NRES 470/670"
date: "Feb 4, 2017"
output:
html_document:
theme: spacelab
toc: yes
toc_float: yes
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, cache = TRUE)
```
## Final projects for NRES 470
Students will work in groups of ~2-3 people to perform a population viability analysis (PVA) to rank conservation or management actions for a species of conservation concern (species of your choice!). Grading will be based on finished products (written and oral presentations) as well as participation and peer evaluations.
## Overview
- Select a species and management question of interest.
- Perform a thorough literature review on your species of interest- collect all information you can about life history, key vital rates and their variability.
- Construct a PVA model, parameterized using the best available information from the literature (free PVA software platforms: InsightMaker, Vortex, R).
- Use your PVA model to address a conservation or management question and write up the results.
- Present your results to the class!
## Timeline
- **PROPOSAL:** Due March 3!
- **INITIAL PVA** Due April 3: description of how your PVA model works and where the parameter estimates come from.
- **DRAFT FINAL PAPER:** Due April 28
- **FINAL FINAL PAPER:** Due May 17
- **FINAL PRESENTATIONS:** May 5 in lab!
Remember that the semester will get crazy at the end (including for your instructors). Plan ahead!
## First project-related assignment: the proposal!
(Due March 3...)
Your project proposal will consist of:
1. **Title**: should indicate what species you are modeling, and what question will be addressed
2. **Project participants**: work in groups of 2-3. Obviously we won't have very many groups this year!
3. **Project rationale**: Describe the rationale for choosing this species and management/conservation question. Be as specific as possible! Convince your instructors that your project is **interesting**!
4. **Data sources**: Describe what data/information sources you plan to use to guide PVA construction and parameterization. Convince your instructors that your project is **possible**!
**NOTE about data sources:** The most important parameters you need for a PVA model are *survival rates* (usually age-structured), *fecundity rates* (often age-structured as well), *stochasticity* (variability in those vital rates), *abundance*, *dispersal rates*, and *carrying capacity*. We have gone over all these concepts in class already- PVA is just a way of putting all these concepts together in a single model! You can either get these parameter estimates directly from the published literature (or unpublished reports), or you estimate these parameters yourself using raw data (which we haven't yet gone over in class). If all else fails, you can use published records for similar species!
## Second project-related assignment: the initial PVA!
(Due April 3...)
Your inital parameterized PVA will consist of:
1. A ready-to-run PVA model, in whatever software framework you are using (Vortex, InsightMaker, R). This model does not need to be the "final" model, but it should work (e.g., produce results) and the parameter estimates should be reasonable and backed by evidence (see below).
2. A description of parameter estimates and rationale/evidence for these estimates.
a. For each major decision you made in constructing the model, describe the information you used to back up your decision (and the source of this information). Decisions include: how many populations, how many stages, how density-dependence operates for your species, allee effects, survival and fecundity rates, environmental stochasticity, catastrophes, etc. Where appropriate, feel free to embed figures, maps, etc. from your information sources.
b. Literature cited (format not important, as long as it includes all key information).
## Third project-related assignment: the written project (rough draft)!
Your final written paper is expected to be in the style of a **scientific manuscript**. That is, it should have an *introduction*, *methods*, *results* and *discussion* sections, and should cite relevant literature.
### Introduction
This is where you introduce the topic and describe why it's important. You can recycle and flesh out the material from your proposal!
Remember to cite lots of literature here!
### Methods
This is where you describe your PVA in enough detail that it could be replicated by another wildlife researcher! You can recycle much of your "initial PVA" assignment here.
Remember to justify all your decisions in terms of parameterization.
Also, you should describe how you addressed your main questions
- What different scenarios did you run?
- How did you use the simulation results to address your questions? How did you visualize the results? Did you perform any statistical analyses?
### Results
This is where you describe and present the relevant outputs from your model. Provide figures and tables to summarize your *relevant* results.
With PVA it can be difficult to decide what to present and what not to present. Always ask yourself: is it *relevant* to your main quesitonS??
### Discussion
This is where you describe what your results really tell us with respect to your main questions.
Also, you should:
- Describe any new questions that came up in the process of building and running your PVA
- Describe any potential flaws with your PVA and how you might improve this in the future
- Describe any future research that could be helpful in addressing your main questions
A rubric for the final written presentation can be found [here](WrittenProject_rubric.docx).
## Fourth project-related assignment: the oral presentation!
Your group presentation should be in the style of an oral presentation at a conference.
Presentations will take place during our final lab period (Friday, May 5 starting at 11). Since this is a small class, we will probably end early!
You will have 15 minutes to give your presentation, with at least 5 additional minutes for presenations.
We will hand out a simple peer-review form so you can give feedback to your peers.
A rubric for the presentations can be found [here](presentationProject_rubric.docx)
## Final paper peer review/feedback session
In class on Thurs May 4 we will have a "peer review" session where we will have a chance to give each other feedback on draft manuscripts.
The way it will work is as follows:
1. By the end of the day on May 2, you will receive another group's draft manuscript via WebCampus (see list below).
2. Before class on May 4, please read the manuscript you have been assigned, and make comments, paying particular attention to the [grading rubric](WrittenProject_rubric.docx).
3. In class, you will first get together with the other students that were also assigned to review the same manuscript. You will have 25 minutes to compare notes and prepare a written "peer review" of the manuscript that highlights both the strengths and the weaknesses. Please make your comments as specific as possible. The goal is to give your classmates feedback that will be useful to them as they prepare their final drafts! *Please hand in your peer-review to the group that wrote the draft AND your instuctor/TA*
4. At the end of class, we will break up into new groups. One representative from each peer-review group will meet with the project group that wrote the draft manuscript, to give the feedback in person.
### In-class peer review: manuscript drafts
The following students will review the draft manuscript by the Pintail group (Cathryn and Bryce): *Ashley and Kristin*
The following students will review the draft manuscript by the Cutthroat trout group (Thomas and Jason): *Bryce and Rachel*
The following students will review the draft manuscript by the Axlotl group (Kenny and Ashley): *Cathryn and Thomas*
The following students will review the draft manuscript by the desert tortoise group (Rachel and Kristin): *Jason and Kenny*
Bring your laptops to class as usual so you can write, save and share your peer-review electronically with your classmates/instructors.
### In-class peer review: presentations
During the final project presentations, please provide feedback to your classmates using [this form](presentation_handout_for_students.docx) (these will be handed out in class on the day of the final project presentaitons)
## Potentially useful links!
Publicly available datasets, potentially for final project...
(many links courtesy Tom Langen)
### BIODIVERSITY DATA CLEARINGHOUSES /ARCHIVES
[International Union for the Conservation of Nature (IUCN) Redlist](http://www.iucnredlist.org/) (Searchable list of the world’s threatened and endangered plants and animal species on the IUCN Redlist.)
[Conservation International Global Biodiversity Hotspots](http://www.biodiversityhotspots.org/Pages/default.aspx) (Detailed data on the attributes and threats to the world’s global biodiversity hotspots.)
[National Biological Information Infrastructure](http://www.nbii.gov/) (Data archive and clearinghouse for biological data from the US. Also provides standards for metadata.)
[Biological Inventories of the World’s Protected Areas](http://www.ice.ucdavis.edu/bioinventory/bioinventory.html) (Searchable species occurrence records and species lists for over 1,400 protected areas around the globe.)
[Global Biodiversity Information Facility](http://data.gbif.org/welcome.htm) (An enormous clearinghouse of biodiversity data)
[USGS avian data portal](https://migbirdapps.fws.gov/mbdc/databases/db_selection.html)
[Global Population Dynamics Data Base(GPDD)](http://www3.imperial.ac.uk/cpb/research/patternsandprocesses/gpdd) (5000 population size time series for 1400 species, most of which have at least ten years of data. There are data on the natural history of the organism and the location & method of sampling.)
[GPDD, alternative link](https://www.imperial.ac.uk/cpb/gpdd2/secure/login.aspx)
[USGS Breeding Bird Survey](http://www.pwrc.usgs.gov/BBS/) (Breeding bird survey data back to 1966)
[Bird Point Count Database](http://www.pwrc.usgs.gov/point/) (Depository of bird point-count data from across the US.)
[Bird Studies Canada Nature Counts](http://www.bsc-eoc.org/birdmon/default/main.jsp) (Bird survey data archive for Canada, includes point counts and many other types of surveys.)
[Avian Knowledge Network](http://www.avianknowledge.net/content/datasets) (Archive of aggregated bird surveys from many organizations and studies across throughout the western hemisphere, including Latin America.)
[NatureServe](http://www.natureserve.org/getData/index.jsp) (Data on species of plants and animals in the Western Hemisphere, including detailed range maps)
[USGS bat data portal](https://my.usgs.gov/bpd/)
[Comadre and Compadre matrix demography database](https://compadredb.wordpress.com/2015/10/05/introducing-the-comadre-animal-matrix-database/)
### GOVERNMENT AGENCY DATA PORTALS
[National Atlas](http://www.nationalatlas.gov/) (Geospatial data on the environment, economy, and people of the US).
[US Department of Agriculture Census of Agricultural Data](http://www.agcensus.usda.gov/) (Authoritative data on all aspects of agriculture in the US.)
[Centers for Disease Control & Prevention Data & Statistics](http://www.cdc.gov/datastatistics/) (Comprehensive data on all aspects of disease epidemiology.)
[USGS Water Data for the Nation](http://waterdata.usgs.gov/nwis) (Hydrological and water-quality data from across the US.)
[USGS Survey Disease Maps](http://diseasemaps.usgs.gov/index.html) (US County-scale maps of incidence patterns of various mosquito-vectored diseases)
[The Multi-resolution Land Characteristics Consortium (MRLC) National Land Cover Database](http://www.mrlc.gov/) (Land cover or land use, canopy cover, and impermeable surface area of the entire US, at a resolution of 30 m x 30 m, based on remote sensing data from satellite imagery.)
[US Fish & Wildlife Service National Wetlands Inventory](http://www.fws.gov/wetlands/) (Wetlands greater than 1 acre are mapped and classified throughout the US, Puerto Rico and US territories. Data can be examined using the [Wetland Mapper](http://www.fws.gov/wetlands/Data/Mapper.html) and then downloaded for use by a GIS application, or can by inspected directly using [Google Earth](http://www.fws.gov/wetlands/Data/GoogleEarth.html))
[USDA Forest Inventory and Analysis National Program](http://fia.fs.fed.us/)
[Forest Inventory Data Online (FIDO)](http://fia.fs.fed.us/tools-data/default.asp) (Highly-detailed periodic surveys of forest composition at sites throughout the US.)
[US Geological Survey](http://www.usgs.gov/) (Reports, data analysis, maps, and raw data on a diversity of topics related to environmental science, including biodiversity and emerging diseases.)
[NOAA National Climate Data Center](http://www.ncdc.noaa.gov/oa/ncdc.html) (Extensive data archives of climate data, including paleoclimate.)
### ENVIRONMENTAL DATA CLEARINGHOUSES
[Ecotrends](http://www.ecotrends.info/EcoTrends/) (Data archive and data visualization tools for ecological data at sites distributed around the US.)
[NASA Global Change Master Directory](http://gcmd.nasa.gov/index.html) (Data on all aspects of global change, includes data on climate, land use, biodiversity and human dimensions.)
[Oak Ridge National Laboratory Distributed Active Archive Center for Biogeochemical Dynamics(ORNL DAAC)](http://daac.ornl.gov/index.shtml) (A NASA-sponsored source for biogeochemical and ecological data and models useful in environmental research.)
[Pole to Pole Ecological Research Lattice of Sites (P2ERLS)](http://www.p2erls.net/) (Portal to research stations and research networks, including their data archives.)
[Weatherspark](http://weatherspark.com/) (Visualized time-series data on local climate at sites around the globe.)
[Long Term Ecological Research (LTER) Network](http://www.lternet.edu/) (Network of research stations that have standardized monitoring programs as well as site-specific research. Sites are mandated to make data publicly available on the web.)
### RESEARCH PROJECT DATA ARCHIVES
[Dryad](http://datadryad.org/) (Data archives for bioscience data from peer-reviewed journal articles from a large consortium of journals)
[Ecological Society of America (ESA) Data Registry](http://esapubs.org/archive/archive_D.htm)
Archive of ecological and environmental data from ESA publications)
[National Center for Ecological Assessment & Synthesis (NCEAS) Data Repository](http://knb.ecoinformatics.org/knb/style/skins/nceas/index.jsp) (Data archive of contributed data sets of all types of ecological data.)
[NCEAS Scientific Computing Database](http://www.nceas.ucsb.edu/scicomp/) (Clearinghouse of climatological, geospatial, and other data. Also has shareware software for analysis.)