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CEREO September 2016

Seminar: Write Winning Grant Proposals

Wednesday, October 19, 2016, University Inn, Best Western, Moscow
Check-In 8:00 – 8:30 a.m., Seminar 8:30 am – 4:30 p.m.

Presented by Peg AtKisson, Ph.D.

This seminar is a prerequisite for the follow-up workshop, Mentored Proposal Writing Workshop Series: Write and Submit a Competitive Grant Application. At the conclusion of the Write Winning Grant Proposals Seminar, tenured or tenure-track faculty may apply to enter this workshop.

In the Mentored Proposal Writing Series, selected faculty work one-on-one with Dr. AtKisson on their proposal from first steps through submission. This interactive opportunity lasts 26 weeks, during which Dr. AtKisson works individually with participants as they develop their proposals. For more information and testimonials on the Mentored Proposal Writing Workshop Series contact Becky James.

Cost: $95 + workbooks, Required workbooks: $75

(includes lunch and handouts)

To Register: Go to Deadline: Oct 12, 2016


NIFA Announces up to $48.1 Million in Funding Available for Specialty Crop Research

The U.S. Department of Agriculture’s (USDA) National Institute of Food and Agriculture (NIFA) released details on up to $48.1 million in available funding to support systems-based research and extension activities to accelerate science-based solutions and new technology for the specialty crop industry. Agriculture Secretary Tom Vilsack announced the grants yesterday at the New York Times Food for Tomorrow Conference in Pocantico Hills, N.Y. The grants are to be funded through NIFA’s Specialty Crop Research Initiative (SCRI).


Simple Mapping in R

Today we discussed using the “maps” package and the “ggplot2” package to make simple maps in R.

Our test dataset is from the “rgbif” data package which makes use of publicly available data (see the “getting data” Topic). To deal with some of the georeferenced data we made use of the “dismo” package .

We made a basic map using ‘maps’:


And then took the same data and mapped it using ggplot2:


Because maps limits its field of view to the “states” basemap, whereas ggplot2 does not, we weren’t able to see this spurious detection way out in the middle of the ocean. Now that we see it, we used subset() to remove it and then made a fancy WSU themed cougar map using ggplot2:


The Script is here: simple-mapping

Changing Data Layout – Dplyr and Reshape

This week we learned about changing the structure of and combining information from various datasheets. Michael showed us some of his data from colleagues which was not particularly clean and which needed reformatted in order to make a stacked bar chart.

He used the two R packages “dplyr” and “reshape2” to reorganize the data so that the ggplot R package could create the desired chart.

Here is the same script that Michael used, only using the built in mtcars dataset from base R: dplyrreshape

2017 CONFERENCE: Climate Impacts to Water

Water users, water managers, researchers, educators, and innovators are meeting January 25-26, 2017 to discuss the impact of climate to waters of the Pacific Northwest. The common theme of the conference will be creating a dialogue amongst the communities that use and value the region’s water supply within the context of a changing climate. Given the increased demand for future food production in the region are expected to be challenged by water supply due to decreased snow pack, in addition to issues associated with water access, and policy and rights. Also, excess water from heavy rain events and untimely precipitation are expected to increase water quality concerns with potential flood events. These uncertainties create difficulty for agriculture producers, water managers and storm water managers when making current and future decisions.

The event will be held at Skamania Lodge in Stevenson, WA on the Columbia River.

To register, submit an abstract, for more information or to sponsor this event.

The meeting is hosted by climate associated groups within Washington State University, University of Idaho and Oregon State University with support from Western Sustainable Agriculture, Research and Education (WSARE).

Barry M. Goldwater Scholarship

Students who are planning a research career in math, science, or engineering and meet the criteria below should be encouraged to apply for the nationally distinguished Barry M. Goldwater Scholarship. The scholarship is for up to $7,500.

All students who are thinking about applying for a Goldwater Scholarship must attend one informational session. These sessions are also appropriate for any student who may be interested in a Goldwater scholarship sometime in the future. Freshman year is not too soon.

Thursday, September 22, 2016 | 12:00 p.m. | CUE 512 Pullman**

Wednesday, September 28, 2015| 4:00 p.m. | CUE 512 Pullman**

Learn More

**Tri-Cities, Spokane, Vancouver: Phone bridge, if needed: (509) 335-9446, passcode = 04745. Dial up for all workshops: 5704745. Technical assistance during meeting: (509) 335-6575.

Bringing in Data and Publicly Available Data Packages

This week we discussed how we bring in data, forms of data, good sources for help, and some packages that pull in publicly available data.

First of all, we talked about R Studio ( R Studio is a great interface for using R and in addition it allows for some “point and click” methods of bring in data. The “input dataset” button on the top right square of the R Studio interface allows you to input data from either a local file on your computer or by connecting to the internet.

Now, data can also be brought in through code. A good resource for ways to import specific types of data is this Quick R page: The most common data type that people work with is .csv files, which are inported using the “read.csv()” command. If you want to read an Excel file you need the “xlsx” package.

If you want to read data from a website, which the point and click method in R Studio lets you do, there are many ways to do it. Two common ways are using the “RCurl” package or the “data.table” package. Examples of that code are below. Remember, to use a package you need to first have the package installed (“buying the book”) and then you need to use the library command to use the package (“taking the book off the shelf”).

myfile <- getURL(‘’, ssl.verifyhost=FALSE, ssl.verifypeer=FALSE)

mydat <- fread(‘’)

Some packages that we discussed which make us of publicly available data are:

Out of these packages EcoRetriever is the hardest to install. You must first install the Retriever program from, then install the ecoretriever package. This will allows you program in queries of the data available at

An example of using one of these packages, the dataRetreival package which is automatically accessed through the package ‘EGRET’ can be found here: r_for_hydrology_script.  This script is from R Working Group contributor Tung Nguyen.

In addition to those packages there were questions about Economic and Social Science data sources. Here are some packages or resources that I tracked down which have data specific for those fields:

2016 Palouse Basin Water Summit

Come to the twelfth annual Palouse Basin Water Summit from 4:30 to 8:00 pm on Wednesday, October 5, at the Schweitzer Event Center in Pullman, WA.

The 2016 Summit – our annual community dialogue about our local water resources – will feature the internationally acclaimed environmentalist Maude Barlow and her recent book, “Blue Future: Protecting Water for People and the Planet Forever“ – a powerful, penetrating, and timely look at the looming global water crisis, and what we can do to prevent it. “The coming grab for the planet’s dwindling resources is the defining issue of our time. Water is not a resource put here for our convenience, pleasure and profit but the source of all life. It is urgent that we clarify the values and principles needed to protect the planet’s fresh water,” notes Barlow.

Be challenged by great presentations from local water experts, area youth and our annual State of the Basin report. The event is free and open to all community-minded Palouse area residents. Additionally, we will draw names for some fabulous prizes, including a low-flow toilet and a $1,000 wisescapingR yard makeover!


February 16-17, 2017, Gonzaga University Spokane, WA

The Washington Higher Education Sustainability Conference (WAHESC) strives to create collective direction and solidarity in higher education for our region. As political, social and environmental issues become more complex, WAHESC convenes and empowers stakeholders who are driving leadership and generating solutions for a more sustainable future.

Registration is already open. Before January 5, 2017, early-bird registration fees are $160 for staff/faculty/community partners, and only $40 for students.

Informational Meeting

Today we discussed the format of the R group and potential topics for the rest of term.

The group functions in small 10-15 minute lessons given by group participants on specific topics. Topics of interest this term are:

Survival Estimation
Writing/creating packages
Social Science specific packages
Data management
Bayesian Statistics

We will cover these and more topics this term.

Next Week’s session will be “Data Sourcing and R Studio”. We will cover online sources of data and some cool packages to get that data, along with a brief intro to R studio shortcuts and use. If you do not have R studio please download it from