Welcome to the 2017 Ecological Genomics course!

This work is licensed under a Creative Commons Attribution 4.0 International License.

Things you'll need to download:

1. R and Rstudio (be sure to install and load the "knitr"" package)
2. Create a github account and download github desktop

Access to my whole project can be found on my github.

It includes this readme file, which I turned into a website you see here, but it also logs research activities on my online notebook.

Common code you'll need to word process in (R)markdown

1. To embed a link, all you need is the URL, implemented in the following way:

[hyperlinked words](URL)

2. To embed an image, you'll need a URL of the image, implemented similarly as above:

![](URL)

To get a URL in (R)markdown: * go to your github repository and click "Issues"
* Click "New"
* Include a title (Pictures); click and drag any image you'd like into the comment section * Click "Submit New Issue" * You will see the image, right click it and copy the URL.

3. To include a table, it is best if you format it first as a csv(comma separated values). (Note, if on a mac, make sure the file type is unicode and unix). With the knitr package, you can generate tables easily from the csv. Here is an example:

Grab a dataset real fast

#packages for reading in data
library(data.table)

#grab dataset online
dat<-fread("https://raw.githubusercontent.com/adnguyen/HelmsCahan_CBP-partA_2016/master/Script_Analyses/Sampling_sites_table.csv")

#making a table
knitr::kable(dat)

n	Locale	State	Site ID	Longitude	Latitude	Tmax
1	Notchview	MA	NO	-73.01277	42.49833	24.8
2	Smokey Mountains	TN	GP	-83.49340	35.63650	25.0
3	Molly Bog	VT	MB	-72.64000	44.50000	25.3
4	Kennebec Highlands	ME	KH	-69.92110	44.56755	25.9
5	Blue Ridge Parkway	NC	BP	-81.95380	35.92640	26.0
6	Bradley	ME	BR	-68.51740	44.98180	26.0
7	Delaware State Forest	PA	DF	-75.01010	41.30233	26.0
8	Harvard Forest	MA	HF	-72.18980	42.53130	26.4
9	Merriman State Forest	NH	MM	-71.13913	44.11107	26.5
10	Sebago Lake	ME	SE	-70.58310	43.92370	26.6
11	Hickory State Park	PA	HP	-75.71751	41.02210	26.8
12	Rugar Woods	NY	RW	-73.48550	44.49060	26.8
13	Bear Brook State Park	NH	BE	-71.34803	43.09943	27.1
14	Blackrock Mountains	NY	BM	-74.02140	41.40405	27.1
15	East Woods	VT	EW	-73.19690	44.43970	27.2
16	Albany Pine Bush	NY	AP	-73.85635	42.71930	28.3
17	Bard College	NY	BA	-73.91630	42.01740	28.8
18	Nockamixon State Park	PA	NK	-75.25890	40.43940	29.1
19	William Penn State Forest	PA	WP	-76.07883	39.72570	29.3
20	Blackwater Creek Park	VA	LA	-79.18100	37.42110	30.7
21	Ljiam Nature Center		IJ	-83.86400	35.95570	30.8
22	Knoxville	TN	DW	-83.94955	35.91995	30.9
23	Durham	NC	RC	-79.07720	36.03640	31.4
24	Uwharrie National Forest	NC	UN	-79.97450	35.36930	31.7
25	Hitchcock Woods	GA	HW	-81.73115	33.55605	33.1

Assignments

1st assignment: Creating maps in R

Final Project

Below are the set of scripts for my final project.

Displaying the organizational structure of your project (repository)

1. In the terminal, install the tree command
   • You may have to install the homebrew
2. use the tree command in the terminal

2017_Ecological_Genomics andrewnguyen$ tree
.
├── 2017_Ecological_Genomics.Rproj
├── Online_notebook.md
├── README.md
├── RasterPCA_demo.Rmd
├── RasterPCA_demo.html
├── index.Rmd
├── index.html
└── index.pdf

0 directories, 8 files