Getting Started in Ecological Genomics

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

Logs research activities in your online notebook template found here.

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 (in R)

#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[1:3])

For a good option to use markdown for taking notes, try Typora

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