seananderson

library(knitr)
themes <- knit_theme$get()

opening <- "
<<>>=
"

opening_no_echo <- "
<<echo=FALSE>>=
"

seananderson

seananderson

# Pull together figs, code, and captions into a knitr TeX document
# Sean Anderson November 24, 2013

# define some knitr chunks to print below:
opening <- "
<<>>=
"
closing <- "@\n"
preamble <- readLines("intro.Rnw")
postamble <- "\\end{document}"

seananderson

diff --git a/inst/ms/ss3sim-ms.md b/inst/ms/ss3sim-ms.md
index 5942428..9c4ece0 100644
--- a/inst/ms/ss3sim-ms.md
+++ b/inst/ms/ss3sim-ms.md
@@ -1,18 +1,17 @@
 # Abstract
 
 Simulation testing is an important approach
-to evaluating fishery stock-assessment methods.
-In the last decade, the fisheries stock-assessment modeling framework

seananderson

diff --git a/inst/ms/ss3sim-ms.md b/inst/ms/ss3sim-ms.md
index 69cf7fc..9c4ece0 100644
--- a/inst/ms/ss3sim-ms.md
+++ b/inst/ms/ss3sim-ms.md
@@ -5,13 +5,13 @@ to evaluating fishery stock assessment methods.
 In the last decade, the fisheries stock assessment modeling framework
 Stock Synthesis (SS3) has become widely-used around the world.
 However, there lacks a generalized
-and scriptable framework for running SS3 simulations.
+and scriptable framework for SS3 simulation testing.

seananderson

// Use Gists to store code you would like to remember later on
console.log(window); // log the "window" object to the console

seananderson

From Stats Beerz on 2015-03-23. Here's the question: How can you substitute values in one column based on values in another column? There are many many ways. Here are a few,

Create some fake data:

d <- data.frame(
  rel = c("yes", "no", "yes"),
  troph = c(1, 2, 3))

d

seananderson

# Vocabulary 

To quote Hadley Wickham from his excellent book *Advanced R* <http://adv-r.had.co.nz/Vocabulary.html>:

"An important part of being fluent in R is having a good working vocabulary. [...] I have listed the functions that I believe constitute such a vocabulary. You don't need to be intimately familiar with the details of every function, but you should at least be aware that they all exist. If there are functions in this list that you've never heard of, I strongly recommend that you read their documentation."

I encourage you to look through Hadley's full list at the link above. 

Below, I have reduced Hadley's list to those most relevant to this workshop. It will help you follow the material if you are at least somewhat aware of the following functions and their purpose.

seananderson

# Because of our limited time, it is critical that you arrive 
# with all of the necessary software and R packages installed.
# If you are having any issues with this, first see if there is 
# a colleague who can help you. If you are stuck, please get in 
# touch with me (Sean, sean "at" seananderson.ca) before the workshop. 
# The following R code should walk you through it.

# You will need to have the latest version of R, version 3.4.0 or above. 
# Check with:
sessionInfo()

seananderson

Process:               RStudio [7928]
Path:                  /Applications/RStudio.app/Contents/MacOS/RStudio
Identifier:            org.rstudio.RStudio
Version:               1.0.136 (1.0.136)
Code Type:             X86-64 (Native)
Parent Process:        ??? [1]
Responsible:           RStudio [7928]
User ID:               501

Date/Time:             2016-12-16 09:49:10.317 -0800