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minor text updates to vignette, also, adding pdf vignette.

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nickreich committed Dec 8, 2015
1 parent 8a7361a commit ed85bda1e6b6f5de68009e280977f973b67ea030
Showing with 7 additions and 7 deletions.
  1. +1 −1 .gitignore
  2. +6 −6 vignettes/ALERTDocumentation.Rnw
  3. BIN vignettes/ALERTDocumentation.pdf
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@@ -6,6 +6,6 @@ vignettes/cache/*
vignettes/figure/*
vignettes/ALERTDocumentation-concordance.tex
vignettes/ALERTDocumentation.tex
vignettes/ALERTDocumentation.pdf
vignettes/ALERTDocumentation.toc
vignettes/ALERTDocumentation.log
vignettes/ALERTDocumentation.synctex.gz
@@ -47,20 +47,20 @@ We demonstrate the use of the ALERT algorithm to evaluate these possible thresho
<<install, eval=FALSE>>=
install.packages("devtools")
require("devtools")
install_github("ALERT", "nickreich")
devtools::install_github("nickreich/ALERT")
@
Then, to load the ALERT package and the sample dataset that comes with the package, run the following commands:
<<setup, message=FALSE>>=
require(ALERT)
<<setup, message=FALSE, warning=FALSE>>=
library(ALERT)
data(fluData)
@
The {\tt fluData} dataset has a particular format that we assume all ALERT datasets will follow. In particular, it is a {\tt data.frame} with a column named ``Date'' and a column named ``Cases''. These represent the number of cases observed in the week of time defined by the date given. This sample dataset is based on a real dataset, but the counts and dates have been modified from the original format based upon data sharing agreements with the owners of the data. This particular dataset has a total of $\Sexpr{sum(fluData$Cases)}$ cases reported across $\Sexpr{nrow(fluData)}$ weeks. The earliest observation is from $\Sexpr{format(min(fluData$Date), "%m/%d/%Y")}$ and the last observation is from $\Sexpr{format(max(fluData$Date), "%m/%d/%Y")}$. This is what the dataset looks like. (NOTE: lines that begin with \#\# indicate they are ouput from R that would be seen by the user who is having an interactive an R session.)
<<dataPeek, fig.height=3.5, fig.width=7>>=
<<dataPeek, fig.height=3.5, fig.width=7, warning=FALSE>>=
head(fluData)
require(ggplot2)
library(ggplot2)
theme_set(theme_bw())
qplot(x=Date, ymin=0, ymax=Cases, data=fluData, geom="linerange")
@
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