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Package accompanying 2009 book by Zuur et. al. (Mixed Effects Models and Extensions in Ecology with R)

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# AED

Package accompanying 2009 book by Zuur et. al. (Mixed Effects Models and Extensions in Ecology with R). AED stands for "Analyzing ecological data".

Please do not contact author(s) of the book about this package on GitHub, as this is an 'unofficial' (but with blessing from the first author) version for your convenience.

This is work in progress and in time, all the datasets and functions will be documented and added. If you feel you can contribute or are willing to learn how, by adding `roxygen2` documentation for data sets (see examples in /R), drop me a line at roman.lustrik@biolitika.si. For further details read on.

## Help wanted

There's a lot of material to be incorporated in the package and any help I can get will be appreciated. Here's what I've done to document `Seal` dataset.

The documentation is written in [`roxygen2` documentation](http://r-pkgs.had.co.nz/man.html) and it needs to be structured in a particular manner. The first paragraph is taken to be details (`\details{}` section in `.Rd` file) and the rest of the lines with tags (`@`) is quite self explanatory. All lines but `NULL` start with `#'`.

* I downloaded the [zip file](https://highstat.com/Books/Book2/ZuurDataMixedModelling.zip) from [Highland Statistics website](https://highstat.com/index.php/mixed-effects-models-and-extensions-in-ecology-with-r) and stored it in a safe location.
 * I opened the book on page 503 and wrote down the description of the dataset and references at the back.
 * Saved the information in a `.R` file structured as evident in the snippet below.
 * Imported the `Seal.txt` using `Seals <- read.table("Seals.txt", header = TRUE)`.
 * Saved the `Seals` data.frame `save(Seals, file = "./data/seals.RData")` to `/data` folder.
 * Commit `.R`, `.Rd` and `.RData` files to GitHub.
 
Notice the lines with `@`. Names immediately behind the are special tags and should not be changed. `\emph{}` is a LaTeX command and will make the text appear in italics.
 
```R
#' Common seal (\emph{Phoca vitulina} L.) data comes from Cronin et al. 2007, where between April 2003 and November 2005, regular
#' standardised haul-out count survey of Bantry Bay and Kenmare River was carried out by boat. Counts of seals at each haul-out
#' site was carried out independently and simultaneously by two observers, initially from 200 m and progressively closer. Read
#' more about the data in Zuur et al. 2007 in chapter 23 (page 503) or in above mentioned Cronin et al. 2007 paper.
#' 
#' @name Seals
#' @title Seals data
#' @description Common seal (\emph{Phoca vitulina} L.) data comes from Cronin et al. 2007.
#' @docType data
#' @usage data(Seals)
#' @references Cronin et al. 2007. An assessment of population size and distribution of hrabour seals in the Republic of Ireland during the moult season in August 2003. Journal of zoology, 273: 131-139
#' @references Zuur et al. 2009. Mixed effects models and extensions in ecology with R. Springer. ISBN: 978-0-387-87457-9.
NULL
```
After running `roxygenize()` on the the package directory an `.Rd` file is produced.

```LaTeX
% Generated by roxygen2 (4.1.0): do not edit by hand
% Please edit documentation in R/seals.R
\docType{data}
\name{Seals}
\alias{Seals}
\title{Seals data}
\usage{
data(Seals)
}
\description{
Common seal (\emph{Phoca vitulina} L.) data comes from Cronin et al. 2007.
}
\details{
Common seal (\emph{Phoca vitulina} L.) data comes from Cronin et al. 2007, where between April 2003 and November 2005, regular
standardised haul-out count survey of Bantry Bay and Kenmare River was carried out by boat. Counts of seals at each haul-out
site was carried out independently and simultaneously by two observers, initially from 200 m and progressively closer. Read
more about the data in Zuur et al. 2007 in chapter 23 (page 503) or in above mentioned Cronin et al. 2007 paper.
}
\references{
Cronin et al. 2007. An assessment of population size and distribution of harbor seals in the Republic of Ireland during the moult season in August 2003. Journal of zoology, 273: 131-139

Zuur et al. 2009. Mixed effects models and extensions in ecology with R. Springer. ISBN: 978-0-387-87457-9.
}
```

Bump version. It should generally be `1.<minor>.<patch>`. Use `<minor>` when adding datasets and `<patch>` when you're fixing typos and other minor stuff.

To make sure everything checks out, run the check from one level above `AED/` folder.

```{bash}
R CMD build AED
R CMD check AED_<version>.tar.gz
```

Warnings about datasets not being used in the code can be ignored.

To try out if everything worked, you can

```{bash}
R CMD INSTALL AED_<version>.tar.gz
R
load(AED)
data(<dataset name>)
```

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