README.Rmd

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## Correlated RAndom Walk Library of R functions
<p float="left">
  <img src="hex_sticker/crawl.png" height="200"/> 
  &nbsp; &nbsp;
  <img src="hex_sticker/noaa.png" height="200"/>
</p>


The [C]orrelated [RA]ndom [W]alk [L]ibrary of R functions was designed for fitting 
continuous-time correlated random walk (CTCRW) models with time indexed 
covariates. The model is fit using the Kalman-Filter on a state space version of 
the continuous-time stochastic movement process. The use case in the estimation
of animal movement paths where the observed locations are determined from
Argos or FastLoc enabled bio-loggers. In addition to the continuous-time
component, `{crawl}` was specifically developed to incorporate the measurement
error often associated with these observed locations. Lastly, `{crawl}` 
provides a framework for multiple imputation workflows for incorporation of
model uncertainty.

## The Future of crawl

The original code base and concepts for `{crawl}` were developed almost 15 years
ago. Much has changed in the world of movement ecology, spatial statistics,
R, bio-logging, and many other fields. In some cases, we've done a fairly good
job keeping pace; in other cases, we've fallen behind. We feel it is time for
a new approach and will, from now on, be focusing our development efforts on
other packages and methods. We will continue to maintain `{crawl}`, improve the documentation,
and ensure compatibility with dependent packages.

## Installation

## Install via CRAN

`{crawl}` is currently available on CRAN and R >= 4.0 is highly recommended. 

```{r, eval = FALSE}
# install latest version of crawl from CRAN
install.packages("crawl")
```

However, should `{crawl}` v 2.3.0 fail to pass CRAN checks it will be archived 
on CRAN and all future bug and check fixes will only be available on this 
repository and the R-universe repository described in the next section. So, if 
you cannot find `{crawl}` on CRAN, this has probably happened. 


### Install via R-Universe

The latest version of `{crawl}` is also available via R-Universe.

```{r, eval = FALSE}
# Install crawl from my R-Universe repository
# Enable repository from dsjohnson

options(repos = c(
  dsjohnson = 'https://dsjohnson.r-universe.dev',
  CRAN = 'https://cloud.r-project.org'))

# Download and install crawl in R
install.packages('crawl')

# Browse the crawl manual pages
help(package = 'crawl')
```

You can also add the repository to your local list of repositories in your
*.Rprofile* and this will ensure `update.packages()` pulls any new releases
of `{crawl}` from R-Universe

```{r, eval = FALSE}
#install.packages("usethis")
usethis::edit_r_profile()

# add the following text or replace existing repos option

options(repos = c(dsjohnson = 'https://dsjohnson.r-universe.dev',
                  CRAN = 'https://cloud.r-project.org'))
```

### Install via Github

A development version  of `{crawl}` is also available from
[GitHub](https://github.com/NMML/crawl). This version should be used with 
caution and only after consulting with package authors.

```{r, eval = FALSE}
# install.packages("remotes")
remotes::install_github("NMML/crawl@devel")
```

### Disclaimer
This repository is a scientific product and is not official communication of the
National Oceanic and Atmospheric Administration, or the United States Department
of Commerce. All NOAA GitHub project code is provided on an ‘as is’ basis and
the user assumes responsibility for its use. NOAA and DOC have relinquished
control of the information and no longer has responsibility to protect the
integrity, confidentiality, or availability of the information. Any claims
against the Department of Commerce or Department of Commerce bureaus stemming
from the use of this GitHub project will be governed by all applicable Federal
law. Any reference to specific commercial products, processes, or services by
service mark, trademark, manufacturer, or otherwise, does not constitute or
imply their endorsement, recommendation or favoring by the Department of
Commerce. The Department of Commerce seal and logo, or the seal and logo of a
DOC bureau, shall not be used in any manner to imply endorsement of any
commercial product or activity by DOC or the United States Government.