install-load-tagtools.RmdWelcome to this vignette! On behalf of the team behind tagtools, thanks for taking some time to get to know this package. We hope it is useful to you.
In this vignette you will complete the first important setup steps of installing the package on your machine and making sure it is loaded in your session.
Estimated time for this vignette: 15 minutes
Before you begin, you must have R and—recommended—RStudio installed on your computer. You can download this software at RStudio.com (you only need the free one).
Alternatively, you can work in RStudio.cloud. This is free too, and it is nice that no download is required. The drawback is that, with your free RStudio.cloud account, you are limited at a certain number of project-hours per month, RAM, and CPU. One who does a lot of work in RStudio, several hours a day, will run out of hours within a week or two. The desktop version has fewer restraints.
If you happen to be new to R also, here is a very nice standalone tutorial.
These practicals assume that you have some basic experience working with R/RStudio, and can execute provided code, making some user-specific changes along the way (e.g. to help R find a file you downloaded).
If you have devtools installed on your computer, you can use it to install the tagtools package directly from github.
If you want or need to install devtools, or want more information about it, see the online installation guide at r-project.org.
The code below gives the devtools command to install. Click “Code” at the right to open the chunk, then you should be able to copy-paste the code into your R console. However, be careful when copy-pasting special characters such as _underscores_, and ‘quotes’. If you get an error, one thing to check is that you have just a single, simple underscore, and 'straight quotes', whether 'single' or "double" (rather than “smart quotes”).
devtools::install_github('stacyderuiter/TagTools/R/tagtools',
build_vignettes = TRUE)If you are asked something like “These packages have more recent versions available”, it is no harm to update them all, and to “install from sources the packages which need compilation”.
With the package as of July 2021, the overall process should take ten to fifteen minutes, depending on the speed of your internet and machine, some eight minutes of which are spent building vignettes. Receiving an abundance of red messages is not the end of the world—this is just how R shows that a package is being installed. If it ends with the message "* DONE (tagtools)", you’re all set!
If you do not want to use the devtools option, you can install the tagtools package from the archive files provided with materials from the WMMC 2019 workshop (in the folder created by unzipping wmmc-2019-workshop-materials.zip). These archive files are also available at the TagTools website. Try http://animaltags.org , or https://animaltags.netlify.app .
Note: if you choose to install from archive files (.zip or .tgz), you will probably also have to manually install all the packages tagtools depends on. If you use the devtools method above, you will not.
Save the appropriate archive to a known location on your computer.
Then, run:
install.packages('YourPath/YourFilename') # you'll have to edit this appropriately(fill in the absolute or relative path to the archive file, and the archive file name). For example, on a Mac, if the file is saved to Downloads, your path might look like this:
install.packages('/Users/YourUsernameHere/Downloads/FileName.tgz')You can also use the “install packages” GUI in RStudio—go to the “Packages” tab, click “Install”, choose “Package Archive File” from the “Install From” pulldown menu, and then navigate to the archive file. Then follow the prompts.
You must also make sure you have installed all the packages that tagtools depends on:
dpnds <- c('CircStats', 'ggformula', 'graphics', 'hht',
'latex2exp', 'lubridate', 'magrittr',
'matlab', 'ncdf4', 'plotly', 'pracma',
'readr', 'rgl', 'signal', 'stats',
'utils', 'zoo', 'zoom')
install.packages(pkgs = dpnds)Note here that we are writing an object dpnds, which is a vector of these 18 (text) strings, concatenated together with c(). Then install.packages() can take all these dependencies as an input.
Once the tagtools are successfully installed, you should be able to run
library(tagtools)You will often get this message: “The following object is masked from ‘package:stats’: smooth”—this means you have loaded it properly; congratulations!
Another check is to make sure that function help files are accessible; for example,
?load_ncNow or at any point in the future when doing a check like this, you might get an error saying the function doesn’t exist. When this happens, make sure you have tagtools loaded in your library. While you won’t have to reinstall the package with install.packages() unless you start working on a different machine, you will have to run library(tagtools) or require(tagtools) every time you restart RStudio.
Having fewer packages loaded is kinder to your computer’s memory, so it is good that R doesn’t automatically load everything. However, it does mean that every time you restart RStudio, you must reload the packages you need, such as tagtools, yourself. Thus at the beginning of each vignette after this one you’ll be reminded to run library(tagtools).
If the command ? load_nc pulls up a help file for the function load_nc like it should, you’re all set.
If you’ve run the devtools command, you can read these vignettes directly in your local RStudio without needing to click through the website! The syntax is very straightforward. To see the list of vignettes in just this package, simply type:
vignette(package = "tagtools")## [1] "Vignettes in package ‘tagtools’:"
## [1] ""
## [1] "complementary-filtering complementary-filtering (source, html)"
## [1] "data-quality-error-correction data-quality-error-correction (source, html)"
## [1] "Detectors Detectors (source, html)"
## [1] "detectors-draft detectors-draft (source, html)"
## [1] "dive-stats dive-stats (source, html)"
## [1] "find-dives find-dives (source, html)"
## [1] "fine-scale-tracking fine-scale-tracking (source, html)"
## [1] "install-load-tagtools install-load-tagtools (source, html)"
## [1] "jerk-transients jerk-transients (source, html)"
## [1] "load-tag-data load-tag-data (source, html)"
## [1] "mahalanobis-distance mahalanobis-distance (source, html)"
## [1] "more-filtering more-filtering (source, html)"
## [1] "plots-and-cropping plots-and-cropping (source, html)"
## [1] "rotation-test rotation-test (source, html)"
## [1] "tag-to-whale-frame tag-to-whale-frame (source, html)"
## [1] "vectors-vs-structures vectors-vs-structures (source, html)"Then you can run any vignette with vignette('package-index', package = 'tagtools'). For instance, in order to see this vignette, you can run:
vignette("install-load-tagtools", package = "tagtools")The package = "tagtools" argument at the end is optional. However, it is a good addition because it clarifies which package you are working in. So, if there happened to be, say, another vectors-vs-structures vignette in some other package, you could load the one that is specific to this package with vignette("vectors-vs-structures", package = "tagtools").
What have you learned so far? Important setup steps that will help avoid confusion and delay moving forward.
Congrats!
If you’d like to continue working through these vignettes, load-tag-data and plots-and-cropping are good options to help you get started with the tools you’ve just installed and loaded.
Perhaps your best starting option is ‘load-tag-data’, helpful for familiarizing yourself with the process of loading in data, as well as making sure that important metadata is included in the data.
vignette('load-tag-data', package = 'tagtools')vectors-vs-structures is a quick review of the way R stores data in structures, and how these can be extracted to individual vectors/scalars.
vignette('vectors-vs-structures', package = 'tagtools')If you already feel confident with setup and structures in R, try plots-and-cropping—you’ll get to start visualizing some data of the types you’ve been learning to load.
vignette('plots-and-cropping', package = 'tagtools')Animaltags home pages: http://animaltags.org/ (old), https://animaltags.netlify.app/ (new), https://github.com/stacyderuiter/TagTools (for latest beta source code), https://stacyderuiter.github.io/TagTools/articles/TagTools (vignettes overview)