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install.txt
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install.txt
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## Installation and Getting Started
### REQUIRED: Updated version of R (>= 3.5.0, released on 23 April 2018):
R is free and open source software for statistical computing. If R is not installed on your computer or if your version of R is <3.5.0, download and install the latest version from https://cran.r-project.org/, following the instructions provided at the site. In particular, "Download" and then "install R for the first time" (if working in Windows), or "Download" and then follow the further instructions on the subsequent web page (if working on Mac OS or Linux-like OS). If you already have an older copy of R installed on your computer, the new version will be installed alongside the old. Unless you know a reason why you want to keep both versions, it is usually a good idea to uninstall the old version to avoid confusion and clutter.
NOTE TO EXPERIENCED R USERS: When you install a new version of R, packages that you previously installed under an older version may not be immediately available to the new R. If not, the easiest way to make them available is to copy the package folders in your old "library" folder into the "library" folder in your new R installation. Then, enter `update.packages()` in R. If asked about a CRAN mirror, choose the nearest location. If you are working in Windows OS and are asked whether you want to install packages "from source", choose "No".
### OPTION 1: Installing GenEst from CRAN (Comprehensive R Archive Network)
A copy of the latest release of GenEst is available on CRAN, which provides a relatively simple pathway for installation. If you are working in Rstudio, click "Tools" and "Install packages". Enter `GenEst` in the form and click "Install". If you are working directly in the R command line, select "Install package(s)" from the "Packages" menu and find GenEst in the LONG list of available packages. If this menu command does not seem to do anything, try entering the following on the R command line: `install.packages("GenEst")`
If asked about a CRAN mirror, choose the nearest location. If asked whether you want to install in a "personal" directory, choose "yes". If asked if you want to install dependencies from source, choose "no".
This should install GenEst and all the third-party packages it requires.
### OPTION 2: Installing GenEst from https://code.usgs.gov/ecosystems/GenEst
GenEst may also be installed from code.usgs.gov. Setup and installation require several steps. Do not skip any steps.
#### Third-party packages:
Several third-party pacakges are required; all are free and open source and available from CRAN. The easiest way to install them is to run the following commands in R (with guidance concerning potential dialog boxes given below the commands):
```
package_req <- c("corpus", "DT", "gsl", "gtools", "hellno", "htmltools", "lubridate", "MASS",
"matrixStats", "mvtnorm", "Rcpp", "shiny", "shinyjs", "survival")
package_new <- package_req[!(package_req %in% installed.packages()[,"Package"])]
if (length(package_new) > 0) install.packages(package_new)
if (packageVersion("htmltools") < "1.5") install.packages("htmltools")
if (packageVersion("shiny") < "1.4.0") install.packages("shiny")
```
\-- If asked about a "CRAN mirror", choose the nearest location.
\-- If asked whether you want to use a "personal library", choose "Yes"
\-- If you are on Windows and are asked whether you want to install packages and their dependencies "from source", choose "No" (unless you are ready to go to lunch, in which case, you can select "Yes" and the installation may well be done by the time you get back).
#### GenEst:
Navigate to https://code.usgs.gov/ecosystems/GenEst/releases.
\-- For Windows, download the compressed folder GenEst_1.4.4.zip (do not unzip) and note where it is stored. You will install from the local .zip folder.
\-- For Mac OS or Unix-like OS, download the compressed file GenEst_1.4.4.tar.gz (do not unzip) and note where it is stored. You will install from the local .tar.gz file.
\-- Next, if you are working directly in R (not R Studio), run the following command:
```
install.packages(file.choose()) # and navigate to the package archive file you just downloaded:
GenEst_1.4.4.zip or GenEst_1.4.4.tar.gz
```
\-- Or, if you are working in R Studio:
Click "Install" in the Packages pane.
Select "Package Archive File (.zip; .tar.gz)" as "Install from:" in the dialog box.
Browse to where you saved the zip file, and open it so it appears in the "Package archive" space.
Click the Install button on the dialog box.
## Getting Started
### Graphical user interface (GUI): easy-to-use buttons and menus
Once the software has been installed, to start the GUI, open R and enter the commands:
```
library(GenEst)
runGenEst()
```
Download the User Guide from a link near the bottom of the "Help" page in the app or from https://pubs.usgs.gov/tm/7c19/tm7c19.pdf
### R command line: more functionality and flexibility
```
library(GenEst)
browseVignettes("GenEst")
?GenEst
```
Also, help files for GenEst functions are accessible in the standard R way, for example:
```
?pkm
```
## Further Reading
GenEst User Guide: https://doi.org/10.3133/tm7C19
GenEst Statistical Models: https://doi.org/10.3133/tm7A2
To download source code, use the cloud download drop-down menu in the upper right of this page.