GenEst is a tool for estimating mortalities fromefficiency, persistence, and carcass data.
This software is preliminary or provisional and is subject torevision. It is being provided to meet the need for timely best science.The software has not received final approval by the U.S. GeologicalSurvey (USGS). No warranty, expressed or implied, is made by the USGS orthe U.S. Government as to the functionality of the software and relatedmaterial nor shall the fact of release constitute any such warranty. Thesoftware is provided on the condition that neither the USGS nor the U.S.Government shall be held liable for any damages resulting from theauthorized or unauthorized use of the software.
Setup and installation require several steps. Do not skip anysteps.
R is free and open source software for statistical computing. If R isnot installed on your computer or if your version of R is <3.5.0,download and install the latest version fromhttps://cran.r-project.org/, following the instructions provided at thesite. In particular, “Download” and then “install R for the first time”(if working in Windows), or “Download” and then follow the furtherinstructions on the subsequent web page (if working on Mac OS orLinux-like OS). If you already have an older copy of R installed on yourcomputer, the new version will be installed alongside the old. Unlessyou know a reason why you want to keep both versions, it is usually agood idea to uninstall the old version to avoid confusion andclutter.
NOTE TO EXPERIENCED R USERS: When you install a new version of R,packages that you previously installed under an older version may not beimmediately available to the new R. If not, the easiest way to make themavailable is to copy the package folders in your old “library” folderinto the “library” folder in your new R installation. Then, enterupdate.packages() in R. If asked about a CRAN mirror,choose the nearest location. If you are working in Windows OS and areasked whether you want to install packages “from source”, choose“No”.
Several third-party pacakges are required; all are free and opensource and available from CRAN. The easiest way to install them is torun the following commands in R (with guidance concerning potentialdialog boxes given below the commands):
package_req <- c("corpus", "DT", "gsl", "gtools", "htmltools", "htmlwidgets", "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("htmlwidgets") < "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 installpackages and their dependencies “from source”, choose “No” (unless youare ready to go to lunch, in which case, you can select “Yes” and theinstallation may well be done by the time you get back).
Click on “Tags” under the “Repository” tab on the left sidebar athttps://code.usgs.gov/ecosystems/GenEst and then click the link for thespecific release you want.
– For Windows, download the compressed folder GenEst_1.x.x.zip (donot 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 fileGenEst_1.x.x.tar.gz and note where it is stored. You will install fromthe local .tar.gz file.
If you are working directly in R (not R Studio), run the followingcommand:
install.packages(file.choose()) # and navigate to the package archive file you just downloaded: GenEst_1.x.x.xxxIf you are working in R Studio:
Click “Install” in the Packages pane.
Select “Package Archive File (.zip; .tar.gz)” as “Install from:” inthe dialog box.
Browse to where you saved the zip file, and open it so it appears inthe “Package archive” space.
Click the Install button on the dialog box.
To start the GUI, open R and enter the command:
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
library(GenEst)browseVignettes("GenEst")?GenEstAlso, help files for GenEst functions are accessible in the standardR way, for example:
?pkmGenEst User Guide: https://doi.org/10.3133/tm7C19
GenEst Statistical Models: https://doi.org/10.3133/tm7A2