GenEst v1.2.0

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Generalized Mortality Estimator

Command-line and 'shiny' GUI implementation of the GenEst models for estimating bird and bat mortality at wind and solar power facilities, following Dalthorp, et al. (2018) <doi:10.3133/tm7A2>.

Readme

GenEst

GenEst: Generalized Fatality Estimator

GenEst is a tool for estimating mortalities from efficiency, persistence, and carcass data.

DISCLAIMER

This software is preliminary or provisional and is subject to revision. It is being provided to meet the need for timely best science. The software has not received final approval by the U.S. Geological Survey (USGS). No warranty, expressed or implied, is made by the USGS or the U.S. Government as to the functionality of the software and related material nor shall the fact of release constitute any such warranty. The software is provided on the condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from the authorized or unauthorized use of the software.

Installation

Setup and installation require several steps. Do not skip any steps.

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".

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_new <- c("cbinom", "corpus", "DT", "gsl", "gtools", "htmltools", "lubridate", 
   "matrixStats", "mvtnorm", "Rcpp", "shiny", "shinyjs", "sticky", "survival", "zip")
package_new <- package_new[!(package_new %in% installed.packages()[,"Package"])] 
if(length(package_new) > 0) install.packages(package_new)

-- 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:

Click on "Tags" under the "Repository" tab on the left sidebar at https://code.usgs.gov/ecosystems/GenEst and then click the link for the specific release you want.

-- For Windows, download the compressed folder GenEst_1.x.x.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.x.x.tar.gz and note where it is stored. You will install from the local .tar.gz file.

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.x.x.xxx

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

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

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

Functions in GenEst

Name Description
Ecbinom Expected value of a continuous binomial with size = 1/g
aicc.pkmSetSize Create the AICc tables for a list of sets of searcher efficiency models
aicc.pkmSize Create the AICc tables for a list of sets of searcher efficiency models
combinePreds Combine predictors
combinePredsAcrossModels Combine predictors across models
cpmSetSizeFailRemove Remove failed cpm models from a cpmSetSize object
cpmSetSpecCPCellPlot Plot cell-specific decay curve for carcass persistence
dlModTabCP Create the download version of the Carcass Persistence model table
dlModTabSE Create the download version of the Searcher Efficiency model table
GenEstInlineCSS Generate the Inline CSS Definition
GenEstServer The GenEst server definition function
SEsi0 Calculate decayed searcher efficiency for a single pk
downloadMFig Download the M figure
SEsi_left Calculate conditional probability of observation at a search
CPcols Produce a named vector of standard CP plot colors
CPdistOptions Produce the options for the distributions in the CP model
SEsi_right Calculate conditional probability of observation after a series of searches
aboutContent Create the Content for the About Pabel
calcRate Estimate the number of fatalities in each search interval throughout the monitoring period.
averageSS Tabulate an average search schedule from a multi-unit SS data table
cButtonStyle Define Clear Button Style
classText Prepare class text header
DWPCols Select the DWP-ok columns from a data table
calcSplits Estimate the number of fatalities by up to two splitting covariates
checkComponents Check for model components
downloadSEFig Download the SE figure
checkDate Checks whether a vector of data can be interpreted as dates
clearNotifications Clear all notifications
kFixedWidget Make a kFixed Widget
GenEstShinyJS Shiny Java Script (via shinyjs) Enabler
cpmFail Check if a CP model is well-fit
cpm Fit cp carcass persistence models
DWPbyCarcass Assign DWP value to each carcass
cpmCPCellPlot Plot cell-specific decay curve for carcass persistence
aicc.cpmSetSize Create the AICc tables for a list of sets of searcher efficiency models
aicc.cpmSet Create the AICc tables for a set of carcass persistence models
calcTsplit Estimate the number of fatalities by time interval
countCarcs Count the minimum number of carcasses in the cells
calcg Calculate cell-level generic detection probability
GenEstUI Create the GenEst User Interface HTML
cpmSetFail Check if cpm models fail
dataInputWidget Create a Data Input Widget for the GenEst User Interface HTML
logit Compute the logit or anti-logit
modelSetModelPredictors Determine the predictors from each model in a model set
estM Estimate mortality
dataTabPanel Create a Data Tab Panel for the GenEst User Interface HTML
estText Prepare the text for the estimation table
msgModSENobs Create the SE data size notification
modelSetPredictors Determine the predictors for a whole model set
defineUnitCol Auto-parsing to find the name of the unit column (unitCol) If a unit column is not explicitly defined by user in the arg list to estM or estg, then defineUnitCol parses the CO, DWP, and SS files to extract the unit column if possible. Criteria that a column must meet to be a unit column are that it is found in both data_CO and data_DWP, all units in data_CO must also be included among units in data_DWP, all units in both data_CO and data_DWP must be included among the column names in data_SS. If data_DWP = NULL, then the unit column must be included in data_CO and all its units must be included among the column names of data_SS.
aicc Generic S3 function for summarizing AICc
gettingStartedContent Create the Content for the Getting Started Pabel
initialOutput Update the output list upon initiation of the app
msgModWarning Create the warning message for a model run (if needed)
modNameSplit Split model names into their components and remove only a desired one
msgList Produce the message list
msgFracNote Create the message for when an incorrect FFS is input
modelInputWidget Create a Model Input Widget for the GenEst User Interface HTML
disclaimersContent Create the Content for the Disclaimers Pabel
estgGenericSize Estimate generic detection probability for multiple size classes
pickSizeclass Locate the sizeclass selected by the inputs
msgSampleSize Create the warning message text for small sample sizes
cpLogLik Calculate the negative log-likelihood of a carcass persistence model
pkmSetAllFail Check if all of the pkm models fail within a given set
pkLogLik Calculate the negative log-likelihood of a searcher efficiency model
msgSplitFail Create the fail message for when splits aren't done correctly
expandModelSetCP Expand a CP model set for plotting
initialReactiveValues Create the main reactive value list for GenEst
cpmSetFailRemove Remove failed cpm models from a cpmSet object
aicc.cpm Extract AIC and AICc for a carcass persistence model
isNeverDecreasing Is a vector never decreasing?
cpmSetSizeFail Check if all of the cpm models fail
dateCols Select the date columns from a data table
pkmSetFail Check if pkm models fail
plotCPCells Plot the cellwise results of a single model in a set of CP models
pkmParamPlot Plot parameter box plots for each cell for either p or k
dateToDay Calculate day of study from calendar date
plotCPFigure Plot results of a single CP model in a set
pkmSECellPlot Plot cell-specific decay curve for searcher efficiency
plot.gGeneric Plot results of a single generic ghat estimation
aicc.pkm extract AICc value from pkm object
checkSpecificModelCP Error check a specific model selection for a CP plot
modelRunWidget Create a Model Run Widget for the GenEst User Interface HTML
modelSelectionWidget Make a Model Selection Widget
plotSEBoxPlots p and k box plots for an SE model set
aicc.pkmSet Create the AICc tables for a set of searcher efficiency models
plotSEBoxTemplate template box plot
msgSSavgFail Create the warning message for when the SS average doesn't work
prettySplitTab Create the pretty version of the split summary table
msgSSinputFail Create the warning message for when the SS based on inputs doesn't work
print.corpus_frame Generic S3 function for printing corpus_frame
downloadTable Download a table
plot.gGenericSize Plot results of a set of size-based generic ghat estimations
plotCPHeader The CP plot header
checkSpecificModelSE Error check a specific model selection for an SE plot
removeCols Remove selected columns from column names
refMod Return the model with the greatest log-likelihood
obsCols_fta Select the columns from a data table that could be CP First Time Absent observations
simpleMplot Plot a total mortality estimation for a simple situation
downloadgFig Download the g figure
obsCols_ltp Select the columns from a data table that could be CP Last Time Present observations
sizeCols Select the potential size class columns from a data table
pkmSetSpecParamPlot p or k box plots for an SE model set
pkmSetSizeFailRemove Remove failed pkm models from a pkmSetSize object
plotNA Produce a blank plot for unsucessful fits
transposeSplits Transpose a splitFull array (preserving attributes)
createvtext Create the version text for GenEst
prepSS Create search schedule data into an prepSS object for convenient splits analyses
dataDownloadWidget Create a Data Download Widget for the GenEst User Interface HTML
trimSetSize Trim a Model-Set-Size Complex to a Single Model Per Size
ltranspose Transpose a list of arrays
plot.splitFull Plot summary statistics for splits of mortality estimates
plot.splitSummary Plot summary statistics for splits of mortality estimates
prepSizeclassText Prepare text for size classes
renderDTns Render a data table without server-side processing
wind_RP Wind Road and Pad (120m) Example
predsCols Select the predictor-ok columns from a data table
rpk Simulate parameters from a fitted pk model
downloadCPFig Download the CP figure
downloadData Download a zipped data set
matchCells Match cells between models.
modelSetCells Determine the cell table for a full model set
estg Estimate all carcass-level detection rates and arrival intervals
estgGeneric Estimate generic g
mock A mock example data set
solar_trough Trough-based solar thermal power simulated example
modNamePaste Paste the parts of a model's name back together
modelSetModelCells Determine the cells from each model in a model set
wind_RPbat Wind Bat-Only Road and Pad (120m) Example
style HTML tag functions
tidyModelSetCP Tidy a CP model set
modelOutputWidget Create a Model Output Widget for the GenEst User Interface HTML
modelOutputPanel Create a Model Output Tab Panel for the GenEst User Interface HTML
prepPredictors Prepare predictors based on inputs
prettyModTabCP Create the pretty version of the Carcass Persistence model table
prettyModTabSE Create the pretty version of the Searcher Efficiency model table
tidyModelSetSE Tidy an SE model set
selectedDataPanel Create a Selected Data Tab Panel for the GenEst User Interface HTML
msgModDone Create a model done message
setFigW Set Figure width and height based on the number of cells
setNotSuspending (Re)set outputOptions to not suspending for given elements
update_output Update the outputs when an event occurs
setkNeed Create the kNeed text
msgModPartialFail Create the warning message text for when only some models are fit successfully
trueLength Get the length of real (non-NA) things
msgModRun Create a model running message
navbar Create the HTML for the navigation bar UI element
obsCols_SE Select the columns from a data table that could be SE observations
msgModFail Create the error message for when no models are fit successfully
update_rv Update the reactive value list when an event occurs
pkmSetSpecSECellPlot Plot cell-specific decay curve for searcher efficiency for a specific model with comparison to the cellwise model
pkmSetSizeFail Check if all of the pkm models fail
pkm Fit pk searcher efficiency models.
pkmSetFailRemove Remove failed pkm models from a pkmSet object
pkmFail Check if a pk model is well-fit
plot.cpm Plot results of a single CP model
plot.cpmSet Plot results of a set of CP models
plotSEHeader The SE plot header
plot.pkm Plot results of a single pk model
plot.estM Plot total mortality estimation
updateColNames_size Update the string of column names that are in all the needed tables
plot.pkmSet Plot results of a set of SE models
plotSECells Plot the cellwise results of a single model in a set of SE models
widgetMaker Input Widget Maker
updatesizeCol Update the name of the size class column based on available names
ppersist Calculate the probability of persistence to detection
plotSEFigure Plot results of a single SE model in a set
reNULL Reset values of a list to NULL
print.cpm Print a cpm model object
rcp Simulate parameters from a fitted cp model
print.pkm Print a pkm model object
reVal Reset values of a reactive values list
readCSV Read in csv files in either format
runGenEst Launch the GenEst Application
solar_PV Photovoltaic Example Dataset
summary.estM Summarize total mortality estimation
selectData Select particular columns from a data set
solar_powerTower Power Tower Example Dataset
summary.gGeneric Summarize the gGeneric list to a simple table
summary.gGenericSize Summarize the gGenericSize list to a list of simple tables
updateSizeclasses Update the size classes
update_input Update the inputs when an event occurs
summary.splitFull Summarize results of mortality estimate splits
wind_cleared Wind cleared plot (60m) Search Example
GenEst Generalized estimation of mortality
SEcols Produce a named vectory with standard SE plot colors
SEsi Calculate decayed searcher efficiency
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Vignettes of GenEst

Name
GenEstGUI.Rmd
command-line-example.Rmd
solar-examples.Rmd
wind-examples.Rmd
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Details

Date 2018-12-06
License CC0
Encoding UTF-8
LazyData true
RoxygenNote 6.1.1
VignetteBuilder knitr
LinkingTo Rcpp
NeedsCompilation yes
Packaged 2018-12-06 17:17:01 UTC; ddalthorp
Repository CRAN
Date/Publication 2018-12-06 22:20:02 UTC

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