From 0a0c4c5ee4ac47a59050f5c81d891ae1fd043a92 Mon Sep 17 00:00:00 2001 From: Doi90 Date: Wed, 24 Apr 2019 19:42:55 +1000 Subject: [PATCH 1/5] Add extra arguments to MaxEnt module. Rebuild documentation --- DESCRIPTION | 2 +- R/MaxEnt.R | 35 +++++++++++++++++++++-------- man/AIC.Rd | 1 + man/AUC.Rd | 1 + man/AddRandomUniformPredictors.Rd | 1 + man/AirNCEP.Rd | 1 + man/AnophelesPlumbeus.Rd | 1 + man/Appify.Rd | 1 + man/Background.Rd | 1 + man/BackgroundAndCrossvalid.Rd | 1 + man/Bioclim.Rd | 4 +++- man/Bioclim_future.Rd | 1 + man/BiomodModel.Rd | 1 + man/Bootstrap.Rd | 1 + man/CWBZimbabwe.Rd | 1 + man/CarolinaWrenPA.Rd | 1 + man/CarolinaWrenPO.Rd | 1 + man/CarolinaWrenRasters.Rd | 1 + man/CarolinaWrenValidation.Rd | 1 + man/Clean.Rd | 1 + man/CoefficientPlot.Rd | 1 + man/CovHistograms.Rd | 1 + man/Crossvalidate.Rd | 1 + man/DataSummary.Rd | 1 + man/Deviance.Rd | 1 + man/Domain.Rd | 1 + man/GBM.Rd | 1 + man/GenerateCovariateReport.Rd | 1 + man/InteractiveCovariateMap.Rd | 1 + man/InteractiveMap.Rd | 1 + man/InteractiveOccurrenceMap.Rd | 1 + man/JitterOccurrence.Rd | 1 + man/LocalOccurrenceData.Rd | 8 ++++--- man/LocalOccurrenceDataFrame.Rd | 1 + man/LocalRaster.Rd | 1 + man/LogisticRegression.Rd | 1 + man/Lorem_ipsum_UK.Rd | 1 + man/MESSMask.Rd | 1 + man/MachineLearn.Rd | 1 + man/MaxEnt.Rd | 16 ++++++++++--- man/MaxLike.Rd | 1 + man/MaxNet.Rd | 5 +++-- man/MyMaxLike.Rd | 1 + man/NATrees.Rd | 1 + man/NCEP.Rd | 4 +++- man/NaiveRandomPresence.Rd | 5 +++-- man/NaiveRandomPresenceAbsence.Rd | 1 + man/NaiveRandomRaster.Rd | 5 +++-- man/NoOutput.Rd | 1 + man/NoProcess.Rd | 1 + man/NullModel.Rd | 1 + man/OneHundredBackground.Rd | 1 + man/OneThousandBackground.Rd | 1 + man/OptGRaF.Rd | 1 + man/PairPlot.Rd | 1 + man/PartitionDisc.Rd | 1 + man/PerformanceMeasures.Rd | 1 + man/PredictNewRasterMap.Rd | 1 + man/PrintMap.Rd | 1 + man/PrintOccurrenceMap.Rd | 5 +++-- man/QuickGRaF.Rd | 1 + man/ROCcurve.Rd | 1 + man/RandomForest.Rd | 1 + man/ReliabilityPlot.Rd | 1 + man/ResponseCurve.Rd | 1 + man/ResponseCurveViz.Rd | 1 + man/ResponsePlot.Rd | 1 + man/SameTimePlaceMap.Rd | 1 + man/SeparatePA.Rd | 1 + man/SpOcc.Rd | 1 + man/StandardiseCov.Rd | 1 + man/StochasticLogisticRegression.Rd | 1 + man/SubsampleOccurrence.Rd | 1 + man/SugarMaple.Rd | 1 + man/SurfaceMap.Rd | 1 + man/TargetGroupBackground.Rd | 1 + man/Transform.Rd | 1 + man/UKAir.Rd | 1 + man/UKAnophelesPlumbeus.Rd | 1 + man/UKBioclim.Rd | 1 + man/VariableImportance.Rd | 1 + man/addInteraction.Rd | 1 + man/mgcv.Rd | 1 + man/spThin.Rd | 1 + 84 files changed, 137 insertions(+), 26 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index da82430..86ce265 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -52,4 +52,4 @@ Suggests: roxygen2 VignetteBuilder: knitr LazyData: TRUE -RoxygenNote: 6.0.1 +RoxygenNote: 6.1.0 diff --git a/R/MaxEnt.R b/R/MaxEnt.R index 85796bf..fb1e441 100644 --- a/R/MaxEnt.R +++ b/R/MaxEnt.R @@ -2,13 +2,13 @@ #' #' @description Model module to fit MaxEnt model via the dismo package #' -#'@details In order to fit a MaxEnt model, you must first download the +#' @details In order to fit a MaxEnt model, you must first download the #' MaxEnt executable file \code{maxent.jar} and save it in the correct location. #' The zoon function \code{GetMaxEnt} can orchestrate this for you. #' Running MaxEnt also requires an up-to-date version of java #' (which you may already have installed). #' -#'@param .df \strong{Internal parameter, do not use in the workflow function}. +#' @param .df \strong{Internal parameter, do not use in the workflow function}. #' \code{.df} is data frame that combines the occurrence data and covariate #' data. \code{.df} is passed automatically in workflow from the process #' module(s) to the model module(s) and should not be passed by the user. @@ -21,20 +21,36 @@ #' (which may or may not be up-to-date) in this forum: #' \url{https://groups.google.com/d/msg/maxent/yRBlvZ1_9rQ/Fj8Two0lmHIJ}. #' +#' @param path Filepath to choose where to save MaxEnt's html output file. Defaults +#' to getwd(). +#' +#' @param factors Character string of the name of variables to be treated as factors. +#' #' @seealso \code{\link{dismo::maxent}} #' -#' @author ZOON Developers, \email{zoonproject@@gmail.com} -#' @section Version: 1.0 +#' @author ZOON Developers, David Wilkinson \email{zoonproject@@gmail.com} +#' @section Version: 1.1 #' @section Date submitted: 2015-11-13 +#' @section Date modified: 2018-04-24 #' @section Data type: presence/background #' #' @name MaxEnt #' @family model -MaxEnt <- function(.df, args = ''){ + +MaxEnt <- function(.df, + args = '', + path = getwd(), + factors = NULL){ zoon::GetPackage('dismo') zoon::GetPackage('rJava') + if(!is.null(factors)){ + + .df[ , factors] <- as.factor(.df[ , factors]) + + } + covs <- as.data.frame(.df[, attr(.df, 'covCols')]) names(covs) <- attr(.df, 'covCols') @@ -49,7 +65,8 @@ MaxEnt <- function(.df, args = ''){ m <- maxent(x = covs, p = .df$value, - args = args) + args = args, + path = path) # create a ZoonModel object and return it ZoonModel(model = m, @@ -62,9 +79,9 @@ MaxEnt <- function(.df, args = ''){ na_idx <- attr(newdata_clean, 'na.action') if (is.null(na_idx)) idx <- 1:nrow(newdata) else idx <- -na_idx - p[idx] <- dismo::predict(model, - newdata_clean, - type = 'response') + p[idx] <- dismo::predict(model, + newdata_clean, + type = 'response') return (p) }, packages = 'dismo') diff --git a/man/AIC.Rd b/man/AIC.Rd index 7900c7a..1c9d2bf 100644 --- a/man/AIC.Rd +++ b/man/AIC.Rd @@ -54,3 +54,4 @@ Other output: \code{\link{AUC}}, \code{\link{Appify}}, \author{ Liz Martin, \email{lizmartinresearch@gmail.com} } +\concept{output} diff --git a/man/AUC.Rd b/man/AUC.Rd index 35434ec..b0cc42c 100644 --- a/man/AUC.Rd +++ b/man/AUC.Rd @@ -52,3 +52,4 @@ Other output: \code{\link{AIC}}, \code{\link{Appify}}, \author{ Liz Martin, \email{emartin@student.unimelb.edu.au} } +\concept{output} diff --git a/man/AddRandomUniformPredictors.Rd b/man/AddRandomUniformPredictors.Rd index 097a084..92350a7 100644 --- a/man/AddRandomUniformPredictors.Rd +++ b/man/AddRandomUniformPredictors.Rd @@ -70,3 +70,4 @@ Other process: \code{\link{BackgroundAndCrossvalid}}, \author{ James Campbell, \email{jamesadamcampbell@gmail.com} } +\concept{process} diff --git a/man/AirNCEP.Rd b/man/AirNCEP.Rd index 4b9ddb1..ec25936 100644 --- a/man/AirNCEP.Rd +++ b/man/AirNCEP.Rd @@ -33,3 +33,4 @@ Other covariate: \code{\link{Bioclim_future}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{covariate} diff --git a/man/AnophelesPlumbeus.Rd b/man/AnophelesPlumbeus.Rd index b66a903..892bbe0 100644 --- a/man/AnophelesPlumbeus.Rd +++ b/man/AnophelesPlumbeus.Rd @@ -42,3 +42,4 @@ Other occurrence: \code{\link{CWBZimbabwe}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{occurrence} diff --git a/man/Appify.Rd b/man/Appify.Rd index df91cee..13b6a30 100644 --- a/man/Appify.Rd +++ b/man/Appify.Rd @@ -56,3 +56,4 @@ Other output: \code{\link{AIC}}, \code{\link{AUC}}, \author{ ZOON Developers, Tom August, \email{zoonproject@gmail.com} } +\concept{output} diff --git a/man/Background.Rd b/man/Background.Rd index c726b73..c9e58ad 100644 --- a/man/Background.Rd +++ b/man/Background.Rd @@ -61,3 +61,4 @@ Other process: \code{\link{AddRandomUniformPredictors}}, \author{ ZOON Developers, Simon Kapitza \email{zoonproject@gmail.com} } +\concept{process} diff --git a/man/BackgroundAndCrossvalid.Rd b/man/BackgroundAndCrossvalid.Rd index a4c7696..81c3c67 100644 --- a/man/BackgroundAndCrossvalid.Rd +++ b/man/BackgroundAndCrossvalid.Rd @@ -48,3 +48,4 @@ Other process: \code{\link{AddRandomUniformPredictors}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{process} diff --git a/man/Bioclim.Rd b/man/Bioclim.Rd index 7ab9534..455c9de 100644 --- a/man/Bioclim.Rd +++ b/man/Bioclim.Rd @@ -4,7 +4,8 @@ \alias{Bioclim} \title{Covariate module: Bioclim} \usage{ -Bioclim(extent = c(-180, 180, -90, 90), resolution = 10, layers = 1:5) +Bioclim(extent = c(-180, 180, -90, 90), resolution = 10, + layers = 1:5) } \arguments{ \item{extent}{Either a length 4 numeric vector giving min longitude, max longitude, min latitude, max latitude; or an object of class Extent} @@ -38,3 +39,4 @@ Other covariate: \code{\link{AirNCEP}}, \author{ ZOON Developers, \email{zoonproject@@gmail.com} } +\concept{covariate} diff --git a/man/Bioclim_future.Rd b/man/Bioclim_future.Rd index 6b38ce4..05d0f26 100644 --- a/man/Bioclim_future.Rd +++ b/man/Bioclim_future.Rd @@ -43,3 +43,4 @@ Other covariate: \code{\link{AirNCEP}}, \author{ F. Rodriguez-Sanchez & E. Van Loon, \email{zoonproject@gmail.com} } +\concept{covariate} diff --git a/man/BiomodModel.Rd b/man/BiomodModel.Rd index 2c3da72..fac1ea6 100644 --- a/man/BiomodModel.Rd +++ b/man/BiomodModel.Rd @@ -53,3 +53,4 @@ Other model: \code{\link{Domain}}, \code{\link{GBM}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{model} diff --git a/man/Bootstrap.Rd b/man/Bootstrap.Rd index 13f5986..06488ec 100644 --- a/man/Bootstrap.Rd +++ b/man/Bootstrap.Rd @@ -54,3 +54,4 @@ Other process: \code{\link{AddRandomUniformPredictors}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{process} diff --git a/man/CWBZimbabwe.Rd b/man/CWBZimbabwe.Rd index 74e620a..bc53a89 100644 --- a/man/CWBZimbabwe.Rd +++ b/man/CWBZimbabwe.Rd @@ -59,3 +59,4 @@ Other occurrence: \code{\link{AnophelesPlumbeus}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{occurrence} diff --git a/man/CarolinaWrenPA.Rd b/man/CarolinaWrenPA.Rd index f5b5a87..78c67c7 100644 --- a/man/CarolinaWrenPA.Rd +++ b/man/CarolinaWrenPA.Rd @@ -44,3 +44,4 @@ Other occurrence: \code{\link{AnophelesPlumbeus}}, \author{ Nick Golding, \email{nick.golding.research@gmail.com} } +\concept{occurrence} diff --git a/man/CarolinaWrenPO.Rd b/man/CarolinaWrenPO.Rd index f39a049..7af4735 100644 --- a/man/CarolinaWrenPO.Rd +++ b/man/CarolinaWrenPO.Rd @@ -38,3 +38,4 @@ Other occurrence: \code{\link{AnophelesPlumbeus}}, \author{ Nick Golding, \email{nick.golding.research@gmail.com} } +\concept{occurrence} diff --git a/man/CarolinaWrenRasters.Rd b/man/CarolinaWrenRasters.Rd index df8d03f..4879e35 100644 --- a/man/CarolinaWrenRasters.Rd +++ b/man/CarolinaWrenRasters.Rd @@ -30,3 +30,4 @@ Other covariate: \code{\link{AirNCEP}}, \author{ Nick Golding, \email{nick.golding.research@gmail.com} } +\concept{covariate} diff --git a/man/CarolinaWrenValidation.Rd b/man/CarolinaWrenValidation.Rd index 71c8f5d..d425c06 100644 --- a/man/CarolinaWrenValidation.Rd +++ b/man/CarolinaWrenValidation.Rd @@ -55,3 +55,4 @@ Other process: \code{\link{AddRandomUniformPredictors}}, \author{ Nick Golding, \email{nick.golding.research@gmail.com} } +\concept{process} diff --git a/man/Clean.Rd b/man/Clean.Rd index d71a5dd..ca890d1 100644 --- a/man/Clean.Rd +++ b/man/Clean.Rd @@ -61,3 +61,4 @@ Other process: \code{\link{AddRandomUniformPredictors}}, \author{ ZOON Developers, David Wilkinson \email{zoonproject@gmail.com} } +\concept{process} diff --git a/man/CoefficientPlot.Rd b/man/CoefficientPlot.Rd index fc9e8af..0a2144b 100644 --- a/man/CoefficientPlot.Rd +++ b/man/CoefficientPlot.Rd @@ -51,3 +51,4 @@ Other output: \code{\link{AIC}}, \code{\link{AUC}}, \author{ Liz Martin, \email{emartin@student.unimelb.edu.au} } +\concept{output} diff --git a/man/CovHistograms.Rd b/man/CovHistograms.Rd index 24d17f6..0614ed8 100644 --- a/man/CovHistograms.Rd +++ b/man/CovHistograms.Rd @@ -51,3 +51,4 @@ Other output: \code{\link{AIC}}, \code{\link{AUC}}, \author{ Saras Windecker, \email{saras.windecker@gmail.com} } +\concept{output} diff --git a/man/Crossvalidate.Rd b/man/Crossvalidate.Rd index 0400e40..6ad70b3 100644 --- a/man/Crossvalidate.Rd +++ b/man/Crossvalidate.Rd @@ -47,3 +47,4 @@ Other process: \code{\link{AddRandomUniformPredictors}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{process} diff --git a/man/DataSummary.Rd b/man/DataSummary.Rd index 231b5d5..2981946 100644 --- a/man/DataSummary.Rd +++ b/man/DataSummary.Rd @@ -51,3 +51,4 @@ Other output: \code{\link{AIC}}, \code{\link{AUC}}, \author{ David Wilkinson, \email{davidpw@student.unimelb.edu.au} } +\concept{output} diff --git a/man/Deviance.Rd b/man/Deviance.Rd index 81280b5..25db0b5 100644 --- a/man/Deviance.Rd +++ b/man/Deviance.Rd @@ -53,3 +53,4 @@ Other output: \code{\link{AIC}}, \code{\link{AUC}}, \author{ Liz Martin, \email{lizmartinresearch@gmail.com} } +\concept{output} diff --git a/man/Domain.Rd b/man/Domain.Rd index dfdbc5c..cf0da06 100644 --- a/man/Domain.Rd +++ b/man/Domain.Rd @@ -43,3 +43,4 @@ Other model: \code{\link{BiomodModel}}, \code{\link{GBM}}, \author{ Nick Golding, \email{nick.golding.research@gmail.com} } +\concept{model} diff --git a/man/GBM.Rd b/man/GBM.Rd index b70e611..6e68e9a 100644 --- a/man/GBM.Rd +++ b/man/GBM.Rd @@ -52,3 +52,4 @@ Other model: \code{\link{BiomodModel}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{model} diff --git a/man/GenerateCovariateReport.Rd b/man/GenerateCovariateReport.Rd index bf4db8c..83f71c3 100644 --- a/man/GenerateCovariateReport.Rd +++ b/man/GenerateCovariateReport.Rd @@ -53,3 +53,4 @@ Other output: \code{\link{AIC}}, \code{\link{AUC}}, \author{ David Wilkinson, \email{davidpw@student.unimelb.edu.au} } +\concept{output} diff --git a/man/InteractiveCovariateMap.Rd b/man/InteractiveCovariateMap.Rd index b45f673..c316755 100644 --- a/man/InteractiveCovariateMap.Rd +++ b/man/InteractiveCovariateMap.Rd @@ -49,3 +49,4 @@ Other output: \code{\link{AIC}}, \code{\link{AUC}}, \author{ ZOON Developers, David Wilkinson, \email{zoonproject@gmail.com} } +\concept{output} diff --git a/man/InteractiveMap.Rd b/man/InteractiveMap.Rd index c72e242..d8fe0fd 100644 --- a/man/InteractiveMap.Rd +++ b/man/InteractiveMap.Rd @@ -47,3 +47,4 @@ Other output: \code{\link{AIC}}, \code{\link{AUC}}, \author{ ZOON Developers, David Wilkinson \email{zoonproject@gmail.com} } +\concept{output} diff --git a/man/InteractiveOccurrenceMap.Rd b/man/InteractiveOccurrenceMap.Rd index db8d398..f405e42 100644 --- a/man/InteractiveOccurrenceMap.Rd +++ b/man/InteractiveOccurrenceMap.Rd @@ -53,3 +53,4 @@ Other output: \code{\link{AIC}}, \code{\link{AUC}}, \author{ David Wilkinson, \email{davidpw@student.unimelb.edu.au} } +\concept{output} diff --git a/man/JitterOccurrence.Rd b/man/JitterOccurrence.Rd index 09c4009..5abbb53 100644 --- a/man/JitterOccurrence.Rd +++ b/man/JitterOccurrence.Rd @@ -48,3 +48,4 @@ Other process: \code{\link{AddRandomUniformPredictors}}, \author{ Nick Golding, \email{nick.golding.research@gmail.com} } +\concept{process} diff --git a/man/LocalOccurrenceData.Rd b/man/LocalOccurrenceData.Rd index c673388..81ca8f2 100644 --- a/man/LocalOccurrenceData.Rd +++ b/man/LocalOccurrenceData.Rd @@ -4,9 +4,10 @@ \alias{LocalOccurrenceData} \title{Occurrence module: LocalOccurrenceData} \usage{ -LocalOccurrenceData(filename = "myData.csv", occurrenceType = "presence", - columns = c(long = "longitude", lat = "latitude", value = "value"), - subsetSpecies = NULL, externalValidation = FALSE) +LocalOccurrenceData(filename = "myData.csv", + occurrenceType = "presence", columns = c(long = "longitude", lat = + "latitude", value = "value"), subsetSpecies = NULL, + externalValidation = FALSE) } \arguments{ \item{filename}{The path to the spreadsheet. The spreadsheet should have a header giving column names. The column names should be "longitude", latitude, and "value". "value" is a numeric such as a proportion, count or presence/absence (1/0). The file can be .csv, .tab, .tsv, or .xlsx} @@ -51,3 +52,4 @@ Other occurrence: \code{\link{AnophelesPlumbeus}}, \author{ ZOON Developers, David Wilkinson, \email{zoonproject@@gmail.com} } +\concept{occurrence} diff --git a/man/LocalOccurrenceDataFrame.Rd b/man/LocalOccurrenceDataFrame.Rd index 33590a0..376e54b 100644 --- a/man/LocalOccurrenceDataFrame.Rd +++ b/man/LocalOccurrenceDataFrame.Rd @@ -52,3 +52,4 @@ Other occurrence: \code{\link{AnophelesPlumbeus}}, \author{ David Wilkinson, ZOON Developers, \email{davidpw@student.unimelb.edu.au} } +\concept{occurrence} diff --git a/man/LocalRaster.Rd b/man/LocalRaster.Rd index cae703c..7401122 100644 --- a/man/LocalRaster.Rd +++ b/man/LocalRaster.Rd @@ -33,3 +33,4 @@ Other covariate: \code{\link{AirNCEP}}, \author{ Tim Lucas, Samuel Bosch, \email{timcdlucas@gmail.com} } +\concept{covariate} diff --git a/man/LogisticRegression.Rd b/man/LogisticRegression.Rd index 777962c..02866b7 100644 --- a/man/LogisticRegression.Rd +++ b/man/LogisticRegression.Rd @@ -40,3 +40,4 @@ Other model: \code{\link{BiomodModel}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{model} diff --git a/man/Lorem_ipsum_UK.Rd b/man/Lorem_ipsum_UK.Rd index 4a62d48..99b48a1 100644 --- a/man/Lorem_ipsum_UK.Rd +++ b/man/Lorem_ipsum_UK.Rd @@ -38,3 +38,4 @@ Other occurrence: \code{\link{AnophelesPlumbeus}}, \author{ A.B. Ceidi, \email{ABCD@anemail.com} } +\concept{occurrence} diff --git a/man/MESSMask.Rd b/man/MESSMask.Rd index 2c1a923..07c29bd 100644 --- a/man/MESSMask.Rd +++ b/man/MESSMask.Rd @@ -52,3 +52,4 @@ Other process: \code{\link{AddRandomUniformPredictors}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{process} diff --git a/man/MachineLearn.Rd b/man/MachineLearn.Rd index f3fb9b9..d102df0 100644 --- a/man/MachineLearn.Rd +++ b/man/MachineLearn.Rd @@ -67,3 +67,4 @@ Other model: \code{\link{BiomodModel}}, \author{ Tim CD Lucas, \email{timcdlucas@gmail.com} } +\concept{model} diff --git a/man/MaxEnt.Rd b/man/MaxEnt.Rd index c0bcfec..fc6ef49 100644 --- a/man/MaxEnt.Rd +++ b/man/MaxEnt.Rd @@ -4,7 +4,7 @@ \alias{MaxEnt} \title{Model module: MaxEnt} \usage{ -MaxEnt(.df, args = "") +MaxEnt(.df, args = "", path = getwd(), factors = NULL) } \arguments{ \item{.df}{\strong{Internal parameter, do not use in the workflow function}. @@ -19,6 +19,11 @@ help files, which list all of the options, aren't available on the web. You could try the MaxEnt graphical user interface, otherwise there is a list (which may or may not be up-to-date) in this forum: \url{https://groups.google.com/d/msg/maxent/yRBlvZ1_9rQ/Fj8Two0lmHIJ}.} + +\item{path}{Filepath to choose where to save MaxEnt's html output file. Defaults +to getwd().} + +\item{factors}{Character string of the name of variables to be treated as factors.} } \description{ Model module to fit MaxEnt model via the dismo package @@ -31,13 +36,17 @@ Running MaxEnt also requires an up-to-date version of java (which you may already have installed). } \section{Version}{ - 1.0 + 1.1 } \section{Date submitted}{ 2015-11-13 } +\section{Date modified}{ + 2018-04-24 +} + \section{Data type}{ presence/background } @@ -56,5 +65,6 @@ Other model: \code{\link{BiomodModel}}, \code{\link{mgcv}} } \author{ -ZOON Developers, \email{zoonproject@gmail.com} +ZOON Developers, David Wilkinson \email{zoonproject@gmail.com} } +\concept{model} diff --git a/man/MaxLike.Rd b/man/MaxLike.Rd index 15ce6be..82c711d 100644 --- a/man/MaxLike.Rd +++ b/man/MaxLike.Rd @@ -71,3 +71,4 @@ Other model: \code{\link{BiomodModel}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{model} diff --git a/man/MaxNet.Rd b/man/MaxNet.Rd index 3511486..677507e 100644 --- a/man/MaxNet.Rd +++ b/man/MaxNet.Rd @@ -4,8 +4,8 @@ \alias{MaxNet} \title{Model module: MaxNet} \usage{ -MaxNet(.df, features = "default", regmult = 1, clamp_predictions = TRUE, - prediction_type = "logistic") +MaxNet(.df, features = "default", regmult = 1, + clamp_predictions = TRUE, prediction_type = "logistic") } \arguments{ \item{.df}{\strong{Internal parameter, do not use in the workflow function}. @@ -76,3 +76,4 @@ Other model: \code{\link{BiomodModel}}, \author{ Nick Golding, \email{nick.golding.research@gmail.com} } +\concept{model} diff --git a/man/MyMaxLike.Rd b/man/MyMaxLike.Rd index c25a31d..79dd478 100644 --- a/man/MyMaxLike.Rd +++ b/man/MyMaxLike.Rd @@ -71,3 +71,4 @@ Other model: \code{\link{BiomodModel}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{model} diff --git a/man/NATrees.Rd b/man/NATrees.Rd index 9aaca08..41ec6f1 100644 --- a/man/NATrees.Rd +++ b/man/NATrees.Rd @@ -44,3 +44,4 @@ Other occurrence: \code{\link{AnophelesPlumbeus}}, \author{ Matt Talluto, \email{mtalluto@gmail.com} } +\concept{occurrence} diff --git a/man/NCEP.Rd b/man/NCEP.Rd index b406a7d..49804f8 100644 --- a/man/NCEP.Rd +++ b/man/NCEP.Rd @@ -4,7 +4,8 @@ \alias{NCEP} \title{Covariate module: NCEP} \usage{ -NCEP(extent = c(-5, 5, 50, 60), variables = "hgt", status.bar = FALSE) +NCEP(extent = c(-5, 5, 50, 60), variables = "hgt", + status.bar = FALSE) } \arguments{ \item{extent}{A numeric vector of length 4 giving the coordinates of the @@ -47,3 +48,4 @@ Other covariate: \code{\link{AirNCEP}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{covariate} diff --git a/man/NaiveRandomPresence.Rd b/man/NaiveRandomPresence.Rd index e419e12..ee02159 100644 --- a/man/NaiveRandomPresence.Rd +++ b/man/NaiveRandomPresence.Rd @@ -4,8 +4,8 @@ \alias{NaiveRandomPresence} \title{Naive Random Presence} \usage{ -NaiveRandomPresence(extent = c(-10, 10, 45, 65), n = 1000, seed = NULL, - projection = NULL) +NaiveRandomPresence(extent = c(-10, 10, 45, 65), n = 1000, + seed = NULL, projection = NULL) } \arguments{ \item{extent}{A numeric vector of length 4 giving the coordinates of the rectangular region within which to create the random points. order: xmin, xmax, ymin, ymax. By default the extent of the UK.} @@ -48,3 +48,4 @@ Other occurrence: \code{\link{AnophelesPlumbeus}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{occurrence} diff --git a/man/NaiveRandomPresenceAbsence.Rd b/man/NaiveRandomPresenceAbsence.Rd index 6a4963d..c5797f8 100644 --- a/man/NaiveRandomPresenceAbsence.Rd +++ b/man/NaiveRandomPresenceAbsence.Rd @@ -50,3 +50,4 @@ Other occurrence: \code{\link{AnophelesPlumbeus}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{occurrence} diff --git a/man/NaiveRandomRaster.Rd b/man/NaiveRandomRaster.Rd index d46f97b..06fcec0 100644 --- a/man/NaiveRandomRaster.Rd +++ b/man/NaiveRandomRaster.Rd @@ -4,8 +4,8 @@ \alias{NaiveRandomRaster} \title{Naive Random Raster} \usage{ -NaiveRandomRaster(extent = c(-10, 10, 45, 65), res = 0.5, seed = NULL, - projection = "+proj=longlat +datum=WGS84") +NaiveRandomRaster(extent = c(-10, 10, 45, 65), res = 0.5, + seed = NULL, projection = "+proj=longlat +datum=WGS84") } \arguments{ \item{extent}{A numeric vector of length 4 giving the coordinates of the rectangular region within which to create the raaster. order: xmin, xmax, ymin, ymax. By default the extent of the UK} @@ -40,3 +40,4 @@ Other covariate: \code{\link{AirNCEP}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{covariate} diff --git a/man/NoOutput.Rd b/man/NoOutput.Rd index 8c1426b..c07ff42 100644 --- a/man/NoOutput.Rd +++ b/man/NoOutput.Rd @@ -52,3 +52,4 @@ Other output: \code{\link{AIC}}, \code{\link{AUC}}, \author{ Tim Lucas, \email{timcdlucas@gmail.com} } +\concept{output} diff --git a/man/NoProcess.Rd b/man/NoProcess.Rd index 10df24a..4c62a0f 100644 --- a/man/NoProcess.Rd +++ b/man/NoProcess.Rd @@ -48,3 +48,4 @@ Other process: \code{\link{AddRandomUniformPredictors}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{process} diff --git a/man/NullModel.Rd b/man/NullModel.Rd index 617a9b1..86039c0 100644 --- a/man/NullModel.Rd +++ b/man/NullModel.Rd @@ -41,3 +41,4 @@ Other model: \code{\link{BiomodModel}}, \author{ Nick Golding, \email{nick.golding.research@gmail.com} } +\concept{model} diff --git a/man/OneHundredBackground.Rd b/man/OneHundredBackground.Rd index 684b6ee..a1c7831 100644 --- a/man/OneHundredBackground.Rd +++ b/man/OneHundredBackground.Rd @@ -46,3 +46,4 @@ Other process: \code{\link{AddRandomUniformPredictors}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{process} diff --git a/man/OneThousandBackground.Rd b/man/OneThousandBackground.Rd index 6e539e6..285ea67 100644 --- a/man/OneThousandBackground.Rd +++ b/man/OneThousandBackground.Rd @@ -46,3 +46,4 @@ Other process: \code{\link{AddRandomUniformPredictors}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{process} diff --git a/man/OptGRaF.Rd b/man/OptGRaF.Rd index 22b1967..c4d5838 100644 --- a/man/OptGRaF.Rd +++ b/man/OptGRaF.Rd @@ -38,3 +38,4 @@ Other model: \code{\link{BiomodModel}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{model} diff --git a/man/PairPlot.Rd b/man/PairPlot.Rd index 9c82098..73f0013 100644 --- a/man/PairPlot.Rd +++ b/man/PairPlot.Rd @@ -52,3 +52,4 @@ Other output: \code{\link{AIC}}, \code{\link{AUC}}, \author{ Saras Windecker, \email{saras.windecker@gmail.com} } +\concept{output} diff --git a/man/PartitionDisc.Rd b/man/PartitionDisc.Rd index adef1ce..5fee96a 100644 --- a/man/PartitionDisc.Rd +++ b/man/PartitionDisc.Rd @@ -52,3 +52,4 @@ Other process: \code{\link{AddRandomUniformPredictors}}, \author{ Tom August, \email{tomaug@ceh.ac.uk} } +\concept{process} diff --git a/man/PerformanceMeasures.Rd b/man/PerformanceMeasures.Rd index 41ecce6..5608b43 100644 --- a/man/PerformanceMeasures.Rd +++ b/man/PerformanceMeasures.Rd @@ -64,3 +64,4 @@ Other output: \code{\link{AIC}}, \code{\link{AUC}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{output} diff --git a/man/PredictNewRasterMap.Rd b/man/PredictNewRasterMap.Rd index bb9c843..9d25a01 100644 --- a/man/PredictNewRasterMap.Rd +++ b/man/PredictNewRasterMap.Rd @@ -57,3 +57,4 @@ Other output: \code{\link{AIC}}, \code{\link{AUC}}, \author{ Zoon developers (modified by F. Rodriguez-Sanchez), \email{zoonproject@gmail.com} } +\concept{output} diff --git a/man/PrintMap.Rd b/man/PrintMap.Rd index 096b7d0..1b3ea10 100644 --- a/man/PrintMap.Rd +++ b/man/PrintMap.Rd @@ -83,3 +83,4 @@ Other output: \code{\link{AIC}}, \code{\link{AUC}}, \author{ ZOON Developers, James Campbell, David Wilkinson \email{zoonproject@gmail.com} } +\concept{output} diff --git a/man/PrintOccurrenceMap.Rd b/man/PrintOccurrenceMap.Rd index 8aa9de6..d4fb97d 100644 --- a/man/PrintOccurrenceMap.Rd +++ b/man/PrintOccurrenceMap.Rd @@ -4,8 +4,8 @@ \alias{PrintOccurrenceMap} \title{Output module: PrintOccurrenceMap} \usage{ -PrintOccurrenceMap(.model, .ras, plot = TRUE, dir = NULL, filename = NULL, - size = c(480, 480), res = 72, ...) +PrintOccurrenceMap(.model, .ras, plot = TRUE, dir = NULL, + filename = NULL, size = c(480, 480), res = 72, ...) } \arguments{ \item{.model}{\strong{Internal parameter, do not use in the workflow function}. \code{.model} is list of a data frame (\code{data}) and a model object (\code{model}). \code{.model} is passed automatically in workflow, combining data from the model module(s) and process module(s), to the output module(s) and should not be passed by the user.} @@ -66,3 +66,4 @@ Other output: \code{\link{AIC}}, \code{\link{AUC}}, \author{ Nick Golding, \email{nick.golding.research@gmail.com} } +\concept{output} diff --git a/man/QuickGRaF.Rd b/man/QuickGRaF.Rd index 3c11729..34a79ec 100644 --- a/man/QuickGRaF.Rd +++ b/man/QuickGRaF.Rd @@ -45,3 +45,4 @@ Other model: \code{\link{BiomodModel}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{model} diff --git a/man/ROCcurve.Rd b/man/ROCcurve.Rd index 57c864e..c912aec 100644 --- a/man/ROCcurve.Rd +++ b/man/ROCcurve.Rd @@ -54,3 +54,4 @@ Other output: \code{\link{AIC}}, \code{\link{AUC}}, \author{ E.E. van Loon, \email{e.e.vanloonD@uva.nl} } +\concept{output} diff --git a/man/RandomForest.Rd b/man/RandomForest.Rd index 01936a4..1d2e1a4 100644 --- a/man/RandomForest.Rd +++ b/man/RandomForest.Rd @@ -41,3 +41,4 @@ Other model: \code{\link{BiomodModel}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{model} diff --git a/man/ReliabilityPlot.Rd b/man/ReliabilityPlot.Rd index 9124d32..c2da01d 100644 --- a/man/ReliabilityPlot.Rd +++ b/man/ReliabilityPlot.Rd @@ -53,3 +53,4 @@ Other output: \code{\link{AIC}}, \code{\link{AUC}}, \author{ Liz Martin, \email{lizmartinresearch@gmail.com} } +\concept{output} diff --git a/man/ResponseCurve.Rd b/man/ResponseCurve.Rd index a66e526..335297d 100644 --- a/man/ResponseCurve.Rd +++ b/man/ResponseCurve.Rd @@ -50,3 +50,4 @@ Other output: \code{\link{AIC}}, \code{\link{AUC}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{output} diff --git a/man/ResponseCurveViz.Rd b/man/ResponseCurveViz.Rd index b6228db..ed7fb6f 100644 --- a/man/ResponseCurveViz.Rd +++ b/man/ResponseCurveViz.Rd @@ -53,3 +53,4 @@ Other output: \code{\link{AIC}}, \code{\link{AUC}}, \author{ G. McInerny, \email{gmcinerny@hotmail.com} } +\concept{output} diff --git a/man/ResponsePlot.Rd b/man/ResponsePlot.Rd index 1ad12ea..4c825d2 100644 --- a/man/ResponsePlot.Rd +++ b/man/ResponsePlot.Rd @@ -54,3 +54,4 @@ Other output: \code{\link{AIC}}, \code{\link{AUC}}, \author{ Liz Martin, \email{emartin@student.unimelb.edu.au} } +\concept{output} diff --git a/man/SameTimePlaceMap.Rd b/man/SameTimePlaceMap.Rd index 439b845..d02ee68 100644 --- a/man/SameTimePlaceMap.Rd +++ b/man/SameTimePlaceMap.Rd @@ -48,3 +48,4 @@ Other output: \code{\link{AIC}}, \code{\link{AUC}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{output} diff --git a/man/SeparatePA.Rd b/man/SeparatePA.Rd index 30a0195..dc64a84 100644 --- a/man/SeparatePA.Rd +++ b/man/SeparatePA.Rd @@ -51,3 +51,4 @@ Other output: \code{\link{AIC}}, \code{\link{AUC}}, \author{ E.E. van Loon, \email{e.e.vanloonD@uva.nl} } +\concept{output} diff --git a/man/SpOcc.Rd b/man/SpOcc.Rd index 0dd49ac..0605a36 100644 --- a/man/SpOcc.Rd +++ b/man/SpOcc.Rd @@ -59,3 +59,4 @@ Other occurrence: \code{\link{AnophelesPlumbeus}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{occurrence} diff --git a/man/StandardiseCov.Rd b/man/StandardiseCov.Rd index cda08ab..c8f01ac 100644 --- a/man/StandardiseCov.Rd +++ b/man/StandardiseCov.Rd @@ -50,3 +50,4 @@ Other process: \code{\link{AddRandomUniformPredictors}}, \author{ Alison Johnston & Carsten F. Dormann, \email{alison.johnston@bto.org} } +\concept{process} diff --git a/man/StochasticLogisticRegression.Rd b/man/StochasticLogisticRegression.Rd index 80452d3..9d1be48 100644 --- a/man/StochasticLogisticRegression.Rd +++ b/man/StochasticLogisticRegression.Rd @@ -40,3 +40,4 @@ Other model: \code{\link{BiomodModel}}, \author{ Nick Golding, \email{nick.golding.research@gmail.com} } +\concept{model} diff --git a/man/SubsampleOccurrence.Rd b/man/SubsampleOccurrence.Rd index 0db9cbf..ea512b2 100644 --- a/man/SubsampleOccurrence.Rd +++ b/man/SubsampleOccurrence.Rd @@ -53,3 +53,4 @@ Other process: \code{\link{AddRandomUniformPredictors}}, \author{ Nick Golding, \email{nick.golding.research@gmail.com} } +\concept{process} diff --git a/man/SugarMaple.Rd b/man/SugarMaple.Rd index 61754cc..13d9e84 100644 --- a/man/SugarMaple.Rd +++ b/man/SugarMaple.Rd @@ -38,3 +38,4 @@ Other occurrence: \code{\link{AnophelesPlumbeus}}, \author{ Matt Talluto & Nick Golding, \email{mtalluto@gmail.com} } +\concept{occurrence} diff --git a/man/SurfaceMap.Rd b/man/SurfaceMap.Rd index b274fb2..09e6ea7 100644 --- a/man/SurfaceMap.Rd +++ b/man/SurfaceMap.Rd @@ -46,3 +46,4 @@ Other output: \code{\link{AIC}}, \code{\link{AUC}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{output} diff --git a/man/TargetGroupBackground.Rd b/man/TargetGroupBackground.Rd index f41b19e..ce1ee50 100644 --- a/man/TargetGroupBackground.Rd +++ b/man/TargetGroupBackground.Rd @@ -51,3 +51,4 @@ Other process: \code{\link{AddRandomUniformPredictors}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{process} diff --git a/man/Transform.Rd b/man/Transform.Rd index df1030c..3586758 100644 --- a/man/Transform.Rd +++ b/man/Transform.Rd @@ -53,3 +53,4 @@ Other process: \code{\link{AddRandomUniformPredictors}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{process} diff --git a/man/UKAir.Rd b/man/UKAir.Rd index 8a92ac2..185c9bd 100644 --- a/man/UKAir.Rd +++ b/man/UKAir.Rd @@ -27,3 +27,4 @@ Other covariate: \code{\link{AirNCEP}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{covariate} diff --git a/man/UKAnophelesPlumbeus.Rd b/man/UKAnophelesPlumbeus.Rd index b14ca84..df99900 100644 --- a/man/UKAnophelesPlumbeus.Rd +++ b/man/UKAnophelesPlumbeus.Rd @@ -36,3 +36,4 @@ Other occurrence: \code{\link{AnophelesPlumbeus}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{occurrence} diff --git a/man/UKBioclim.Rd b/man/UKBioclim.Rd index 1b6fd7f..a6eb95f 100644 --- a/man/UKBioclim.Rd +++ b/man/UKBioclim.Rd @@ -35,3 +35,4 @@ Other covariate: \code{\link{AirNCEP}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{covariate} diff --git a/man/VariableImportance.Rd b/man/VariableImportance.Rd index da3e556..1d9b29f 100644 --- a/man/VariableImportance.Rd +++ b/man/VariableImportance.Rd @@ -53,3 +53,4 @@ Other output: \code{\link{AIC}}, \code{\link{AUC}}, \author{ Tom August, \email{tomaug@ceh.ac.uk} } +\concept{output} diff --git a/man/addInteraction.Rd b/man/addInteraction.Rd index 9a1333c..8c07f55 100644 --- a/man/addInteraction.Rd +++ b/man/addInteraction.Rd @@ -50,3 +50,4 @@ Other process: \code{\link{AddRandomUniformPredictors}}, \author{ Alison Johnston & Carsten F. Dormann, \email{alison.johnston@bto.org} } +\concept{process} diff --git a/man/mgcv.Rd b/man/mgcv.Rd index 0fe2817..eb6c26f 100644 --- a/man/mgcv.Rd +++ b/man/mgcv.Rd @@ -52,3 +52,4 @@ Other model: \code{\link{BiomodModel}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{model} diff --git a/man/spThin.Rd b/man/spThin.Rd index be340d9..579ab6a 100644 --- a/man/spThin.Rd +++ b/man/spThin.Rd @@ -48,3 +48,4 @@ Other process: \code{\link{AddRandomUniformPredictors}}, \author{ Nick Golding, \email{nick.golding.research@gmail.com} } +\concept{process} From 1d8be4a87bc0680250bd0465b961bccb652fa213 Mon Sep 17 00:00:00 2001 From: Doi90 Date: Wed, 24 Apr 2019 19:48:02 +1000 Subject: [PATCH 2/5] Rebuild documentation --- man/AnophelesPlumbeus.Rd | 3 +- man/CWBZimbabwe.Rd | 3 +- man/CarolinaWrenPA.Rd | 3 +- man/CarolinaWrenPO.Rd | 3 +- man/LocalOccurrenceData.Rd | 3 +- man/LocalOccurrenceDataFrame.Rd | 3 +- man/LonLatToCovariates.Rd | 1 + man/Lorem_ipsum_UK.Rd | 3 +- man/NATrees.Rd | 3 +- man/NaiveRandomPresence.Rd | 3 +- man/NaiveRandomPresenceAbsence.Rd | 3 +- man/RemoveNAs.Rd | 1 + man/SpOcc.Rd | 3 +- man/SugarMaple.Rd | 3 +- man/UKAnophelesPlumbeus.Rd | 3 +- man/malariaAtlas_PR.Rd | 4 +- man/malariaAtlas_VecOcc.Rd | 64 +++++++++++++++++++++++++++++++ man/malariaAtlas_covariates.Rd | 1 + 18 files changed, 96 insertions(+), 14 deletions(-) create mode 100644 man/malariaAtlas_VecOcc.Rd diff --git a/man/AnophelesPlumbeus.Rd b/man/AnophelesPlumbeus.Rd index 068841f..d919aaa 100644 --- a/man/AnophelesPlumbeus.Rd +++ b/man/AnophelesPlumbeus.Rd @@ -38,7 +38,8 @@ Other occurrence: \code{\link{CWBZimbabwe}}, \code{\link{NaiveRandomPresence}}, \code{\link{SpOcc}}, \code{\link{SugarMaple}}, \code{\link{UKAnophelesPlumbeus}}, - \code{\link{malariaAtlas_PR}} + \code{\link{malariaAtlas_PR}}, + \code{\link{malariaAtlas_VecOcc}} } \author{ ZOON Developers, \email{zoonproject@gmail.com} diff --git a/man/CWBZimbabwe.Rd b/man/CWBZimbabwe.Rd index ad607cd..96561fb 100644 --- a/man/CWBZimbabwe.Rd +++ b/man/CWBZimbabwe.Rd @@ -55,7 +55,8 @@ Other occurrence: \code{\link{AnophelesPlumbeus}}, \code{\link{NaiveRandomPresence}}, \code{\link{SpOcc}}, \code{\link{SugarMaple}}, \code{\link{UKAnophelesPlumbeus}}, - \code{\link{malariaAtlas_PR}} + \code{\link{malariaAtlas_PR}}, + \code{\link{malariaAtlas_VecOcc}} } \author{ ZOON Developers, \email{zoonproject@gmail.com} diff --git a/man/CarolinaWrenPA.Rd b/man/CarolinaWrenPA.Rd index 7db714b..9241dab 100644 --- a/man/CarolinaWrenPA.Rd +++ b/man/CarolinaWrenPA.Rd @@ -40,7 +40,8 @@ Other occurrence: \code{\link{AnophelesPlumbeus}}, \code{\link{NaiveRandomPresence}}, \code{\link{SpOcc}}, \code{\link{SugarMaple}}, \code{\link{UKAnophelesPlumbeus}}, - \code{\link{malariaAtlas_PR}} + \code{\link{malariaAtlas_PR}}, + \code{\link{malariaAtlas_VecOcc}} } \author{ Nick Golding, \email{nick.golding.research@gmail.com} diff --git a/man/CarolinaWrenPO.Rd b/man/CarolinaWrenPO.Rd index 9c678e6..1da956c 100644 --- a/man/CarolinaWrenPO.Rd +++ b/man/CarolinaWrenPO.Rd @@ -34,7 +34,8 @@ Other occurrence: \code{\link{AnophelesPlumbeus}}, \code{\link{NaiveRandomPresence}}, \code{\link{SpOcc}}, \code{\link{SugarMaple}}, \code{\link{UKAnophelesPlumbeus}}, - \code{\link{malariaAtlas_PR}} + \code{\link{malariaAtlas_PR}}, + \code{\link{malariaAtlas_VecOcc}} } \author{ Nick Golding, \email{nick.golding.research@gmail.com} diff --git a/man/LocalOccurrenceData.Rd b/man/LocalOccurrenceData.Rd index 29ed88b..1448ed4 100644 --- a/man/LocalOccurrenceData.Rd +++ b/man/LocalOccurrenceData.Rd @@ -48,7 +48,8 @@ Other occurrence: \code{\link{AnophelesPlumbeus}}, \code{\link{NaiveRandomPresence}}, \code{\link{SpOcc}}, \code{\link{SugarMaple}}, \code{\link{UKAnophelesPlumbeus}}, - \code{\link{malariaAtlas_PR}} + \code{\link{malariaAtlas_PR}}, + \code{\link{malariaAtlas_VecOcc}} } \author{ ZOON Developers, David Wilkinson, \email{zoonproject@@gmail.com} diff --git a/man/LocalOccurrenceDataFrame.Rd b/man/LocalOccurrenceDataFrame.Rd index 7d69333..027ea2a 100644 --- a/man/LocalOccurrenceDataFrame.Rd +++ b/man/LocalOccurrenceDataFrame.Rd @@ -48,7 +48,8 @@ Other occurrence: \code{\link{AnophelesPlumbeus}}, \code{\link{NaiveRandomPresence}}, \code{\link{SpOcc}}, \code{\link{SugarMaple}}, \code{\link{UKAnophelesPlumbeus}}, - \code{\link{malariaAtlas_PR}} + \code{\link{malariaAtlas_PR}}, + \code{\link{malariaAtlas_VecOcc}} } \author{ David Wilkinson, ZOON Developers, \email{davidpw@student.unimelb.edu.au} diff --git a/man/LonLatToCovariates.Rd b/man/LonLatToCovariates.Rd index 61e807f..48fb30f 100644 --- a/man/LonLatToCovariates.Rd +++ b/man/LonLatToCovariates.Rd @@ -51,3 +51,4 @@ Other process: \code{\link{AddRandomUniformPredictors}}, \author{ Tim Lucas, \email{timcdlucas@gmail.com} } +\concept{process} diff --git a/man/Lorem_ipsum_UK.Rd b/man/Lorem_ipsum_UK.Rd index f12f5ba..d3e7f03 100644 --- a/man/Lorem_ipsum_UK.Rd +++ b/man/Lorem_ipsum_UK.Rd @@ -34,7 +34,8 @@ Other occurrence: \code{\link{AnophelesPlumbeus}}, \code{\link{NaiveRandomPresence}}, \code{\link{SpOcc}}, \code{\link{SugarMaple}}, \code{\link{UKAnophelesPlumbeus}}, - \code{\link{malariaAtlas_PR}} + \code{\link{malariaAtlas_PR}}, + \code{\link{malariaAtlas_VecOcc}} } \author{ A.B. Ceidi, \email{ABCD@anemail.com} diff --git a/man/NATrees.Rd b/man/NATrees.Rd index a8b2154..7a76697 100644 --- a/man/NATrees.Rd +++ b/man/NATrees.Rd @@ -40,7 +40,8 @@ Other occurrence: \code{\link{AnophelesPlumbeus}}, \code{\link{NaiveRandomPresence}}, \code{\link{SpOcc}}, \code{\link{SugarMaple}}, \code{\link{UKAnophelesPlumbeus}}, - \code{\link{malariaAtlas_PR}} + \code{\link{malariaAtlas_PR}}, + \code{\link{malariaAtlas_VecOcc}} } \author{ Matt Talluto, \email{mtalluto@gmail.com} diff --git a/man/NaiveRandomPresence.Rd b/man/NaiveRandomPresence.Rd index d63e424..1c82653 100644 --- a/man/NaiveRandomPresence.Rd +++ b/man/NaiveRandomPresence.Rd @@ -44,7 +44,8 @@ Other occurrence: \code{\link{AnophelesPlumbeus}}, \code{\link{NaiveRandomPresenceAbsence}}, \code{\link{SpOcc}}, \code{\link{SugarMaple}}, \code{\link{UKAnophelesPlumbeus}}, - \code{\link{malariaAtlas_PR}} + \code{\link{malariaAtlas_PR}}, + \code{\link{malariaAtlas_VecOcc}} } \author{ ZOON Developers, \email{zoonproject@gmail.com} diff --git a/man/NaiveRandomPresenceAbsence.Rd b/man/NaiveRandomPresenceAbsence.Rd index cdccdfe..41ee9f0 100644 --- a/man/NaiveRandomPresenceAbsence.Rd +++ b/man/NaiveRandomPresenceAbsence.Rd @@ -46,7 +46,8 @@ Other occurrence: \code{\link{AnophelesPlumbeus}}, \code{\link{NaiveRandomPresence}}, \code{\link{SpOcc}}, \code{\link{SugarMaple}}, \code{\link{UKAnophelesPlumbeus}}, - \code{\link{malariaAtlas_PR}} + \code{\link{malariaAtlas_PR}}, + \code{\link{malariaAtlas_VecOcc}} } \author{ ZOON Developers, \email{zoonproject@gmail.com} diff --git a/man/RemoveNAs.Rd b/man/RemoveNAs.Rd index 68dd708..9c9a6dd 100644 --- a/man/RemoveNAs.Rd +++ b/man/RemoveNAs.Rd @@ -52,3 +52,4 @@ Other process: \code{\link{AddRandomUniformPredictors}}, \author{ ZOON Developers, \email{zoonproject@gmail.com} } +\concept{process} diff --git a/man/SpOcc.Rd b/man/SpOcc.Rd index 638e3e2..0b51c43 100644 --- a/man/SpOcc.Rd +++ b/man/SpOcc.Rd @@ -55,7 +55,8 @@ Other occurrence: \code{\link{AnophelesPlumbeus}}, \code{\link{NaiveRandomPresence}}, \code{\link{SugarMaple}}, \code{\link{UKAnophelesPlumbeus}}, - \code{\link{malariaAtlas_PR}} + \code{\link{malariaAtlas_PR}}, + \code{\link{malariaAtlas_VecOcc}} } \author{ ZOON Developers, \email{zoonproject@gmail.com} diff --git a/man/SugarMaple.Rd b/man/SugarMaple.Rd index 2e63bec..885ee08 100644 --- a/man/SugarMaple.Rd +++ b/man/SugarMaple.Rd @@ -34,7 +34,8 @@ Other occurrence: \code{\link{AnophelesPlumbeus}}, \code{\link{NaiveRandomPresenceAbsence}}, \code{\link{NaiveRandomPresence}}, \code{\link{SpOcc}}, \code{\link{UKAnophelesPlumbeus}}, - \code{\link{malariaAtlas_PR}} + \code{\link{malariaAtlas_PR}}, + \code{\link{malariaAtlas_VecOcc}} } \author{ Matt Talluto & Nick Golding, \email{mtalluto@gmail.com} diff --git a/man/UKAnophelesPlumbeus.Rd b/man/UKAnophelesPlumbeus.Rd index 44c7cd9..abda3c6 100644 --- a/man/UKAnophelesPlumbeus.Rd +++ b/man/UKAnophelesPlumbeus.Rd @@ -31,7 +31,8 @@ Other occurrence: \code{\link{AnophelesPlumbeus}}, \code{\link{Lorem_ipsum_UK}}, \code{\link{NATrees}}, \code{\link{NaiveRandomPresenceAbsence}}, \code{\link{NaiveRandomPresence}}, \code{\link{SpOcc}}, - \code{\link{SugarMaple}}, \code{\link{malariaAtlas_PR}} + \code{\link{SugarMaple}}, \code{\link{malariaAtlas_PR}}, + \code{\link{malariaAtlas_VecOcc}} } \author{ ZOON Developers, \email{zoonproject@gmail.com} diff --git a/man/malariaAtlas_PR.Rd b/man/malariaAtlas_PR.Rd index 4cbea53..b9969f6 100644 --- a/man/malariaAtlas_PR.Rd +++ b/man/malariaAtlas_PR.Rd @@ -78,8 +78,10 @@ Other occurrence: \code{\link{AnophelesPlumbeus}}, \code{\link{NaiveRandomPresenceAbsence}}, \code{\link{NaiveRandomPresence}}, \code{\link{SpOcc}}, \code{\link{SugarMaple}}, - \code{\link{UKAnophelesPlumbeus}} + \code{\link{UKAnophelesPlumbeus}}, + \code{\link{malariaAtlas_VecOcc}} } \author{ Tim Lucas, \email{timcdlucas@gmail.com} } +\concept{occurrence} diff --git a/man/malariaAtlas_VecOcc.Rd b/man/malariaAtlas_VecOcc.Rd new file mode 100644 index 0000000..d4cfbfe --- /dev/null +++ b/man/malariaAtlas_VecOcc.Rd @@ -0,0 +1,64 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/malariaAtlas_VecOcc.R +\name{malariaAtlas_VecOcc} +\alias{malariaAtlas_VecOcc} +\title{Occurrence module: malariaAtlas_VecOcc} +\usage{ +malariaAtlas_VecOcc(country = NULL, ISO = "MMR", extent = NULL, + species = "Anopheles dirus", year = NULL, fold = 1) +} +\arguments{ +\item{country}{Character vector containing names of desired countries, +e.g. c("Country1", "Country2", ...) OR = "ALL" (use exactly one of +country, ISO and extent).} + +\item{ISO}{Character vector containing ISO3 code for desired country, +e.g. c("XXX", "YYY", ...) OR = "ALL" (use exactly one of + country, ISO and extent).} + +\item{extent}{Numeric vector containing bounding box values for desired +area. In the order xmin, xman, ymin, ymax. (use exactly one of + country, ISO and extent).} + +\item{species}{String containing name of desired species} + +\item{year}{Vector of years for which to keep data. NULL keeps all years.} + +\item{fold}{Control the validation. If 0, all data is validation data. +If 1, all data is training data.} +} +\description{ +Occurrence module to collect malaria vector occurrence data + from the Malaria Atlas Project database. +} +\section{Version}{ + 1.0 +} + +\section{Date submitted}{ + 2018-09-26 +} + +\section{Data type}{ + presence-only +} + +\seealso{ +\code{\link{malariaAtlas::getVecOcc}} + +Other occurrence: \code{\link{AnophelesPlumbeus}}, + \code{\link{CWBZimbabwe}}, \code{\link{CarolinaWrenPA}}, + \code{\link{CarolinaWrenPO}}, + \code{\link{LocalOccurrenceDataFrame}}, + \code{\link{LocalOccurrenceData}}, + \code{\link{Lorem_ipsum_UK}}, \code{\link{NATrees}}, + \code{\link{NaiveRandomPresenceAbsence}}, + \code{\link{NaiveRandomPresence}}, \code{\link{SpOcc}}, + \code{\link{SugarMaple}}, + \code{\link{UKAnophelesPlumbeus}}, + \code{\link{malariaAtlas_PR}} +} +\author{ +Suzanne H Keddie, \email{suzanne.keddie@bdi.ox.ac.uk} +} +\concept{occurrence} diff --git a/man/malariaAtlas_covariates.Rd b/man/malariaAtlas_covariates.Rd index 45cb129..9297d46 100644 --- a/man/malariaAtlas_covariates.Rd +++ b/man/malariaAtlas_covariates.Rd @@ -48,3 +48,4 @@ Other covariate: \code{\link{AirNCEP}}, \author{ Tim Lucas, \email{timcdlucas@gmail.com} } +\concept{covariate} From 7416ef2c0912f80ffca91de7d7fdcab3142b0ecb Mon Sep 17 00:00:00 2001 From: Doi90 Date: Wed, 1 May 2019 17:24:27 +1000 Subject: [PATCH 3/5] Change travis checks to intall GRaF from GitHub instead of CRAN. --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index 67e0c9d..2b97567 100644 --- a/.travis.yml +++ b/.travis.yml @@ -18,6 +18,7 @@ r_binary_packages: # Install zoon from Github r_github_packages: - zoonproject/zoon + - goldingn/GRaF # Install devtools to allow travis to work. r_packages: From 262639ca4c17cd7ad6abf737df5f30de05acf981 Mon Sep 17 00:00:00 2001 From: Doi90 Date: Thu, 2 May 2019 16:27:01 +1000 Subject: [PATCH 4/5] Empty commit to restart Travis From 9aa0881a70fc0c57b3fa822304e61cd07834c854 Mon Sep 17 00:00:00 2001 From: Doi90 Date: Mon, 13 May 2019 12:33:15 +1000 Subject: [PATCH 5/5] Remove GRaF from DESCRIPTION to hopefully get it to install via GitHub instead --- DESCRIPTION | 1 - 1 file changed, 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 7c066f5..a7962da 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -34,7 +34,6 @@ Depends: glmnet, rJava, mgcv, - GRaF, sperrorest, SDMTools, randomForest,