From efe791529812ddd44fb05d66803dd29cd213a591 Mon Sep 17 00:00:00 2001 From: Andre Chalom Date: Sun, 11 Jun 2017 14:17:39 -0300 Subject: [PATCH] Bumping Roxygen version --- DESCRIPTION | 2 +- man/LHS.Rd | 12 ++++++------ man/LHScorcorr.Rd | 1 - man/PLUE.Rd | 3 +-- man/accessors.Rd | 5 ++--- man/cv.Rd | 1 - man/external.Rd | 1 - man/machinefile.Rd | 1 - man/pic.Rd | 5 ++--- man/plots.Rd | 8 ++++---- man/sbma.Rd | 3 +-- man/target.sbma.Rd | 1 - 12 files changed, 17 insertions(+), 26 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 5662cfe..6b6cc73 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -25,4 +25,4 @@ Description: Functions for creating Latin Hypercubes with License: GPL-3 URL: https://github.com/andrechalom/pse BugReports: https://github.com/andrechalom/pse -RoxygenNote: 5.0.1 +RoxygenNote: 6.0.1 diff --git a/man/LHS.Rd b/man/LHS.Rd index e4510bf..866f336 100644 --- a/man/LHS.Rd +++ b/man/LHS.Rd @@ -67,9 +67,9 @@ stochastic models for details} \item{x}{An LHS/PLUE object. For "tell", an incomplete LHS object (created with model=NULL)} -\item{y}{A data.frame containing the model responses} - \item{\dots}{Currently ignored} + +\item{y}{A data.frame containing the model responses} } \description{ Generates the Latin Hypercube sampling for uncertainty and sensitivity analyses. @@ -107,6 +107,7 @@ NOTE: the tell method from sensitivity objects (like 'fast99') modifies the object passed as argument as a side effect. This is NOT the case with the LHS tell method. } + \examples{ completeLHS <- LHS(model=function(x) x[,1]+x[,2]*x[,3], factors=3, N=20) incompleteLHS <- LHS(factors=5, N=30) @@ -118,9 +119,6 @@ clusterLHS <- LHS(model=function(x) x[,1]/x[,2], factors=2, N=100, cl = new.clus stopCluster(new.cluster) } } -\author{ -Andre Chalom -} \references{ McKay, M.D. and Beckman, R.J. 1979. A comparison of three methods for selecting values of input variables in the analysis of output from a computer code, @@ -129,4 +127,6 @@ McKay, M.D. and Beckman, R.J. 1979. A comparison of three methods for selecting Chalom, A. and Prado, P.I.K.L. 2012. Parameter space exploration of ecological models \emph{arXiv}:1210.6278 [q-bio.QM] } - +\author{ +Andre Chalom +} diff --git a/man/LHScorcorr.Rd b/man/LHScorcorr.Rd index f8ca4ba..55a4c7a 100644 --- a/man/LHScorcorr.Rd +++ b/man/LHScorcorr.Rd @@ -54,4 +54,3 @@ Huntington, D.E. and Lyrintzis, C.S. 1998 Improvements to and limitations of Chalom, A. and Prado, P.I.K.L. 2012. Parameter space exploration of ecological models \emph{arXiv}:1210.6278 [q-bio.QM] } - diff --git a/man/PLUE.Rd b/man/PLUE.Rd index 5a2868e..1c466c5 100644 --- a/man/PLUE.Rd +++ b/man/PLUE.Rd @@ -2,8 +2,8 @@ % Please edit documentation in R/PLUE.R \name{PLUE} \alias{PLUE} -\alias{plot.PLUE} \alias{print.PLUE} +\alias{plot.PLUE} \title{Profiled Likelihood Uncertainty Estimation} \usage{ PLUE(model = NULL, factors, N, LL, start, res.names = NULL, @@ -65,4 +65,3 @@ A detailed description can be found on Chalom & Prado (2015). Chalom, A. and Prado, P.I.K.L. 2015. Uncertainty analysis and composite hypothesis under the likelihood paradigm. \emph{arXiv}:1508.03354 [q-bio.QM] } - diff --git a/man/accessors.Rd b/man/accessors.Rd index a8442b1..25c9210 100644 --- a/man/accessors.Rd +++ b/man/accessors.Rd @@ -1,12 +1,12 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/accessors.R \name{get.results} -\alias{get.N} +\alias{get.results} \alias{get.data} +\alias{get.N} \alias{get.ninputs} \alias{get.noutputs} \alias{get.repetitions} -\alias{get.results} \title{LHS Accessor Functions.} \usage{ get.results(obj, get.mean = TRUE) @@ -50,4 +50,3 @@ response variables. created by \code{LHS(model, factors, N, repetitions=X)}, or by \code{tell}ing several result sets to the same LHS object (or PLUE object). } - diff --git a/man/cv.Rd b/man/cv.Rd index b3ee028..7add6aa 100644 --- a/man/cv.Rd +++ b/man/cv.Rd @@ -14,4 +14,3 @@ cv(x, ...) \description{ Returns the coefficient of variation of a sample. } - diff --git a/man/external.Rd b/man/external.Rd index bb4ae18..499859d 100644 --- a/man/external.Rd +++ b/man/external.Rd @@ -14,4 +14,3 @@ \description{ This function is derived from package "sensitivity", please proceed to its help files. } - diff --git a/man/machinefile.Rd b/man/machinefile.Rd index 1b91d11..ee61e85 100644 --- a/man/machinefile.Rd +++ b/man/machinefile.Rd @@ -28,4 +28,3 @@ glastonbury:2 stopCluster(cl) } } - diff --git a/man/pic.Rd b/man/pic.Rd index 70caf0d..154e772 100644 --- a/man/pic.Rd +++ b/man/pic.Rd @@ -32,9 +32,9 @@ of experiments (model output variables).} \item{conf}{Confidence of the bootstrap interval} -\item{x}{The object returned by \code{pic}.} - \item{\dots}{Currently ignored.} + +\item{x}{The object returned by \code{pic}.} } \description{ Partial Inclination Coefficient @@ -44,4 +44,3 @@ in relation with all model input variables. \author{ Andre Chalom, based on code by Gilles Pujol, Bertrand Iooss, Alexandre Janon } - diff --git a/man/plots.Rd b/man/plots.Rd index 7e42092..1ce108c 100644 --- a/man/plots.Rd +++ b/man/plots.Rd @@ -1,5 +1,6 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/plotcv.R, R/plotecdf.R, R/plotprcc.R, R/plotscatter.R +% Please edit documentation in R/plotcv.R, R/plotecdf.R, R/plotprcc.R, +% R/plotscatter.R \name{plotcv} \alias{plotcv} \alias{plotecdf} @@ -35,6 +36,8 @@ all variables identified by different colors.} \item{quant}{Maximum quantile to be plotted on the ecdf (used to cut off extreme values in the labels)} +\item{\dots}{Additional parameters to be passed to the lower level plotting function.} + \item{xlab, ylab}{Labels for the x axis (ecdf) or y axis(prcc). The functions use the name provided in the res.names argument from the LHS function if left blank.} @@ -44,8 +47,6 @@ The functions use the name provided in the res.names argument from the LHS funct \item{index.data}{An optional vector with the indices of the data columns to be plotted.} \item{add.lm}{Boolean. Whether to include a simple linear model on the plots. Defaults to TRUE.} - -\item{\dots}{Additional parameters to be passed to the lower level plotting function.} } \description{ The functions listed here are used in uncertainty and sensitivity estimation. @@ -74,4 +75,3 @@ plotecdf(myLHS, main="ECDF plot") plotprcc(myLHS, main="PRCC plot") plotscatter(myLHS) } - diff --git a/man/sbma.Rd b/man/sbma.Rd index 12d9dcc..493cd85 100644 --- a/man/sbma.Rd +++ b/man/sbma.Rd @@ -2,8 +2,8 @@ % Please edit documentation in R/sbma.R \name{sbma} \alias{sbma} -\alias{sbma.LHS} \alias{sbma.default} +\alias{sbma.LHS} \title{Calculates the Symetrized Blest Measure of Agreement between two samples} \usage{ sbma(sample1, sample2, absolute = TRUE, ...) @@ -47,4 +47,3 @@ cor(c(1,2,3,4), c(1,2,4,3), method="spearman") Maturi, T.A. and Elsayigh, A. 2010. A comparison of correlation coefficients via a three-step bootstrap approach. \emph{Journal of Mathematics Research} 2(2): 3-10. } - diff --git a/man/target.sbma.Rd b/man/target.sbma.Rd index e76f428..3789269 100644 --- a/man/target.sbma.Rd +++ b/man/target.sbma.Rd @@ -54,4 +54,3 @@ Returns the largest LHS generated. Generates a series of Latin Hypercube Samples for a model until a pair of LHS present a measure of agreement equal to or greater than a specified target. } -