From eb6af5c54779710b75cfff36acae3eec20189a2d Mon Sep 17 00:00:00 2001 From: julia-wrobel Date: Sat, 16 Apr 2022 11:03:06 -0600 Subject: [PATCH] documentation fixes for cran push --- R/CD4-data.R | 30 ++++++++++++++---------------- R/pffr-ff.R | 2 +- R/pffr.R | 2 +- R/plot.lpeer.R | 2 +- R/plot.peer.R | 2 +- README.md | 2 +- man/cd4.Rd | 4 +--- man/ff.Rd | 2 +- man/pffr.Rd | 2 +- 9 files changed, 22 insertions(+), 26 deletions(-) diff --git a/R/CD4-data.R b/R/CD4-data.R index ac511c83..64ee4129 100755 --- a/R/CD4-data.R +++ b/R/CD4-data.R @@ -1,16 +1,14 @@ -##' Observed CD4 cell counts -##' -##' CD4 cell counts for 366 subjects between months -18 and 42 since -##' seroconversion. Each subject's observations are contained in a single row. -##' -##' -##' @name cd4 -##' @docType data -##' @format A data frame made up of \describe{ \item{list("cd4")}{A 366 x 61 -##' matrix of CD4 cell counts.}\item{ }{A 366 x 61 matrix of CD4 cell counts.} -##' } -##' @references Goldsmith, J., Greven, S., and Crainiceanu, C. (2013). -##' Corrected confidence bands for functional data using principal components. -##' \emph{Biometrics}, 69(1), 41--51. -##' @keywords datasets -NULL +##' Observed CD4 cell counts +##' +##' CD4 cell counts for 366 subjects between months -18 and 42 since +##' seroconversion. Each subject's observations are contained in a single row. +##' +##' @name cd4 +##' @docType data +##' @format A data frame made up of a 366 x 61 matrix of CD4 cell counts +##' +##' @references Goldsmith, J., Greven, S., and Crainiceanu, C. (2013). +##' Corrected confidence bands for functional data using principal components. +##' \emph{Biometrics}, 69(1), 41--51. +##' @keywords datasets +NULL diff --git a/R/pffr-ff.R b/R/pffr-ff.R index a863236d..ff327d98 100644 --- a/R/pffr-ff.R +++ b/R/pffr-ff.R @@ -69,7 +69,7 @@ #' @references For background on \code{check.ident}:\cr Scheipl, F., Greven, #' S. (2016). Identifiability in penalized function-on-function regression #' models. Electronic Journal of Statistics, 10(1), 495--526. -#' \url{https://projecteuclid.org/journals/electronic-journal-of-statistics/volume-10/issue-1/Identifiability-in-penalized-function-on-function-regression-models/10.1214/16-EJS1123.full} +#' \url{https://projecteuclid.org/journals/electronic-journal-of-statistics/volume-10/issue-1/Identifiability-in-penalized-function-on-function-regression-models/10.1214} #' @export #' @importFrom MASS Null # FIXME: weights for Simpson's rule on non-equidistant grids diff --git a/R/pffr.R b/R/pffr.R index 3f737a8d..16861208 100644 --- a/R/pffr.R +++ b/R/pffr.R @@ -173,7 +173,7 @@ #' #' F. Scheipl, J. Gertheiss, S. Greven (2016): Generalized Functional Additive Mixed Models, #' Electronic Journal of Statistics, 10(1), 1455--1492. -#' \url{https://projecteuclid.org/journals/electronic-journal-of-statistics/volume-10/issue-1/Generalized-functional-additive-mixed-models/10.1214/16-EJS1145.full} +#' \url{https://projecteuclid.org/journals/electronic-journal-of-statistics/volume-10/issue-1/Generalized-functional-additive-mixed-models/10.1214} #' @export #' @importFrom mgcv ti jagam gam gam.fit bam gamm #' @importFrom gamm4 gamm4 diff --git a/R/plot.lpeer.R b/R/plot.lpeer.R index f6ba205b..3d09f703 100644 --- a/R/plot.lpeer.R +++ b/R/plot.lpeer.R @@ -32,7 +32,7 @@ ##' } ### Function to plot estimated regression function plot.lpeer<- function(x, conf=0.95, ...){ - if(!class(x)=='lpeer') return (cat("Error: The object is not an lpeer object.\n")) + if(!inherits(x, "lpeer")) return (cat("Error: The object is not an lpeer object.\n")) if(conf>0.99 | conf<0.70) return (cat("Error: Confidence level should be within 0.70 and 0.99\n")) d<- x$d status<- x$status diff --git a/R/plot.peer.R b/R/plot.peer.R index 83b90756..1f65249c 100644 --- a/R/plot.peer.R +++ b/R/plot.peer.R @@ -29,7 +29,7 @@ ### Function to plot estimated regression function plot.peer<- function(x, conf=0.95, ylab='Estimated regression function', main=expression(gamma),...){ - if(!class(x)=='peer') return (cat("Error: The object is not an peer object.\n")) + if(!inherits(x, "peer")) return (cat("Error: The object is not an peer object.\n")) if(conf>0.99 | conf<0.70) return (cat("Error: Confidence level should be within 0.70 and 0.99\n")) status<- x$status est<- x$GammaHat diff --git a/README.md b/README.md index f488adf9..5e9e24cf 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ # `refund` [![](https://travis-ci.org/refunders/refund.svg?branch=master)](https://travis-ci.org/refunders/refund) -[![](http://cranlogs.r-pkg.org/badges/refund)](http://cran.rstudio.com/web/packages/refund/index.html) +[![](http://cranlogs.r-pkg.org/badges/refund)](https://cran.rstudio.com/web/packages/refund/index.html) ## Methods for regression with functional data diff --git a/man/cd4.Rd b/man/cd4.Rd index 571d538f..57ffa6b2 100644 --- a/man/cd4.Rd +++ b/man/cd4.Rd @@ -5,9 +5,7 @@ \alias{cd4} \title{Observed CD4 cell counts} \format{ -A data frame made up of \describe{ \item{list("cd4")}{A 366 x 61 -matrix of CD4 cell counts.}\item{ }{A 366 x 61 matrix of CD4 cell counts.} -} +A data frame made up of a 366 x 61 matrix of CD4 cell counts } \description{ CD4 cell counts for 366 subjects between months -18 and 42 since diff --git a/man/ff.Rd b/man/ff.Rd index 6c9010cc..b17c327d 100755 --- a/man/ff.Rd +++ b/man/ff.Rd @@ -97,7 +97,7 @@ of eigenvalues accounting for at least 0.995 of the total variance in For background on \code{check.ident}:\cr Scheipl, F., Greven, S. (2016). Identifiability in penalized function-on-function regression models. Electronic Journal of Statistics, 10(1), 495--526. - \url{https://projecteuclid.org/journals/electronic-journal-of-statistics/volume-10/issue-1/Identifiability-in-penalized-function-on-function-regression-models/10.1214/16-EJS1123.full} + \url{https://projecteuclid.org/journals/electronic-journal-of-statistics/volume-10/issue-1/Identifiability-in-penalized-function-on-function-regression-models/10.1214} } \seealso{ \code{mgcv}'s \code{\link[mgcv]{linear.functional.terms}} diff --git a/man/pffr.Rd b/man/pffr.Rd index 0ca20cea..f68e1b36 100644 --- a/man/pffr.Rd +++ b/man/pffr.Rd @@ -253,7 +253,7 @@ Ivanescu, A., Staicu, A.-M., Scheipl, F. and Greven, S. (2015). F. Scheipl, J. Gertheiss, S. Greven (2016): Generalized Functional Additive Mixed Models, Electronic Journal of Statistics, 10(1), 1455--1492. - \url{https://projecteuclid.org/journals/electronic-journal-of-statistics/volume-10/issue-1/Generalized-functional-additive-mixed-models/10.1214/16-EJS1145.full} + \url{https://projecteuclid.org/journals/electronic-journal-of-statistics/volume-10/issue-1/Generalized-functional-additive-mixed-models/10.1214} } \seealso{ \code{\link[mgcv]{smooth.terms}} for details of \code{mgcv} syntax