documentation fixes for cran push

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

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

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

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

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

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