Merge branch 'master' into inherits

Author: davidruegamer

R/FDboost.R

@@ -456,7 +456,7 @@ FDboost <- function(formula,          ### response ~ xvars
   ### save formula of FDboost before it is changed
   formulaFDboost <- formula
 
-  tf <- terms.formula(formula, specials = c("c"))
+  tf <- terms.formula(formula, specials = "c")
   trmstrings <- attr(tf, "term.labels")
   equalBrackets <- NULL
   if(length(trmstrings) > 0){
@@ -465,8 +465,8 @@ FDboost <- function(formula,          ### response ~ xvars
     ## check if number of opening brackets is equal to number of closing brackets
     equalBrackets <- sapply(seq_along(trmstrings2), function(i)
     {
-      sapply(regmatches(trmstrings2[i], gregexpr("\\(", trmstrings2[i])), length) ==
-        sapply(regmatches(trmstrings2[i], gregexpr("\\)", trmstrings2[i])), length)
+      lengths(regmatches(trmstrings2[i], gregexpr("\\(", trmstrings2[i]))) ==
+        lengths(regmatches(trmstrings2[i], gregexpr("\\)", trmstrings2[i])))
     })
   }
 
@@ -621,7 +621,7 @@ FDboost <- function(formula,          ### response ~ xvars
       nr <- nrow(response)
       if(!is.list(time))
         stopifnot(ncol(response) == length(time)) else
-          stopifnot(all(ncol(response) == sapply(time[sapply(time, is.vector)], length)))
+          stopifnot(all(ncol(response) == lengths(time[sapply(time, is.vector)])))
       nc <- ncol(response)
       dresponse <- as.vector(response) # column-wise stacking of response 
       ## convert characters to factor 
@@ -633,7 +633,7 @@ FDboost <- function(formula,          ### response ~ xvars
       stopifnot(is.null(dim(response))) ## stopifnot(is.vector(response))
       # check length of response and its time and index
       if(is.list(time))
-        stopifnot(all(length(response) == sapply(time, length)) & length(response) == length(id)) else
+        stopifnot(all(length(response) == lengths(time)) & length(response) == length(id)) else
           stopifnot(length(response) == length(time) & length(response) == length(id))
 
       if(anyNA(response)) warning("For non-grid observations the response should not contain missing values.")
@@ -944,7 +944,7 @@ FDboost <- function(formula,          ### response ~ xvars
   ### multiply integration weights numInt to weights and w
   if(is.numeric(numInt)){
     .numInt_len_check <- if(is.list(time))
-      all(length(numInt) == sapply(time, length))  else 
+      all(length(numInt) == lengths(time))  else 
         length(numInt) == length(time)
     if(!.numInt_len_check) 
       stop("Length of integration weights and time vector are not equal.")

R/crossvalidation.R

@@ -1248,7 +1248,7 @@ plot.validateFDboost <- function(x, riskopt=c("mean", "median"),
             c(min(c(0, ylim[1] * ifelse(ylim[1] < 0, 2, 0.5))), 
               riskMean[paste(mOptMean)]), lty = 2)
       legend("topright", legend=paste(c(mOptMean)),
-             lty=c(2), col=c("black"))
+             lty=2, col="black")
 
     }
 
@@ -1261,7 +1261,7 @@ plot.validateFDboost <- function(x, riskopt=c("mean", "median"),
               riskMedian[paste(mOptMedian)]), lty = 2)
 
       legend("topright", legend=paste(c(mOptMedian)),
-             lty=c(2), col=c("black"))
+             lty=2, col="black")
     }
 
   }

R/utilityFunctions.R

@@ -12,7 +12,7 @@
 #' @export 
 o_control <- function(k_min=20, rule=2, silent=TRUE, cyclic=FALSE, knots=NULL) { 
   RET <- list(k_min=k_min, rule=rule, silent=silent, cyclic=cyclic, knots=knots)
-  class(RET) <- c("offset_control")
+  class(RET) <- "offset_control"
   RET
 }
 

README.md

@@ -1,27 +1,28 @@
-FDboost
-======
+# FDboost
 
-[![Build Status (Linux)](https://travis-ci.org/boost-R/FDboost.svg?branch=master)](https://travis-ci.org/boost-R/FDboost)
-<!--[![Build status (Windows)](https://ci.appveyor.com/api/projects/status/5mkvicgin1j6pfc6/branch/master?svg=true)](https://ci.appveyor.com/project/hofnerb/mboost-h73a1/branch/master)  -->
-[![CRAN Status Badge](https://www.r-pkg.org/badges/version/FDboost)](https://cran.r-project.org/package=FDboost)
-<!--[![Coverage Status](https://coveralls.io/repos/github/boost-R/mboost/badge.svg?branch=master)](https://coveralls.io/github/boost-R/mboost?branch=master) -->
-[![](https://cranlogs.r-pkg.org/badges/FDboost)](https://cran.rstudio.com/web/packages/FDboost/index.html)
+<!-- badges: start -->
+
+[![CRAN status](https://www.r-pkg.org/badges/version/FDboost)](https://CRAN.R-project.org/package=FDboost)
+[![CRAN RStudio mirror downloads](https://cranlogs.r-pkg.org/badges/FDboost)](https://www.r-pkg.org/pkg/FDboost)
+
+<!-- badges: end -->
 
 `FDboost` Boosting Functional Regression Models.
 
-The package FDboost fits regression models for functional data, i.e., 
+The package FDboost fits regression models for functional data, i.e.,
 scalar-on-function, function-on-scalar, and function-on-function regression models,
-by a component-wise gradient boosting algorithm. 
+by a component-wise gradient boosting algorithm.
 Furthermore, it can be used to fit density-on-scalar regression models.
 
 ## Using FDboost
 
 For installation instructions see below.
 
 Instructions on how to use `FDboost` can be found in various places:
+
 - Read the tutorial paper [doi:10.18637/jss.v094.i10](doi:10.18637/jss.v094.i10)
 - Have a look at the manual, which also contains example code
-- Check the vignettes: 
+- Check the vignettes:
   - [function-on-function regression](https://cran.r-project.org/web/packages/FDboost/vignettes/FLAM_canada.pdf)
   - [scalar-on-function regression](https://cran.r-project.org/web/packages/FDboost/vignettes/FLAM_fuel.pdf)
   - [function-on-scalar regression](https://cran.r-project.org/web/packages/FDboost/vignettes/FLAM_viscosity.pdf)
@@ -31,30 +32,17 @@ Instructions on how to use `FDboost` can be found in various places:
 
 For issues, bugs, feature requests etc. please use the [GitHub Issues](https://github.com/boost-R/FDboost/issues).
 
-## Installation Instructions
-
-- Current version (from CRAN):
-  ```r
-  install.packages("FDboost")
-  ```
-
-- Latest **patch version** (patched version of CRAN package; under development) from GitHub:
-  ```r
-  library("devtools")
-  install_github("boost-R/FDboost") 
-  library("FDboost")
-  ```
-
-<!-- - Latest **development version** (version with new features; under development) from GitHub:
-  ```r
-  library("devtools")
-  install_github("boost-R/mboost", ref = "devel")
-  library("mboost")
-  ```
--->
-
-  To be able to use the `install_github()` command, one needs to install `devtools` first:
-  ```r
-  install.packages("devtools")
-  ```
+## Installation
+
+Install the last release from [CRAN](https://cran.r-project.org):
+
+```r
+install.packages("FDboost")
+```
+
+Install the development version from [GitHub](https://github.com/):
 
+```r
+# install.packages("pak")
+pak::pak("boost-R/FDboost")
+```