225 lines
6.8 KiB
R
225 lines
6.8 KiB
R
|
|
## Without this def. roxygen (i.e. C-c C-o C-t or C-c C-o C-r) will fail
|
|
setGeneric("slplot", function(object, ...) { plot(object, ...) })
|
|
|
|
##' \code{loadings(object)} and then design your own plotting method.
|
|
##' @title Side by side scores and loadings plot
|
|
##' @usage slplot(object, pcs=c(1,2), scoresLoadings=c(TRUE, TRUE),
|
|
##' sl="def", ll="def", hotelling=0.95, rug=TRUE, sub=NULL,...)
|
|
##' @param object
|
|
##' @param pcs
|
|
##' @param tjo
|
|
##' @return None, used for side effect.
|
|
##' @export
|
|
##' @author Henning Redestig
|
|
setMethod("slplot", "pcaRes",
|
|
function(object, pcs=c(1,2), tjo) {
|
|
#(ess-roxy-get-function-args)
|
|
opar <- par(no.readonly=TRUE)
|
|
cl <- match.call()
|
|
})
|
|
|
|
##' .. content for \description{} (no empty lines) ..
|
|
##'
|
|
##' .. content for \details{} ..
|
|
##' @title Must have a title
|
|
##' @param a any
|
|
##' @param b any
|
|
##' @param d any
|
|
##' @param asd any
|
|
##' @return invisible
|
|
##' @author Henning Redestig
|
|
trickyInArgsComments <- function(a,#comment
|
|
b,#hejhopp trams
|
|
d,asd) {
|
|
print("hello")
|
|
}
|
|
|
|
##' .. content for \description{} (no empty lines) ..
|
|
##'
|
|
##' @title Function example where arguments have defaults
|
|
##' @param a any
|
|
##' @param b string
|
|
##' @param cc
|
|
##' @return invisible
|
|
##' @author Henning Redestig
|
|
withdef <- function(a, b=c("asd","ffd", "asd", "ffd",
|
|
"asd",
|
|
"ffd","asd",
|
|
"ffd"), cc) {
|
|
print("hello")
|
|
|
|
}
|
|
|
|
setClass(Class="inference", representation=representation(model="character"
|
|
, sample.size="numeric"
|
|
, robust.se="logical"
|
|
, two.sided="logical"
|
|
, ci.level="numeric"), contains=c("matrix"))
|
|
|
|
##' .. content for \description{} (no empty lines)
|
|
##'
|
|
##' .. content for \details{} ..
|
|
##' @title asd
|
|
##' @param a
|
|
##' @param asdsd
|
|
##' @param sd
|
|
##' @param ...
|
|
##' @return s
|
|
##' @author Henning Redestig
|
|
tempFixNasFunction <- function(a,asdsd, sd, ...) {
|
|
asds
|
|
}
|
|
|
|
setGeneric("updateMu", function(respM, gamma, ...)
|
|
standardGeneric("updateMu"))
|
|
|
|
|
|
## (make-local-variable 'adaptive-fill-regexp)
|
|
## (setq adaptive-fill-regexp (concat ess-roxy-str adaptive-fill-regexp))
|
|
## (make-local-variable 'adaptive-fill-first-line-regexp)
|
|
## (setq adaptive-fill-first-line-regexp (concat ess-roxy-str adaptive-fill-first-line-regexp))
|
|
## (make-local-variable 'paragraph-start)
|
|
## (setq paragraph-start (concat "\\(" ess-roxy-str "\\)*" paragraph-start))
|
|
## (make-local-variable 'paragraph-separate)
|
|
## (setq paragraph-separate (concat "\\(" ess-roxy-str "\\)*" paragraph-separate))
|
|
## (auto-fill-mode)
|
|
asd
|
|
|
|
##' aqdasd lksa odnsl dlsakdn lsakdn sladn asijdi j 1. asdsd alksnd
|
|
##' lasdn ldnad
|
|
##'
|
|
##'
|
|
##' alkdnal dl lakd lasdnladna ld aldan lda dlakd nladn a amd lakdn
|
|
##' ajdn asjdns
|
|
##'
|
|
##' lajnsd jasdn aksjdnaksjnd asjdnaksdnajsdnajsd aksdn askdjn
|
|
##' akjdn aksdnkasjdnka
|
|
##'
|
|
##' 1. aldn adlnsald ladn saldnlaksd naskl
|
|
##' 2. ad asdjnksadn adjn skajan kda dksadkas dkjan dkasndkadn
|
|
##' ajsd nkj dakjd sd
|
|
##' @title hej
|
|
##' @param fitta asdadsd
|
|
##' 1.
|
|
##' 2. asd
|
|
##' @param diagonals pung asa as a sad s dsa da das d asd asd add
|
|
##' @param tjo asd
|
|
##' @param asdasd
|
|
##' @return me
|
|
##' @author Henning Redestig
|
|
tempFixNas <- function(fitta, diagonals, tjo, asdasd) {
|
|
|
|
for(i in index) {
|
|
data <- otherdata[i]
|
|
}
|
|
|
|
}
|
|
|
|
|
|
##' Simply replace completely ajksbdkjsa djskbdkajbd
|
|
##'
|
|
##' ksdb skdb skasdaj ahd (ess-roxy-beg-of-field) (newline-and-indent)
|
|
##' aksndlsakndlksdn jkahd ksn dkjands
|
|
##' @title Temporary fix for missing values
|
|
##' @param diagonals The diagonal to be replaced, i.e. the first,
|
|
##' second and so on when looking at the fat version of the matrix
|
|
##' @param tjo asdsdsdw
|
|
##' @return The original matrix with completely missing rows/cols
|
|
##' filled with zeroes. oasndsnd aksdnkasdnskans dkas ndkjasndksdn
|
|
##' skandkand ksjandknsd
|
|
##' @export
|
|
##' @examples
|
|
##' tempFixNas(iris)
|
|
##' pi <- 1
|
|
##' plot(x)
|
|
##' @author Henning Redestig
|
|
tempFixNas <- function(diagonals, tjo) {
|
|
(ess-roxy-delete-args)
|
|
wilcox.test
|
|
(ess-roxy-goto-end-of-entry)
|
|
badRows <- apply(mat, 1, function(x) all(is.na(x)))
|
|
badCols <- apply(mat, 2, function(x) all(is.na(x)))
|
|
mat[ badRows,] <- 0 (ess-roxy-get-args-list-from-def)
|
|
mat[,badCols ] <- 0 (ess-roxy-get-args-list-from-entry)
|
|
mat
|
|
}
|
|
|
|
##' <description>
|
|
##'
|
|
##' <details>
|
|
##' @title asdsd
|
|
##' @param asd asd
|
|
##' @param test1 asd
|
|
##' @param asdsd
|
|
##' @param tjo asdasd
|
|
##' @return aa
|
|
##' @author Henning Redestig
|
|
tempFixNas <- function(asd,test1,asdsd,tjo=c("asd", "asdasd")) {
|
|
## (ess-roxy-goto-end-of-entry)
|
|
## (setq fun (ess-roxy-get-args-list-from-def))
|
|
## (setq ent (ess-roxy-get-args-list-from-entry))
|
|
## (ess-roxy-merge-args fun ent)
|
|
## (ess-roxy-mrg-args fun ent)
|
|
## (ess-roxy-get-args-list-from-entry)
|
|
## (ess-roxy-get-function-args)
|
|
## (ess-roxy-goto-end-of-entry)
|
|
|
|
## (setq here (ess-roxy-delete-args))
|
|
## (ess-roxy-insert-args (ess-roxy-get-args-list-from-def) here)
|
|
badRows <- apply(mat, 1, function(x) all(is.na(x)))
|
|
badCols <- apply(mat, 2, function(x) all(is.na(x)))
|
|
mat[ badRows,] <- 0
|
|
mat[,badCols ] <- 0
|
|
mat
|
|
}
|
|
|
|
##' <description>
|
|
##'
|
|
##' <details>
|
|
##' @title my title
|
|
##' @param test1
|
|
##' @param tjo
|
|
##' @param pung
|
|
##' @param str
|
|
##' @return value
|
|
##' @author Henning Redestig
|
|
tempFixNasBad <- function(test1,tjo=c("asd", "asdasd"), pung, str) {
|
|
asdsd# (car (cdr (ess-end-of-function nil t)))
|
|
}
|
|
|
|
##' Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse
|
|
##' Non-Linear PCA and the conventional SVD PCA. A cluster based
|
|
##' method for missing value estimation is included for comparison.
|
|
##' BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete
|
|
##' data as well as for accurate missing value estimation. A set of
|
|
##' methods for printing and plotting the results is also provided.
|
|
##' All PCA methods make use of the same data structure (pcaRes) to
|
|
##' provide a unique interface to the PCA results. Developed at the
|
|
##' Max-Planck Institute for Molecular Plant Physiology, Golm,
|
|
##' Germany, RIKEN Plant Science Center Yokohama, Japan, and CAS-MPG
|
|
##' Partner Institute for Computational Biology (PICB) Shanghai,
|
|
##' P.R. China
|
|
##'
|
|
##' @name pcaMethods
|
|
##' @aliases pcaMethods
|
|
##' @docType package
|
|
##' @title pcaMethods
|
|
##' @useDynLib pcaMethods
|
|
##' @author Wolfram Stacklies, Henning Redestig
|
|
NULL
|
|
|
|
|
|
#' Title
|
|
#'
|
|
#' @param par Lorem ipsum dolor sit amet, consectetur adipiscing
|
|
#' elit. Vivamus ligula purus, ultricies quis odio non, vulputate
|
|
#' finibus risus. Donec eleifend quis dolor ut rhoncus.
|
|
#' @param par2 Lorem ipsum dolor sit amet, consectetur adipiscing
|
|
#' elit. Vivamus ligula purus, ultricies quis odio non.
|
|
#' @examples
|
|
#' # This long comment line can be paragraph-filled without squashing
|
|
#' # the following lines of code into the comment
|
|
#' fun(arg)
|
|
#' print(object)
|