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Generalize uwerrcf #316

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Generalize uwerrcf #316

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2833871
UWerr: We can also specify a main when plotting an UWerr-result with …
christianegross Nov 14, 2023
8608c33
cf: when we call uwerr.cf, we can also specify the parameter S now
christianegross Nov 14, 2023
dec9d57
cf: when calling uwerr on cf, we can now also plot the results
christianegross Nov 14, 2023
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15 changes: 8 additions & 7 deletions R/UWerr.R
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@
#' @param pl logical: if TRUE, the autocorrelation function, the integrated
#' autocorrelation time as function of the integration cut-off and (for primary
#' quantities) the time history of the observable are plotted with plot.uwerr
#' @param main character, title of the plots
#' @param ... arguments passed to function \code{f}.
#' @return In case of a primary observable (\code{uwerrprimary}), an object of
#' class \code{uwerr} with basis class \code{\link{list}} containing the
Expand Down Expand Up @@ -60,7 +61,7 @@
#' plot(plaq.res)
#'
#' @export uwerr
uwerr <- function(f, data, nrep, S=1.5, pl=FALSE, ...) {
uwerr <- function(f, data, nrep, S=1.5, pl=FALSE, main="", ...) {
# f: scalar function handle, needed for derived quantities
# data: the matrix of data with dim. (Nalpha x N)
# N = total number of measurements
Expand All @@ -71,18 +72,18 @@ uwerr <- function(f, data, nrep, S=1.5, pl=FALSE, ...) {
if(missing(nrep)) {
nrep <- c(length(data))
}
return(invisible(uwerrprimary(data=data, nrep=nrep, S=S, pl=pl)))
return(invisible(uwerrprimary(data=data, nrep=nrep, S=S, pl=pl, main=main)))
}
else {
if(missing(nrep)) {
nrep <- c(length(data[1,]))
}
return(invisible(uwerrderived(f=f, data=data, nrep=nrep, S=S, pl=pl, ...)))
return(invisible(uwerrderived(f=f, data=data, nrep=nrep, S=S, pl=pl, main=main, ...)))
}
}

#' @export
uwerrprimary <- function(data, nrep, S=1.5, pl=FALSE) {
uwerrprimary <- function(data, nrep, S=1.5, pl=FALSE, main="") {

N = length(data)
if(missing(nrep)) {
Expand Down Expand Up @@ -202,14 +203,14 @@ uwerrprimary <- function(data, nrep, S=1.5, pl=FALSE) {
attr(res, "class") <- c("uwerr", "list")

if(pl) {
plot(res)
plot(res, main=main)
}

return(invisible(res))
}

#' @export
uwerrderived <- function(f, data, nrep, S=1.5, pl=FALSE, ...) {
uwerrderived <- function(f, data, nrep, S=1.5, pl=FALSE, main="", ...) {
Nalpha <- dim(data)[2]
N <- dim(data)[1]
if(missing(nrep)) {
Expand Down Expand Up @@ -392,7 +393,7 @@ uwerrderived <- function(f, data, nrep, S=1.5, pl=FALSE, ...) {
attr(res, "class") <- c("uwerr", "list")

if(pl) {
plot(res)
plot(res, main=main)
}

options(error = NULL)
Expand Down
21 changes: 14 additions & 7 deletions R/cf.R
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Expand Up @@ -673,6 +673,12 @@ jackknife.cf <- function(cf, boot.l = 1) {
#' Gamma method analysis on all time-slices in a 'cf' object
#'
#' @param cf Object of type `cf` containing `cf_orig`
#' @param S initial guess for the ratio tau/tauint, with tau the exponetial
#' autocorrelation length.
#' @param pl logical: if TRUE, the autocorrelation function, the integrated
#' autocorrelation time as function of the integration cut-off and (for primary
#' quantities) the time history of the observable are plotted with plot.uwerr
#' @param main character, title of the plots
#'
#' @return A list with a named element `uwcf` which contains a data frame
#' with six columns, `value`, `dvalue`, `ddvalue`, `tauint`, `dtauint`
Expand All @@ -690,31 +696,32 @@ jackknife.cf <- function(cf, boot.l = 1) {
#' uwerr.cf(samplecf)
#'
#' @export
uwerr.cf <- function(cf){
uwerr.cf <- function(cf, S=1.5, pl=FALSE, main=""){
stopifnot(inherits(cf, 'cf_orig'))

uw_wrapper <- function(x){
uw_tmp <- try(uwerrprimary(data=x), silent=TRUE)
uw_wrapper <- function(x, S, pl, main){
uw_tmp <- try(uwerrprimary(data=x, S=S, pl=pl, main=main), silent=TRUE)
if( any(class(uw_tmp) == "try-error") ){
c(value=NA, dvalue=NA, ddvalue=NA, tauint=NA, dtauint=NA)
c(value=NA, dvalue=NA, ddvalue=NA, tauint=NA, dtauint=NA, S=S)
} else {
c(value=uw_tmp$value, dvalue=uw_tmp$dvalue, ddvalue=uw_tmp$ddvalue,
tauint=uw_tmp$tauint, dtauint=uw_tmp$dtauint)
tauint=uw_tmp$tauint, dtauint=uw_tmp$dtauint, S=S)
}
}

res <- list()
res[["uwcf"]] <- cbind(as.data.frame(t(apply(X=cf$cf, MARGIN=2L, FUN=uw_wrapper))),
res[["uwcf"]] <- cbind(as.data.frame(t(apply(X=cf$cf, MARGIN=2L, FUN=uw_wrapper, S=S, pl=pl, main=main))),
t=(1:ncol(cf$cf)))
if( has_icf(cf) ){
res[["uwicf"]] <- cbind(as.data.frame(t(apply(X=cf$icf, MARGIN=2L, FUN=uw_wrapper))),
res[["uwicf"]] <- cbind(as.data.frame(t(apply(X=cf$icf, MARGIN=2L, FUN=uw_wrapper, S=S, pl=pl, main=main))),
t=(1:ncol(cf$icf)))
}
return(res)
}




#' add a configuration index to an \code{cf} object
#'
#' add a configuration number index to \code{cf} object.
Expand Down