tseries class

DESCRIPTION

@@ -57,13 +57,15 @@ Description: Toolkit to perform statistical analyses of correlation
 Imports:
     abind,
     boot,
-    dplyr,
+    dplyr (>= 1.0.0),
     R6,
     Rcpp,
     stringr
 LinkingTo: 
     Rcpp
 Suggests: 
+    grr,
+    pbmcapply,
     minpack.lm,
     parallel,
     rhdf5,
@@ -76,12 +78,13 @@ Suggests:
     staplr,
     markdown,
     rmarkdown,
-    errors
+    errors,
+    reshape2
 License: GPL-3
 URL: https://github.com/HISKP-LQCD/hadron
 BugReports: https://github.com/HISKP-LQCD/hadron/issues
 LazyData: true
 Roxygen: list(markdown = TRUE, old_usage = TRUE, r6 = FALSE)
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.0
 Encoding: UTF-8
 VignetteBuilder: knitr

R/UWerr.R

@@ -81,6 +81,22 @@ uwerr <- function(f, data, nrep, S=1.5, pl=FALSE, ...) {
   }
 }
 
+#' @export
+apply_uwerrprimary <- function(X, S=1.5){
+  stopifnot(length(dim(X)) == 2)
+  tmp <- t(apply(
+    X = X,
+    MARGIN = 2L,
+    FUN = function(x){
+      uw <- uwerrprimary(data = x, S = S, pl = FALSE)
+      return( c(uw$value, uw$dvalue, uw$ddvalue, uw$tauint, uw$dtauint) )
+    }
+  ))
+  colnames(tmp) <- c("value", "dvalue", "ddvalue", "tauint", "dtauint")
+  return(invisible(as.data.frame(tmp)))
+}
+
+
 #' @export
 uwerrprimary <- function(data, nrep, S=1.5, pl=FALSE) {
 

R/bootstrap.nlsfit.R

@@ -110,7 +110,7 @@ parametric.nlsfit <- function (fn, par.guess, boot.R, y, dy, x, dx,
                                lower = rep(x = -Inf, times = length(par.guess)),
                                upper = rep(x = +Inf, times = length(par.guess)),
                                ..., bootstrap=TRUE) {
-  stopifnot(length(x) == length(y))
+  stopifnot(length(x) %% length(y) == 0)
   stopifnot(missing(dx) || length(dx) == length(x))
   stopifnot(missing(dy) || length(dy) == length(y))
   stopifnot(length(lower) == length(par.guess))
@@ -156,7 +156,7 @@ parametric.nlsfit.cov <- function (fn, par.guess, boot.R, y, x, cov,
                                    lower = rep(x = -Inf, times = length(par.guess)),
                                    upper = rep(x = +Inf, times = length(par.guess)),
                                    ..., bootstrap=TRUE, na.rm = FALSE) {
-  stopifnot(length(x) == length(y))
+  stopifnot(length(x) %% length(y) == 0)
   stopifnot(length(lower) == length(par.guess))
   stopifnot(length(upper) == length(par.guess))
 
@@ -1280,20 +1280,6 @@ plot.bootstrapfit <- function(x, ..., col.line="black", col.band="gray", opacity
   }
 }
 
-#' residual_plot
-#'
-#' generic residual_plot method
-#'
-#' @param x the object to plot
-#' @param ... additional parameters to be passed on to specialised functions
-#' 
-#' @return
-#' No return value.
-#' 
-#' @export
-residual_plot <- function (x, ...) {
-  UseMethod("residual_plot", x)
-}
 
 #' @export
 residual_plot.bootstrapfit <- function (x, ..., error_fn = x$error.function, operation = `/`) {

R/cf.R

@@ -419,7 +419,7 @@ is_empty.cf <- function (.cf) {
 #'         with elements `boot`, `boot.R`, `boot.l`, `sim`, `endcorr`,
 #'         `resampling_method`, `boot_dim`, `icf` and, optionally
 #'         `iboot_dim` (if both `cf1` and `cf2` contain imaginary parts).
-resampling_is_compatible <- function(cf1, cf2){
+resampling_is_compatible.cf <- function(cf1, cf2){
 
   res <- list()
   res$boot <- ( inherits(cf1, 'cf_boot') & inherits(cf2, 'cf_boot') )
@@ -453,7 +453,7 @@ resampling_is_compatible <- function(cf1, cf2){
 #'         with elements `boot`, `boot.R`, `boot.l`, `sim`, `endcorr`,
 #'         `resampling_method`, `boot_nrow`, `icf` and, optionally
 #'         `iboot_nrow` (if both `cf1` and `cf2` contain imaginary parts).
-resampling_is_concatenable <- function(cf1, cf2){
+resampling_is_concatenable.cf <- function(cf1, cf2){
   res <- list()
   res$boot <- ( inherits(cf1, 'cf_boot') & inherits(cf2, 'cf_boot') )
   res$seed <- (cf1$seed == cf2$seed)

R/cvc_readutils.R

@@ -22,7 +22,7 @@ cvc_local_loop_key <- function(loop_type, istoch, gamma, p)
 #' @title Generate key to identify a momentum and spin-projected loop 
 #' @param loop_type String, loop type.
 #' @param istoch Integer, index of the stochastic sample.
-#' @param gamma Integer, CVC convention gamma matrix identifier.
+#' @param gamma Integer or string, gamma matrix identifier.
 #' @param p Integer vector of length 3, (x,y,z) components of the momentum
 #'          vector in lattice units.
 #' @return
@@ -40,51 +40,91 @@ cvc_local_loop_key <- function(loop_type, istoch, gamma, p)
           p[1], p[2], p[3])
 }
 
-#' @title Generate HDF5 key for CVC 'correlators' meson 2pt function
+#' @title Generate HDF5 key for meson 2pt functions labelled with CVC-like pathnames.
+#'
+#' @details
+#' The key for a meson two-point function has the form:
+#' 
+#'  /u+-g-d-g/s1/t10/gf5/pfx0pfy0pfz0/gi5/pix0piy0piz0
+#' 
+#' where, from left to right:
+#' \itemize{
+#'  \item 'u' is the flavour of the "backward" propagator
+#'  \item '+' indicates that 'u' is daggered
+#'  \item 'g' indicates a gamma insertion 
+#'  \item 'd' is the flavour of the "forward" propagator
+#'  \item 'g' indicates a Dirac structure at the source
+#'  \item 'sN' is an optional stochastic sample identifier
+#'  \item 'tXX' is the source time slice
+#'  \item 'gfN' gamma structure at the sink
+#'  \item 'pfxXpfyYpfzZ' is the sink momentum in CVC convention (sink and source phases are both e^{ipx})
+#'  \item 'giN' gamma structure at the souce in CVC indexing
+#'  \item 'pixXpiyYpizZ' at the source in CVC convention
+#' }
+#'
 #' @param fwd_flav String, "forward" quark flavour identifier.
 #' @param bwd_flav String, "backward" quark flavour identifier.
 #' @param src_ts Integer, source time slice.
-#' @param snk_gamma Integer, CVC convention gamma matrix identifier at the source.
-#' @param src_gamma Integer, CVC convention gamma matrix identified at the sink.
+#' @param snk_gamma Integer or string, gamma matrix identifier at the source.
+#' @param src_gamma Integer or string, gamma matrix identifier at the sink.
 #' @param src_p Integer vector of length 3. (x,y,z) components of the source momentum
 #'              vector in lattice units.
 #' @param snk_p Integer vector of length 3. (x,y,z) components of the sink momentum
 #'              vector in lattice units.
+#' @param istoch Integer, optional stochastic sample identifier.
 #' @return
-#' A character vector with the HDF5 key.
+#' A character vector with the HDF5 pathname.
 #' 
 #' @export
-correlators_key_meson_2pt <- function(fwd_flav, bwd_flav, src_ts, snk_gamma, src_gamma, src_p, snk_p)
+correlators_key_meson_2pt <- function(fwd_flav, bwd_flav, src_ts, snk_gamma, src_gamma, src_p, snk_p, istoch = NA)
 {
   stopifnot( length(snk_p) == 3 )
   stopifnot( length(src_p) == 3 )
   stopifnot( is.character(fwd_flav) )
   stopifnot( is.character(bwd_flav) )
   stopifnot( is.integer(src_ts) )
-  stopifnot( is.integer(snk_gamma) )
-  stopifnot( is.integer(src_gamma) )
+  if( !is.na(istoch) ){ stopifnot( is.integer(istoch) ) }
 
-  sprintf("/%s+-g-%s-g/t%d/gf%d/pfx%dpfy%dpfz%d/gi%d/pix%dpiy%dpiz%d",
+  sprintf("/%s+-g-%s-g/%st%d/gf%s/pfx%dpfy%dpfz%d/gi%s/pix%dpiy%dpiz%d",
           bwd_flav,
           fwd_flav,
+          ifelse(is.na(istoch), "", sprintf("s%d/", istoch)),
           src_ts,
           snk_gamma,
           snk_p[1],snk_p[2],snk_p[3],
           src_gamma,
           src_p[1],src_p[2],src_p[3])
 }
 
-#' @title Generate key string to identify a meson 2pt function
+#' @title Generate identifier string to identify a meson 2pt function with a CVC-like pathname
+#'
+#' @details
+#' The identifier string for a meson two-point function has the form:
+#' 
+#'  /u+-g-d-g/gf5/pfx0pfy0pfz0/gi5/pix0piy0piz0
+#' 
+#' where, from left to right:
+#' \itemize{
+#'  \item 'u' is the flavour of the "backward" propagator
+#'  \item '+' indicates that 'u' is daggered
+#'  \item 'g' indicates a gamma insertion 
+#'  \item 'd' is the flavour of the "forward" propagator
+#'  \item 'g' indicates a Dirac structure at the source
+#'  \item 'gfN' gamma structure at the sink
+#'  \item 'pfxXpfyYpfzZ' is the sink momentum in CVC convention (sink and source phases are both e^{ipx})
+#'  \item 'giN' gamma structure at the souce in CVC indexing
+#'  \item 'pixXpiyYpizZ' at the source in CVC convention
+#' }
 #' @param fwd_flav String, "forward" quark flavour identifier.
 #' @param bwd_flav String, "backward" quark flavour identifier.
-#' @param snk_gamma Integer, CVC convention gamma matrix identifier at the source.
-#' @param src_gamma Integer, CVC convention gamma matrix identified at the sink.
+#' @param snk_gamma Integer or string, gamma matrix identifier at the source.
+#' @param src_gamma Integer or string, gamma matrix identifier at the sink.
 #' @param src_p Integer vector of length 3. (x,y,z) components of the source momentum
 #'              vector in lattice units.
 #' @param snk_p Integer vector of length 3. (x,y,z) components of the sink momentum
 #'              vector in lattice units.
 #' @return
-#' A character vector with the HDF5 key.
+#' A character vector with the identifier string.
 #' 
 #' @export
 cf_key_meson_2pt <- function(fwd_flav, bwd_flav, snk_gamma, src_gamma, src_p, snk_p)
@@ -93,10 +133,8 @@ cf_key_meson_2pt <- function(fwd_flav, bwd_flav, snk_gamma, src_gamma, src_p, sn
   stopifnot( length(src_p) == 3 )
   stopifnot( is.character(fwd_flav) )
   stopifnot( is.character(bwd_flav) )
-  stopifnot( is.integer(snk_gamma) )
-  stopifnot( is.integer(src_gamma) )
 
-  sprintf("/%s+-g-%s-g/gf%d/pfx%dpfy%dpfz%d/gi%d/pix%dpiy%dpiz%d",
+  sprintf("/%s+-g-%s-g/gf%s/pfx%dpfy%dpfz%d/gi%s/pix%dpiy%dpiz%d",
           bwd_flav,
           fwd_flav,
           snk_gamma,
@@ -105,11 +143,12 @@ cf_key_meson_2pt <- function(fwd_flav, bwd_flav, snk_gamma, src_gamma, src_p, sn
           src_p[1],src_p[2],src_p[3])
 }
 
-#' @title Generate HDF5 key for CVC 'correlators' meson 3pt function with a local or derivative insertion
+#' @title Generate HDF5 key for meson 3pt function with a local or derivative insertion
 #' 
+#' @details
 #' The key for a meson three-point function has the form:
 #' 
-#'  /sud+-g-u-g/t10/dt12/gf5/pfx0pfy0pfz0/gc0/Ddim0_dir0/Ddim1_dir1/D[...]/gi5/pix0piy0piz0
+#'  /sud+-g-u-g/s1/t10/dt12/gf5/pfx0pfy0pfz0/gc0/Ddim0_dir0/Ddim1_dir1/D[...]/gi5/pix0piy0piz0
 #' 
 #' where, from left to right:
 #' \itemize{
@@ -119,11 +158,12 @@ cf_key_meson_2pt <- function(fwd_flav, bwd_flav, snk_gamma, src_gamma, src_p, sn
 #'  \item 'g' indicates a gamma insertion 
 #'  \item 'u' is the flavour of the foward propagator
 #'  \item 'g' indicates a Dirac structure at the source
+#'  \item 'sN' is an optional stochastic sample identifier
 #'  \item 'tXX' is the source time slice
 #'  \item 'dtYY' is the source-sink separation
-#'  \item 'gfN' gamma structure at the sink in CVC indexing
+#'  \item 'gfN' gamma structure at the sink
 #'  \item 'pfxXpfyYpfzZ' is the sink momentum in CVC convention (sink and source phases are both e^{ipx})
-#'  \item 'gcN' gamma structure at the current insertion point in CVC indexing
+#'  \item 'gcN' gamma structure at the current insertion point in
 #'  \item 'DdimJ_dirK' covariant displacement applied in dimension 'J', direction 'K'
 #'         where it should be noted that this is. in operator notation, i.e., the right-most
 #'         displacement is the one applied first.
@@ -137,8 +177,8 @@ cf_key_meson_2pt <- function(fwd_flav, bwd_flav, snk_gamma, src_gamma, src_p, sn
 #' @param seq_flav String, "sequential" quark flavour identifier.
 #' @param src_ts Integer, source time slice.
 #' @param dt Integer, source-sink separation.
-#' @param snk_gamma Integer, CVC convention gamma matrix identifier at the source.
-#' @param cur_gamma Integer, CVC convention gamma matrix identified at the insertion.
+#' @param snk_gamma Integer or string, gamma matrix identifier at the sink.
+#' @param cur_gamma Integer or string, gamma matrix identifier at the insertion.
 #' @param cur_displ_dim Integer vector of dimensions (0,1,2,3 <-> t,x,y,z) in which
 #'                      covariant displacements have been applied. This vector will be
 #'                      parsed in reverse order, such that the first element here
@@ -150,11 +190,12 @@ cf_key_meson_2pt <- function(fwd_flav, bwd_flav, snk_gamma, src_gamma, src_p, sn
 #'                      which the covariant displacements have been applied. Parsing
 #'                      as for 'cur_displ_dim'. Length must be matched to 'cur_displ_dim'.
 #'                      Defaults to 'NA' for no displacements.
-#' @param src_gamma Integer, CVC convention gamma matrix identified at the sink.
+#' @param src_gamma Integer or string, gamma matrix identifier at the source.
 #' @param src_p Integer vector of length 3. (x,y,z) components of the source momentum
 #'              vector in lattice units.
 #' @param snk_p Integer vector of length 3. (x,y,z) components of the sink momentum
 #'              vector in lattice units.
+#' @param istoch Integer, optional stochastic sample identifier.
 #' @return
 #' A character vector with the HDF5 key.
 #' 
@@ -164,17 +205,16 @@ correlators_key_meson_3pt <- function(fwd_flav, bwd_flav, seq_flav,
                                       snk_gamma,
                                       cur_gamma, cur_displ_dim = NA, cur_displ_dir = NA,
                                       src_gamma, 
-                                      src_p, snk_p)
+                                      src_p, snk_p,
+                                      istoch = NA)
 {
   stopifnot( length(snk_p) == 3 )
   stopifnot( length(src_p) == 3 )
   stopifnot( is.character(fwd_flav) )
   stopifnot( is.character(bwd_flav) )
   stopifnot( is.integer(src_ts) )
   stopifnot( is.integer(dt) )
-  stopifnot( is.integer(snk_gamma) )
-  stopifnot( is.integer(src_gamma) )
-
+  if( !is.na(istoch) ){ stopifnot( is.integer(istoch) ) } 
   if( !is.na(cur_displ_dim) | !is.na(cur_displ_dir) ){
     stopifnot( all(cur_displ_dim %in% c(0:3)) )
     stopifnot( all(cur_displ_dir %in% c(0,1)) )
@@ -208,11 +248,12 @@ correlators_key_meson_3pt <- function(fwd_flav, bwd_flav, seq_flav,
   return(key)
 }
 
-#' @title Generate HDF5 key for CVC 'correlators' meson 3pt function with a local or derivative insertion
+#' @title Generate an identifier string for a meson 3pt function labelled with a CVC-like pathname with a local or derivative insertion
 #' 
-#' The key for a meson three-point function has the form:
+#' @details
+#' The identifier string for a meson three-point function has the form:
 #' 
-#'  /sud+-g-u-g/t10/dt12/gf5/pfx0pfy0pfz0/gc0/Ddim0_dir0/Ddim1_dir1/D[...]/gi5/pix0piy0piz0
+#'  /sud+-g-u-g/dt12/gf5/pfx0pfy0pfz0/gc0/Ddim0_dir0/Ddim1_dir1/D[...]/gi5/pix0piy0piz0
 #' 
 #' where, from left to right:
 #' \itemize{
@@ -222,25 +263,24 @@ correlators_key_meson_3pt <- function(fwd_flav, bwd_flav, seq_flav,
 #'  \item 'g' indicates a gamma insertion 
 #'  \item 'u' is the flavour of the foward propagator
 #'  \item 'g' indicates a Dirac structure at the source
-#'  \item 'tXX' is the source time slice
 #'  \item 'dtYY' is the source-sink separation
-#'  \item 'gfN' gamma structure at the sink in CVC indexing
+#'  \item 'gfN' gamma structure at the sink in CVC indexing ('N' can be numeric or a string)
 #'  \item 'pfxXpfyYpfzZ' is the sink momentum in CVC convention (sink and source phases are both e^{ipx})
-#'  \item 'gcN' gamma structure at the current insertion point in CVC indexing
+#'  \item 'gcN' gamma structure at the current insertion point ('N' can be numeric or a string)
 #'  \item 'DdimJ_dirK' covariant displacement applied in dimension 'J', direction 'K'
 #'         where it should be noted that this is. in operator notation, i.e., the right-most
 #'         displacement is the one applied first.
 #'  \item [...]
-#'  \item 'giN' gamma structure at the souce in CVC indexing
+#'  \item 'giN' gamma structure at the source ('N' can be numeric or a string)
 #'  \item 'pixXpiyYpizZ' at the source in CVC convention
 #' }
 #'
 #' @param fwd_flav String, "forward" quark flavour identifier.
 #' @param bwd_flav String, "backward" quark flavour identifier.
 #' @param seq_flav String, "sequential" quark flavour identifier.
 #' @param dt Integer, source-sink separation.
-#' @param snk_gamma Integer, CVC convention gamma matrix identifier at the source.
-#' @param cur_gamma Integer, CVC convention gamma matrix identified at the insertion.
+#' @param snk_gamma Integer or string, gamma matrix identifier at the sink.
+#' @param cur_gamma Integer or string, gamma matrix identifier at the insertion.
 #' @param cur_displ_dim Integer vector of dimensions (0,1,2,3 <-> t,x,y,z) in which
 #'                      covariant displacements have been applied. This vector will be
 #'                      parsed in reverse order, such that the first element here
@@ -252,13 +292,13 @@ correlators_key_meson_3pt <- function(fwd_flav, bwd_flav, seq_flav,
 #'                      which the covariant displacements have been applied. Parsing
 #'                      as for 'cur_displ_dim'. Length must be matched to 'cur_displ_dim'.
 #'                      Defaults to 'NA' for no displacements.
-#' @param src_gamma Integer, CVC convention gamma matrix identified at the sink.
+#' @param src_gamma Integer or string, gamma matrix identifier at the source.
 #' @param src_p Integer vector of length 3. (x,y,z) components of the source momentum
 #'              vector in lattice units.
 #' @param snk_p Integer vector of length 3. (x,y,z) components of the sink momentum
 #'              vector in lattice units.
 #' @return
-#' A character vector with the HDF5 key.
+#' A character vector with the identifier string.
 #' 
 #' @export
 cf_key_meson_3pt <- function(fwd_flav, bwd_flav, seq_flav,
@@ -273,8 +313,6 @@ cf_key_meson_3pt <- function(fwd_flav, bwd_flav, seq_flav,
   stopifnot( is.character(fwd_flav) )
   stopifnot( is.character(bwd_flav) )
   stopifnot( is.integer(dt) )
-  stopifnot( is.integer(snk_gamma) )
-  stopifnot( is.integer(src_gamma) )
   if( !is.na(cur_displ_dim) | !is.na(cur_displ_dir) ){
     stopifnot( all(cur_displ_dim %in% c(0:3)) )
     stopifnot( all(cur_displ_dir %in% c(0,1)) )
@@ -337,7 +375,7 @@ cvc_to_raw_cf <- function(cf_dat, dims = c(1,1))
   # internal dimensions and time in the 'wrong' order
   cf_dat <- array(complex(real = cf_dat[ridcs],
                           imaginary = cf_dat[iidcs]),
-                          dim = c(1,dims,nts))
+                  dim = c(1,dims,nts))
   cf_dims <- dim(cf_dat)
   # reshape the array, ordering 'measurement' (a single one), 'time',
   # internal dimensions