diff --git a/DESCRIPTION b/DESCRIPTION index 7d06108..d4a484b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -39,7 +39,8 @@ Imports: caret, mgcv, xtable, - Rdpack + Rdpack, + data.table Suggests: knitr, rmarkdown, diff --git a/R/twdtw_reduce_time.R b/R/twdtw_reduce_time.R index e214a9d..bd0bdd6 100644 --- a/R/twdtw_reduce_time.R +++ b/R/twdtw_reduce_time.R @@ -38,8 +38,10 @@ px <- x[,names(x)!="date",drop=FALSE] tx <- as.Date(x$date) + ## Basic use case + # Comput TWDTW alignments for all patterns - aligs <- do.call("rbind", lapply(seq_along(y), function(l){ + aligs <- lapply(seq_along(y), function(l){ # Split pattern time series from dates py <- y[[l]][,names(y[[l]])!="date",drop=FALSE] @@ -55,7 +57,6 @@ cm <- proxy::dist(py, px, method = dist.method) if(!is.null(weight.fun)){ - # Get day of the year for pattern and time series doyy <- as.numeric(format(ty, "%j")) doyx <- as.numeric(format(tx, "%j")) @@ -65,9 +66,7 @@ # Apply time-weight to local cost matrix cm <- w * cm - } - # Compute accumulated DTW cost matrix internals <- .computecost(cm = cm, step.matrix = step.matrix) @@ -107,11 +106,14 @@ distance = candidates$d[I], label = l ) - + tictoc::toc() return(res) - })) + }) + # Bind rows + aligs <- data.table::rbindlist(aligs) + # Create classification intervals breaks <- seq(as.Date(from), as.Date(to), by = by) # Find best macthes for the intervals @@ -123,7 +125,7 @@ breaks = breaks, overlap = overlap, fill = 99999)$IM - + # Build output out <- as.data.frame(best_matches[,c(1,3)]) names(out) <- c("label", "Alig.N") diff --git a/R/zzz.R b/R/zzz.R index dd809fc..989e4c0 100644 --- a/R/zzz.R +++ b/R/zzz.R @@ -49,6 +49,7 @@ #' @importFrom xtable xtable print.xtable #' @importFrom utils packageDescription flush.console #' @importFrom Rdpack reprompt +#' @importFrom data.table rbindlist #' @useDynLib dtwSat, .registration = TRUE #' NULL diff --git a/inst/lucc_MT/patterns/araguaia.csv b/inst/lucc_MT/patterns/araguaia.csv new file mode 100644 index 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