From ad8cbd2febfe6091a9a60e30a82bafd119f4c020 Mon Sep 17 00:00:00 2001 From: Nicolau Manubens Date: Mon, 14 Jan 2019 21:25:47 +0100 Subject: [PATCH 1/9] Fixed bug of dimnames not propagating. --- R/Apply.R | 7 ++++++- tests/testthat/test-use-cases.R | 22 ++++++++++++++++++++++ 2 files changed, 28 insertions(+), 1 deletion(-) diff --git a/R/Apply.R b/R/Apply.R index e130e90..f1b324b 100644 --- a/R/Apply.R +++ b/R/Apply.R @@ -31,7 +31,8 @@ #' @importFrom plyr splat llply #' @importFrom utils capture.output Apply <- function(data, target_dims = NULL, fun, ..., - output_dims = NULL, margins = NULL, guess_dim_names = TRUE, + output_dims = NULL, margins = NULL, + guess_dim_names = TRUE, ncores = NULL, split_factor = 1) { # Check data if (!is.list(data)) { @@ -470,6 +471,10 @@ Apply <- function(data, target_dims = NULL, fun, ..., iteration_input[[i]] <- do.call('[', c(list(x = data[[i]]), iteration_indices_to_take[[i]], list(drop = FALSE))) + num_targets <- length(target_dims_names[[i]]) + if (num_targets > 0) { + names(dim(iteration_input[[i]])) <- names(dim(data[[i]])) + } num_margins <- length(margins_names[[i]]) if (num_margins > 0) { if (num_margins == length(dim(iteration_input[[i]]))) { diff --git a/tests/testthat/test-use-cases.R b/tests/testthat/test-use-cases.R index 2b27f58..62d3399 100644 --- a/tests/testthat/test-use-cases.R +++ b/tests/testthat/test-use-cases.R @@ -1267,6 +1267,28 @@ test_that(".aperm2", { ) }) +# Test dim names passed on properly +test_that("Dimension names are propagated correctly.", { + a <- array(1:prod(1:6), dim = c(a = 1, b = 2, c = 3, d = 4, e = 5, f = 6)) + b <- array(1:prod(c(1, 2, 3, 5, 6)), dim = c(a = 1, b = 2, c = 3, e = 5, f = 6)) + + x <- "" + y <- "" + + f <- function(a, b) { + x <<- names(dim(a)) + y <<- names(dim(b)) + } + + r <- multiApply::Apply(list(a, b), + list(c('b', 'c', 'd'), + c('b', 'c')), + f) + + expect_equal(x, c('b', 'c', 'd')) + expect_equal(y, c('b', 'c')) +}) + # TODOS: # TESTS FOR MARGINS # TESTS FOR DISORDERED TARGET_DIMS -- GitLab From d996b1276ba80f810e9dfa45268e9da0815ce31d Mon Sep 17 00:00:00 2001 From: Nicolau Manubens Date: Mon, 14 Jan 2019 23:23:05 +0100 Subject: [PATCH 2/9] Added parameters 'use_attributes' and 'extra_info'. Tests pending. --- R/Apply.R | 90 ++++++++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 89 insertions(+), 1 deletion(-) diff --git a/R/Apply.R b/R/Apply.R index e130e90..9724994 100644 --- a/R/Apply.R +++ b/R/Apply.R @@ -8,6 +8,8 @@ #' @param ... Additional fixed arguments expected by the function provided in the parameter 'fun'. #' @param output_dims Optional list of vectors containing the names of the dimensions to be output from the fun for each of the objects it returns (or a single vector if the function has only one output). #' @param margins One or a list of vectors (or NULLs) containing the 'margin' dimensions to be looped over for each input in 'data'. If a single vector of margins is specified and multiple inputs are provided in 'data', then the single set of margins is re-used for all of the inputs. These vectors can contain either integers specifying the position of the margins, or character strings corresponding to the dimension names. If both 'margins' and 'target_dims' are specified, 'margins' takes priority. +#' @param use_attributes List of vectors of character strings with names of attributes of each object in 'data' to be propagated to the subsets of data sent as inputs to the function specified in 'fun'. If this parameter is not specified (NULL), all attributes are dropped. This parameter can be specified as a named list (then the names of this list must match those of the names of parameter 'data'), or as an unnamed list (then the vectors of attribute names will be assigned in order to the input arrays in 'data'). +#' @param extra_info Named list of extra variables to be defined for them to be accessible from within the function specified in 'fun'. The variable names will automatically be prepended a heading dot ('.'). So, if the variable 'name = "Tony"' is sent through this parameter, it will be accessible from within 'fun' via '.name'. #' @param guess_dim_names Whether to automatically guess missing dimension names for dimensions of equal length across different inputs in 'data' with a warning (TRUE; default), or to crash whenever unnamed dimensions of equa length are identified across different inputs (FALSE). #' @param ncores The number of parallel processes to spawn for the use for parallel computation in multiple cores. #' @param split_factor Factor telling to which degree the input data should be split into smaller pieces to be processed by the available cores. By default (split_factor = 1) the data is split into 4 pieces for each of the cores (as specified in ncores). A split_factor of 2 will result in 8 pieces for each of the cores, and so on. The special value 'greatest' will split the input data into as many pieces as possible. @@ -31,7 +33,9 @@ #' @importFrom plyr splat llply #' @importFrom utils capture.output Apply <- function(data, target_dims = NULL, fun, ..., - output_dims = NULL, margins = NULL, guess_dim_names = TRUE, + output_dims = NULL, margins = NULL, + use_attributes = NULL, extra_info = NULL, + guess_dim_names = TRUE, ncores = NULL, split_factor = 1) { # Check data if (!is.list(data)) { @@ -294,6 +298,76 @@ Apply <- function(data, target_dims = NULL, fun, ..., } } + # Check use_attributes + if (!is.null(use_attributes)) { + if (!is.list(use_attributes)) { + stop("Parameter 'use_attributes' must be a list.") + } + if (is.null(names(data)) && !is.null(names(use_attributes))) { + warning("Parameter 'use_attributes' provided with names, but ", + "no names provided for 'data'. All names will be ", + "disregarded.") + names(use_attributes) <- NULL + } + if (!is.null(names(use_attributes))) { + if (!all(sapply(names(use_attributes), function(x) nchar(x) > 0))) { + stop("If providing names for the list 'use_attributes', all ", + "components must be named.") + } + if (length(unique(names(use_attributes))) != + length(names(use_attributes))) { + stop("The list in parameter 'use_attributes' must not ", + "contain repeated names.") + } + if (any(!(names(use_attributes) %in% names(data)))) { + stop("Provided some names in parameter 'use_attributes' not present ", + "in parameter 'data'.") + } + use_attributes <- use_attributes[names(data)] + } else { + if (length(use_attributes) != length(data)) { + warning("Provided different number of items in 'use_attributes' ", + "and in 'data'. Assuming same order.") + } + use_attributes <- use_attributes[1:length(data)] + } + } else { + use_attributes <- vector('list', length = length(data)) + } + for (i in 1:length(data)) { + if (any(!(use_attributes[[i]] %in% names(attributes(data[[i]]))))) { + stop("Parameter 'use_attributes' contains some attribute names ", + "that are not present in the attributes of the corresponding ", + "object in parameter 'data'.") + } + } + + # Check extra_info + if (is.null(extra_info)) { + extra_info <- list() + } + raise_error <- FALSE + if (!is.list(extra_info)) { + raise_error <- TRUE + } + if (length(extra_info) > 0) { + if (is.null(names(extra_info))) { + raise_error <- TRUE + } + if (any(sapply(names(extra_info), function(x) nchar(x) == 0))) { + raise_error <- TRUE + } + names(extra_info) <- paste0(names(extra_info), '.') + } + if (raise_error) { + stop("Parameter 'extra_info' must be a list with all components named.") + } + + # Check guess_dimnames + if (!is.logical(guess_dimnames)) { + stop("Parameter 'guess_dimnames' must be logical.") + } + # Check ncores if (is.null(ncores)) { ncores <- 1 @@ -434,10 +508,22 @@ Apply <- function(data, target_dims = NULL, fun, ..., names(first_marg_indices) <- names(mad) sub_arrays_of_results <- list() found_first_sub_result <- FALSE + attributes_to_send <- vector('list', length = length(data)) iteration_indices_to_take <- list() for (i in 1:length(data)) { iteration_indices_to_take[[i]] <- as.list(rep(TRUE, length(dim(data[[i]])))) names(iteration_indices_to_take[[i]]) <- names(dim(data[[i]])) + if (length(use_attributes[[i]]) > 0) { + attributes_to_send[[i]] <- attributes(data[[i]]) + if ('dim' %in% names(attributes_to_send[[i]])) { + attributes_to_send[[i]][['dim']] <- NULL + } + attributes_to_send[[i]] <- attributes_to_send[[i]][use_attributes[[i]]] + } + } + + for (i in 1:length(extra_info)) { + assign(names(extra_info)[i], extra_info[[i]]) } add_one_multidim <- function(index, dims) { @@ -480,6 +566,8 @@ Apply <- function(data, target_dims = NULL, fun, ..., #if only one dim remains, make as.vector } } + attributes(iteration_input[[i]]) <- c(attributes(iteration_input[[i]]), + attributes_to_send[[i]]) } if (!is.null(mad)) { first_marg_indices <- add_one_multidim(first_marg_indices, mad) -- GitLab From d80722bde722fb4ee3633d6d4044dcff50028689 Mon Sep 17 00:00:00 2001 From: Nicolau Manubens Date: Mon, 14 Jan 2019 23:28:04 +0100 Subject: [PATCH 3/9] Sending .margin_index to the atomic function. --- R/Apply.R | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/R/Apply.R b/R/Apply.R index 9724994..1b73626 100644 --- a/R/Apply.R +++ b/R/Apply.R @@ -569,13 +569,16 @@ Apply <- function(data, target_dims = NULL, fun, ..., attributes(iteration_input[[i]]) <- c(attributes(iteration_input[[i]]), attributes_to_send[[i]]) } - if (!is.null(mad)) { - first_marg_indices <- add_one_multidim(first_marg_indices, mad) - } + + assign('.margin_indices', first_marg_indices) # SPLATTED_F result <- splatted_f(iteration_input, ...) + if (!is.null(mad)) { + first_marg_indices <- add_one_multidim(first_marg_indices, mad) + } + # SUB-ITERATION OUTRO if (!is.list(result)) { result <- list(result) -- GitLab From 1a7ed1562e76a510275114304c6986a1f87e2570 Mon Sep 17 00:00:00 2001 From: Nicolau Manubens Date: Tue, 15 Jan 2019 19:17:56 +0100 Subject: [PATCH 4/9] Progress and debugging. --- R/Apply.R | 25 +++++++++++++------------ man/Apply.Rd | 8 ++++++-- tests/testthat/test-use-cases.R | 28 ++++++++++++++++++++++++++++ 3 files changed, 47 insertions(+), 14 deletions(-) diff --git a/R/Apply.R b/R/Apply.R index 1b73626..9fb5158 100644 --- a/R/Apply.R +++ b/R/Apply.R @@ -349,23 +349,22 @@ Apply <- function(data, target_dims = NULL, fun, ..., raise_error <- FALSE if (!is.list(extra_info)) { raise_error <- TRUE - } - if (length(extra_info) > 0) { + } else if (length(extra_info) > 0) { if (is.null(names(extra_info))) { raise_error <- TRUE } if (any(sapply(names(extra_info), function(x) nchar(x) == 0))) { raise_error <- TRUE } - names(extra_info) <- paste0(names(extra_info), '.') + names(extra_info) <- paste0('.', names(extra_info)) } if (raise_error) { stop("Parameter 'extra_info' must be a list with all components named.") } - # Check guess_dimnames - if (!is.logical(guess_dimnames)) { - stop("Parameter 'guess_dimnames' must be logical.") + # Check guess_dim_names + if (!is.logical(guess_dim_names)) { + stop("Parameter 'guess_dim_names' must be logical.") } # Check ncores @@ -480,6 +479,13 @@ Apply <- function(data, target_dims = NULL, fun, ..., chunk_sizes <- c(chunk_sizes, total_size %% chunk_size) } + fun_env <- new.env() + for (i in seq_along(extra_info)) { + assign(names(extra_info)[i], extra_info[[i]], envir = fun_env) + } + environment(fun) <- fun_env + splatted_f <- splat(fun) + input_margin_weights <- vector('list', length(data)) for (i in 1:length(data)) { marg_sizes <- dim(data[[i]])[margins[[i]]] @@ -488,7 +494,6 @@ Apply <- function(data, target_dims = NULL, fun, ..., } # TODO: need to add progress bar - splatted_f <- splat(fun) # For a selected use case, these are the timings: # - total: 17 s # - preparation + post: 1 s @@ -522,10 +527,6 @@ Apply <- function(data, target_dims = NULL, fun, ..., } } - for (i in 1:length(extra_info)) { - assign(names(extra_info)[i], extra_info[[i]]) - } - add_one_multidim <- function(index, dims) { stop_iterating <- FALSE check_dim <- 1 @@ -570,7 +571,7 @@ Apply <- function(data, target_dims = NULL, fun, ..., attributes_to_send[[i]]) } - assign('.margin_indices', first_marg_indices) + assign('.margin_indices', as.list(first_marg_indices), envir = fun_env) # SPLATTED_F result <- splatted_f(iteration_input, ...) diff --git a/man/Apply.Rd b/man/Apply.Rd index 4fe37e9..b93c173 100644 --- a/man/Apply.Rd +++ b/man/Apply.Rd @@ -5,8 +5,8 @@ \title{Apply Functions to Multiple Multidimensional Arrays or Vectors} \usage{ Apply(data, target_dims = NULL, fun, ..., output_dims = NULL, - margins = NULL, guess_dim_names = TRUE, ncores = NULL, - split_factor = 1) + margins = NULL, use_attributes = NULL, extra_info = NULL, + guess_dim_names = TRUE, ncores = NULL, split_factor = 1) } \arguments{ \item{data}{One or a list of numeric object (vector, matrix or array). They must be in the same order as expected by the function provided in the parameter 'fun'. The dimensions do not necessarily have to be ordered. If the 'target_dims' require a different order than the provided, \code{Apply} will automatically reorder the dimensions as needed.} @@ -21,6 +21,10 @@ Apply(data, target_dims = NULL, fun, ..., output_dims = NULL, \item{margins}{One or a list of vectors (or NULLs) containing the 'margin' dimensions to be looped over for each input in 'data'. If a single vector of margins is specified and multiple inputs are provided in 'data', then the single set of margins is re-used for all of the inputs. These vectors can contain either integers specifying the position of the margins, or character strings corresponding to the dimension names. If both 'margins' and 'target_dims' are specified, 'margins' takes priority.} +\item{use_attributes}{List of vectors of character strings with names of attributes of each object in 'data' to be propagated to the subsets of data sent as inputs to the function specified in 'fun'. If this parameter is not specified (NULL), all attributes are dropped. This parameter can be specified as a named list (then the names of this list must match those of the names of parameter 'data'), or as an unnamed list (then the vectors of attribute names will be assigned in order to the input arrays in 'data').} + +\item{extra_info}{Named list of extra variables to be defined for them to be accessible from within the function specified in 'fun'. The variable names will automatically be prepended a heading dot ('.'). So, if the variable 'name = "Tony"' is sent through this parameter, it will be accessible from within 'fun' via '.name'.} + \item{guess_dim_names}{Whether to automatically guess missing dimension names for dimensions of equal length across different inputs in 'data' with a warning (TRUE; default), or to crash whenever unnamed dimensions of equa length are identified across different inputs (FALSE).} \item{ncores}{The number of parallel processes to spawn for the use for parallel computation in multiple cores.} diff --git a/tests/testthat/test-use-cases.R b/tests/testthat/test-use-cases.R index 2b27f58..8cd94b0 100644 --- a/tests/testthat/test-use-cases.R +++ b/tests/testthat/test-use-cases.R @@ -1255,6 +1255,34 @@ test_that("real use case - standardization", { }) +# Test margin indices and extra info +test_that("Margin indices and extra info are provided correctly.", { + a <- array(1:prod(1:6), dim = c(a = 1, b = 2, c = 3, d = 4, e = 5, f = 6)) + b <- array(1:prod(c(1, 2, 3, 5, 6)), dim = c(a = 1, b = 2, c = 3, e = 5, f = 6)) + + x <- NULL + y <- NULL + z <- NULL + + f <- function(a, b) { + if (all(.margin_indices == 1)) { + x <<- .margin_indices + } + y <<- .margin_indices + z <<- .test_info + } + + r <- multiApply::Apply(list(a, b), + list(c('b', 'c', 'd'), + c('b', 'c')), + extra_info = list(test_info = 'test'), + f) + + expect_equal(x, list(a = 1, e = 1, f = 1)) + expect_equal(y, list(a = 1, e = 5, f = 6)) + expect_equal(z, 'test') +}) + # Test .aperm2 test_that(".aperm2", { data <- seq(as.POSIXct('1990-11-01'), -- GitLab From e542a576c8e0c48ea4b367eb618e6b884f7833f1 Mon Sep 17 00:00:00 2001 From: Nicolau Manubens Date: Tue, 15 Jan 2019 19:21:47 +0100 Subject: [PATCH 5/9] Added support for all types. --- DESCRIPTION | 2 +- R/Apply.R | 12 ++++++------ 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index b49b7f5..3a5505b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -11,7 +11,7 @@ Description: The base apply function and its variants, as well as the related single argument (or a list of vectorized arguments in the case of mapply). The 'multiApply' package extends this paradigm with its only function, Apply, which efficiently applies functions taking one or a list of multiple unidimensional - or multidimensional numeric arrays (or combinations thereof) as input. The input + or multidimensional arrays (or combinations thereof) as input. The input arrays can have different numbers of dimensions as well as different dimension lengths, and the applied function can return one or a list of unidimensional or multidimensional arrays as output. This saves development time by preventing the diff --git a/R/Apply.R b/R/Apply.R index e130e90..b4a75d1 100644 --- a/R/Apply.R +++ b/R/Apply.R @@ -1,10 +1,10 @@ #' Apply Functions to Multiple Multidimensional Arrays or Vectors #' -#' This function efficiently applies a given function, which takes N vectors or multi-dimensional arrays as inputs (which may have different numbers of dimensions and dimension lengths), and applies it to a list of N vectors or multi-dimensional arrays with at least as many dimensions as expected by the given function. The user can specify which dimensions of each array the function is to be applied over with the \code{margins} or \code{target_dims} parameters. The function to be applied can receive other helper parameters and return any number of numeric vectors or multidimensional arrays. The target dimensions or margins can be specified by their names, as long as the inputs are provided with dimension names (recommended). This function can also use multi-core in a transparent way if requested via the \code{ncores} parameter.\cr\cr The following steps help to understand how \code{Apply} works:\cr\cr - The function receives N arrays with Dn dimensions each.\cr - The user specifies, for each of the arrays, which of its dimensions are 'target' dimensions (dimensions which the function provided in 'fun' operates with) and which are 'margins' (dimensions to be looped over).\cr - \code{Apply} will generate an array with as many dimensions as margins in all of the input arrays. If a margin is repeated across different inputs, it will appear only once in the resulting array.\cr - For each element of this resulting array, the function provided in the parameter'fun' is applied to the corresponding sub-arrays in 'data'.\cr - If the function returns a vector or a multidimensional array, the additional dimensions will be prepended to the resulting array (in left-most positions).\cr - If the provided function returns more than one vector or array, the process above is carried out for each of the outputs, resulting in a list with multiple arrays, each with the combination of all target dimensions (at the right-most positions) and resulting dimensions (at the left-most positions). +#' This function efficiently applies a given function, which takes N vectors or multi-dimensional arrays as inputs (which may have different numbers of dimensions and dimension lengths), and applies it to a list of N vectors or multi-dimensional arrays with at least as many dimensions as expected by the given function. The user can specify which dimensions of each array the function is to be applied over with the \code{margins} or \code{target_dims} parameters. The function to be applied can receive other helper parameters and return any number of vectors or multidimensional arrays. The target dimensions or margins can be specified by their names, as long as the inputs are provided with dimension names (recommended). This function can also use multi-core in a transparent way if requested via the \code{ncores} parameter.\cr\cr The following steps help to understand how \code{Apply} works:\cr\cr - The function receives N arrays with Dn dimensions each.\cr - The user specifies, for each of the arrays, which of its dimensions are 'target' dimensions (dimensions which the function provided in 'fun' operates with) and which are 'margins' (dimensions to be looped over).\cr - \code{Apply} will generate an array with as many dimensions as margins in all of the input arrays. If a margin is repeated across different inputs, it will appear only once in the resulting array.\cr - For each element of this resulting array, the function provided in the parameter'fun' is applied to the corresponding sub-arrays in 'data'.\cr - If the function returns a vector or a multidimensional array, the additional dimensions will be prepended to the resulting array (in left-most positions).\cr - If the provided function returns more than one vector or array, the process above is carried out for each of the outputs, resulting in a list with multiple arrays, each with the combination of all target dimensions (at the right-most positions) and resulting dimensions (at the left-most positions). #' -#' @param data One or a list of numeric object (vector, matrix or array). They must be in the same order as expected by the function provided in the parameter 'fun'. The dimensions do not necessarily have to be ordered. If the 'target_dims' require a different order than the provided, \code{Apply} will automatically reorder the dimensions as needed. +#' @param data One or a list of vectors, matrices or arrays. They must be in the same order as expected by the function provided in the parameter 'fun'. The dimensions do not necessarily have to be ordered. If the 'target_dims' require a different order than the provided, \code{Apply} will automatically reorder the dimensions as needed. #' @param target_dims One or a list of vectors (or NULLs) containing the dimensions to be input into fun for each of the objects in the data. If a single vector of target dimensions is specified and multiple inputs are provided in 'data, then the single set of target dimensions is re-used for all of the inputs. These vectors can contain either integers specifying the position of the dimensions, or character strings corresponding to the dimension names. This parameter is mandatory if 'margins' are not specified. If both 'margins' and 'target_dims' are specified, 'margins' takes priority. -#' @param fun Function to be applied to the arrays. Must receive as many inputs as provided in 'data', each with as many dimensions as specified in 'target_dims' or as the total number of dimensions in 'data' minus the ones specified in 'margins'. The function can receive other additional fixed parameters (see parameter '...' of \code{Apply}). The function can return one or a list of numeric vectors or multidimensional arrays, optionally with dimension names which will be propagated to the final result. The returned list can optionally be named, with a name for each output, which will be propagated to the resulting array. The function can optionally be provided with the attributes 'target_dims' and 'output_dims'. In that case, the corresponding parameters of \code{Apply} do not need to be provided. The function can expect named dimensions for each of its inputs, in the same order as specified in 'target_dims' or, if no 'target_dims' have been provided, in the same order as provided in 'data'. +#' @param fun Function to be applied to the arrays. Must receive as many inputs as provided in 'data', each with as many dimensions as specified in 'target_dims' or as the total number of dimensions in 'data' minus the ones specified in 'margins'. The function can receive other additional fixed parameters (see parameter '...' of \code{Apply}). The function can return one or a list of vectors or multidimensional arrays, optionally with dimension names which will be propagated to the final result. The returned list can optionally be named, with a name for each output, which will be propagated to the resulting array. The function can optionally be provided with the attributes 'target_dims' and 'output_dims'. In that case, the corresponding parameters of \code{Apply} do not need to be provided. The function can expect named dimensions for each of its inputs, in the same order as specified in 'target_dims' or, if no 'target_dims' have been provided, in the same order as provided in 'data'. #' @param ... Additional fixed arguments expected by the function provided in the parameter 'fun'. #' @param output_dims Optional list of vectors containing the names of the dimensions to be output from the fun for each of the objects it returns (or a single vector if the function has only one output). #' @param margins One or a list of vectors (or NULLs) containing the 'margin' dimensions to be looped over for each input in 'data'. If a single vector of margins is specified and multiple inputs are provided in 'data', then the single set of margins is re-used for all of the inputs. These vectors can contain either integers specifying the position of the margins, or character strings corresponding to the dimension names. If both 'margins' and 'target_dims' are specified, 'margins' takes priority. @@ -37,9 +37,9 @@ Apply <- function(data, target_dims = NULL, fun, ..., if (!is.list(data)) { data <- list(data) } - if (any(!sapply(data, is.numeric))) { - stop("Parameter 'data' must be one or a list of numeric objects.") - } + #if (any(!sapply(data, is.numeric))) { + # stop("Parameter 'data' must be one or a list of numeric objects.") + #} is_vector <- rep(FALSE, length(data)) is_unnamed <- rep(FALSE, length(data)) unnamed_dims <- c() -- GitLab From 3392a8c728e6293a1e5d0eadb98c846614a61a49 Mon Sep 17 00:00:00 2001 From: Nicolau Manubens Date: Tue, 15 Jan 2019 20:04:50 +0100 Subject: [PATCH 6/9] Margin indices, extra info and attributes propagated correctly to atomic function. --- R/Apply.R | 5 ++++- R/zzz.R | 5 +++++ tests/testthat/test-use-cases.R | 38 +++++++++++++++++++++++---------- 3 files changed, 36 insertions(+), 12 deletions(-) diff --git a/R/Apply.R b/R/Apply.R index 9fb5158..9fa01bc 100644 --- a/R/Apply.R +++ b/R/Apply.R @@ -571,7 +571,10 @@ Apply <- function(data, target_dims = NULL, fun, ..., attributes_to_send[[i]]) } - assign('.margin_indices', as.list(first_marg_indices), envir = fun_env) + assign(".margin_indices", + setNames(as.integer(first_marg_indices), + names(first_marg_indices)), + envir = fun_env) # SPLATTED_F result <- splatted_f(iteration_input, ...) diff --git a/R/zzz.R b/R/zzz.R index 2bf747e..662624d 100644 --- a/R/zzz.R +++ b/R/zzz.R @@ -1,6 +1,10 @@ # Function to permute arrays of non-atomic elements (e.g. POSIXct) .aperm2 <- function(x, new_order) { old_dims <- dim(x) + attr_bk <- attributes(x) + if ('dim' %in% names(attr_bk)) { + attr_bk[['dim']] <- NULL + } if (is.numeric(x)) { x <- aperm(x, new_order) } else { @@ -9,5 +13,6 @@ x <- x[as.vector(y)] } dim(x) <- old_dims[new_order] + attributes(x) <- c(attributes(x), attr_bk) x } diff --git a/tests/testthat/test-use-cases.R b/tests/testthat/test-use-cases.R index 8cd94b0..37e3327 100644 --- a/tests/testthat/test-use-cases.R +++ b/tests/testthat/test-use-cases.R @@ -1260,27 +1260,43 @@ test_that("Margin indices and extra info are provided correctly.", { a <- array(1:prod(1:6), dim = c(a = 1, b = 2, c = 3, d = 4, e = 5, f = 6)) b <- array(1:prod(c(1, 2, 3, 5, 6)), dim = c(a = 1, b = 2, c = 3, e = 5, f = 6)) - x <- NULL - y <- NULL - z <- NULL + attr(a, 'test_attr_a') <- 'test_a' + attr(b, 'test_attr_b') <- list(x = 1, z = 2) f <- function(a, b) { - if (all(.margin_indices == 1)) { - x <<- .margin_indices - } - y <<- .margin_indices - z <<- .test_info + stopifnot(length(.margin_indices) == 3) + stopifnot(identical(names(.margin_indices), c('a', 'e', 'f'))) + stopifnot(all(is.integer(.margin_indices))) + stopifnot(identical(.test_info, 'test')) + stopifnot(!is.null(attr(a, 'test_attr_a'))) + stopifnot(identical(attr(a, 'test_attr_a'), 'test_a')) + stopifnot(!is.null(attr(b, 'test_attr_b'))) + stopifnot(identical(attr(b, 'test_attr_b'), list(x = 1, z = 2))) } r <- multiApply::Apply(list(a, b), list(c('b', 'c', 'd'), c('b', 'c')), extra_info = list(test_info = 'test'), + use_attributes = list(a = 'test_attr_a', + b = 'test_attr_b'), f) - expect_equal(x, list(a = 1, e = 1, f = 1)) - expect_equal(y, list(a = 1, e = 5, f = 6)) - expect_equal(z, 'test') + r <- multiApply::Apply(list(a = a, b = b), + list(c('b', 'c', 'd'), + c('b', 'c')), + extra_info = list(test_info = 'test'), + use_attributes = list(a = 'test_attr_a', + b = 'test_attr_b'), + f) + + r <- multiApply::Apply(list(a = a, b = b), + list(c('b', 'c', 'd'), + c('b', 'c')), + extra_info = list(test_info = 'test'), + use_attributes = list(b = 'test_attr_b', + a = 'test_attr_a'), + f) }) # Test .aperm2 -- GitLab From db22638500a6c23725571c62badeb7781c85ea92 Mon Sep 17 00:00:00 2001 From: Nicolau Manubens Date: Tue, 15 Jan 2019 20:31:20 +0100 Subject: [PATCH 7/9] Improved documentation. --- R/Apply.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/Apply.R b/R/Apply.R index 9fa01bc..d305447 100644 --- a/R/Apply.R +++ b/R/Apply.R @@ -4,7 +4,7 @@ #' #' @param data One or a list of numeric object (vector, matrix or array). They must be in the same order as expected by the function provided in the parameter 'fun'. The dimensions do not necessarily have to be ordered. If the 'target_dims' require a different order than the provided, \code{Apply} will automatically reorder the dimensions as needed. #' @param target_dims One or a list of vectors (or NULLs) containing the dimensions to be input into fun for each of the objects in the data. If a single vector of target dimensions is specified and multiple inputs are provided in 'data, then the single set of target dimensions is re-used for all of the inputs. These vectors can contain either integers specifying the position of the dimensions, or character strings corresponding to the dimension names. This parameter is mandatory if 'margins' are not specified. If both 'margins' and 'target_dims' are specified, 'margins' takes priority. -#' @param fun Function to be applied to the arrays. Must receive as many inputs as provided in 'data', each with as many dimensions as specified in 'target_dims' or as the total number of dimensions in 'data' minus the ones specified in 'margins'. The function can receive other additional fixed parameters (see parameter '...' of \code{Apply}). The function can return one or a list of numeric vectors or multidimensional arrays, optionally with dimension names which will be propagated to the final result. The returned list can optionally be named, with a name for each output, which will be propagated to the resulting array. The function can optionally be provided with the attributes 'target_dims' and 'output_dims'. In that case, the corresponding parameters of \code{Apply} do not need to be provided. The function can expect named dimensions for each of its inputs, in the same order as specified in 'target_dims' or, if no 'target_dims' have been provided, in the same order as provided in 'data'. +#' @param fun Function to be applied to the arrays. Must receive as many inputs as provided in 'data', each with as many dimensions as specified in 'target_dims' or as the total number of dimensions in 'data' minus the ones specified in 'margins'. The function can receive other additional fixed parameters (see parameter '...' of \code{Apply}). The function can return one or a list of numeric vectors or multidimensional arrays, optionally with dimension names which will be propagated to the final result. The returned list can optionally be named, with a name for each output, which will be propagated to the resulting array. The function can optionally be provided with the attributes 'target_dims' and 'output_dims'. In that case, the corresponding parameters of \code{Apply} do not need to be provided. The function can expect named dimensions for each of its inputs, in the same order as specified in 'target_dims' or, if no 'target_dims' have been provided, in the same order as provided in 'data'. The function can access the variable \code{.margin_indices}, a named numeric vector that provides the indices of the current iteration over the margins, as well as any other variables specified in the parameter \code{extra_info} or input attributes specified in the parameter \code{use_attributes}. #' @param ... Additional fixed arguments expected by the function provided in the parameter 'fun'. #' @param output_dims Optional list of vectors containing the names of the dimensions to be output from the fun for each of the objects it returns (or a single vector if the function has only one output). #' @param margins One or a list of vectors (or NULLs) containing the 'margin' dimensions to be looped over for each input in 'data'. If a single vector of margins is specified and multiple inputs are provided in 'data', then the single set of margins is re-used for all of the inputs. These vectors can contain either integers specifying the position of the margins, or character strings corresponding to the dimension names. If both 'margins' and 'target_dims' are specified, 'margins' takes priority. -- GitLab From 92f6163aa218f9a1361be658965fb2fba02548e9 Mon Sep 17 00:00:00 2001 From: Nicolau Manubens Date: Wed, 16 Jan 2019 19:38:26 +0100 Subject: [PATCH 8/9] Possible to send sub-attributes. --- R/Apply.R | 54 ++++++++++++++++++++++++++++----- tests/testthat/test-use-cases.R | 30 ++++++++++++++++++ 2 files changed, 76 insertions(+), 8 deletions(-) diff --git a/R/Apply.R b/R/Apply.R index d305447..14ecb8c 100644 --- a/R/Apply.R +++ b/R/Apply.R @@ -335,10 +335,37 @@ Apply <- function(data, target_dims = NULL, fun, ..., use_attributes <- vector('list', length = length(data)) } for (i in 1:length(data)) { - if (any(!(use_attributes[[i]] %in% names(attributes(data[[i]]))))) { - stop("Parameter 'use_attributes' contains some attribute names ", - "that are not present in the attributes of the corresponding ", - "object in parameter 'data'.") + if (is.character(use_attributes[[i]])) { + use_attributes[[i]] <- as.list(use_attributes[[i]]) + } + if (is.list(use_attributes[[i]])) { + if (length(use_attributes[[i]]) == 0) { + use_attributes[i] <- list(NULL) + } else { + if (!all(sapply(use_attributes[[i]], + function(x) all(is.character(x) & nchar(x) > 0)))) { + stop("All entries in 'use_attributes' must be character strings ", + "of length > 0.") + } + } + } else if (!is.null(use_attributes[[i]])) { + stop("Parameter 'use_attributes' must be a list of character vectors or ", + "a list of lists of character vectors.") + } + for (j in seq_along(use_attributes[[i]])) { + if (length(use_attributes[[i]][[j]]) == 1 && + use_attributes[[i]][[j]] == 'dim') { + stop("Requesting the attribute 'dim' via the parameter ", + "'use_attributes' is forbidden.") + } + found_entry <- FALSE + entry <- try({`[[`(attributes(data[[i]]), + use_attributes[[i]][[j]])}, silent = TRUE) + if ('try-error' %in% class(entry)) { + stop("Parameter 'use_attributes' contains some attribute names ", + "that are not present in the attributes of the corresponding ", + "object in parameter 'data'.") + } } } @@ -519,11 +546,22 @@ Apply <- function(data, target_dims = NULL, fun, ..., iteration_indices_to_take[[i]] <- as.list(rep(TRUE, length(dim(data[[i]])))) names(iteration_indices_to_take[[i]]) <- names(dim(data[[i]])) if (length(use_attributes[[i]]) > 0) { - attributes_to_send[[i]] <- attributes(data[[i]]) - if ('dim' %in% names(attributes_to_send[[i]])) { - attributes_to_send[[i]][['dim']] <- NULL + attributes_to_send[[i]] <- list() + for (j in seq_along(use_attributes[[i]])) { + found_entry <- FALSE + entry <- try({`[[`(attributes(data[[i]]), + use_attributes[[i]][[j]]) + }, silent = TRUE) + if ('try-error' %in% class(entry)) { + stop("Unexpected error with the attributes of the inputs.") + } + save_string <- "attributes_to_send[[i]]" + access_string <- "`[[`(attributes(data[[i]]), use_attributes[[i]][[j]])" + for (k in seq_along(use_attributes[[i]][[j]])) { + save_string <- paste0(save_string, '$', use_attributes[[i]][[j]][[k]]) + } + eval(parse(text = paste(save_string, '<-', access_string))) } - attributes_to_send[[i]] <- attributes_to_send[[i]][use_attributes[[i]]] } } diff --git a/tests/testthat/test-use-cases.R b/tests/testthat/test-use-cases.R index 37e3327..ab39fbc 100644 --- a/tests/testthat/test-use-cases.R +++ b/tests/testthat/test-use-cases.R @@ -1297,6 +1297,36 @@ test_that("Margin indices and extra info are provided correctly.", { use_attributes = list(b = 'test_attr_b', a = 'test_attr_a'), f) + + attr(b, 'test_attr_b') <- list(x = 1, z = 2) + attr(b, 'z') <- 3 + + f <- function(a, b) { + stopifnot(identical(attr(b, 'test_attr_b')$z, 2)) + stopifnot(identical(attr(b, 'z'), 3)) + } + + r <- multiApply::Apply(list(a = a, b = b), + list(c('b', 'c', 'd'), + c('b', 'c')), + extra_info = list(test_info = 'test'), + use_attributes = list(b = c('test_attr_b', 'z'), + a = 'test_attr_a'), + f) + + f <- function(a, b) { + stopifnot(identical(attr(b, 'test_attr_b')$z, 2)) + stopifnot(is.null(attr(b, 'test_attr_b')$x)) + stopifnot(is.null(attr(b, 'z'))) + } + + r <- multiApply::Apply(list(a = a, b = b), + list(c('b', 'c', 'd'), + c('b', 'c')), + extra_info = list(test_info = 'test'), + use_attributes = list(b = list(c('test_attr_b', 'z')), + a = 'test_attr_a'), + f) }) # Test .aperm2 -- GitLab From cd995660c11402696b92d327b8fd0f404a6214a9 Mon Sep 17 00:00:00 2001 From: Nicolau Manubens Date: Wed, 16 Jan 2019 22:43:15 +0100 Subject: [PATCH 9/9] Bumped version to v2.1.0. Fixed test. --- DESCRIPTION | 2 +- man/Apply.Rd | 6 +++--- multiApply-manual.pdf | Bin 72020 -> 73326 bytes tests/testthat/test-use-cases.R | 10 ++-------- 4 files changed, 6 insertions(+), 12 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 3a5505b..3f6fffe 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: multiApply Title: Apply Functions to Multiple Multidimensional Arrays or Vectors -Version: 2.0.1 +Version: 2.1.0 Authors@R: c( person("BSC-CNS", role = c("aut", "cph")), person("Nicolau", "Manubens", , "nicolau.manubens@bsc.es", role = "aut"), diff --git a/man/Apply.Rd b/man/Apply.Rd index b93c173..a368553 100644 --- a/man/Apply.Rd +++ b/man/Apply.Rd @@ -9,11 +9,11 @@ Apply(data, target_dims = NULL, fun, ..., output_dims = NULL, guess_dim_names = TRUE, ncores = NULL, split_factor = 1) } \arguments{ -\item{data}{One or a list of numeric object (vector, matrix or array). They must be in the same order as expected by the function provided in the parameter 'fun'. The dimensions do not necessarily have to be ordered. If the 'target_dims' require a different order than the provided, \code{Apply} will automatically reorder the dimensions as needed.} +\item{data}{One or a list of vectors, matrices or arrays. They must be in the same order as expected by the function provided in the parameter 'fun'. The dimensions do not necessarily have to be ordered. If the 'target_dims' require a different order than the provided, \code{Apply} will automatically reorder the dimensions as needed.} \item{target_dims}{One or a list of vectors (or NULLs) containing the dimensions to be input into fun for each of the objects in the data. If a single vector of target dimensions is specified and multiple inputs are provided in 'data, then the single set of target dimensions is re-used for all of the inputs. These vectors can contain either integers specifying the position of the dimensions, or character strings corresponding to the dimension names. This parameter is mandatory if 'margins' are not specified. If both 'margins' and 'target_dims' are specified, 'margins' takes priority.} -\item{fun}{Function to be applied to the arrays. Must receive as many inputs as provided in 'data', each with as many dimensions as specified in 'target_dims' or as the total number of dimensions in 'data' minus the ones specified in 'margins'. The function can receive other additional fixed parameters (see parameter '...' of \code{Apply}). The function can return one or a list of numeric vectors or multidimensional arrays, optionally with dimension names which will be propagated to the final result. The returned list can optionally be named, with a name for each output, which will be propagated to the resulting array. The function can optionally be provided with the attributes 'target_dims' and 'output_dims'. In that case, the corresponding parameters of \code{Apply} do not need to be provided. The function can expect named dimensions for each of its inputs, in the same order as specified in 'target_dims' or, if no 'target_dims' have been provided, in the same order as provided in 'data'.} +\item{fun}{Function to be applied to the arrays. Must receive as many inputs as provided in 'data', each with as many dimensions as specified in 'target_dims' or as the total number of dimensions in 'data' minus the ones specified in 'margins'. The function can receive other additional fixed parameters (see parameter '...' of \code{Apply}). The function can return one or a list of vectors or multidimensional arrays, optionally with dimension names which will be propagated to the final result. The returned list can optionally be named, with a name for each output, which will be propagated to the resulting array. The function can optionally be provided with the attributes 'target_dims' and 'output_dims'. In that case, the corresponding parameters of \code{Apply} do not need to be provided. The function can expect named dimensions for each of its inputs, in the same order as specified in 'target_dims' or, if no 'target_dims' have been provided, in the same order as provided in 'data'. The function can access the variable \code{.margin_indices}, a named numeric vector that provides the indices of the current iteration over the margins, as well as any other variables specified in the parameter \code{extra_info} or input attributes specified in the parameter \code{use_attributes}.} \item{...}{Additional fixed arguments expected by the function provided in the parameter 'fun'.} @@ -35,7 +35,7 @@ Apply(data, target_dims = NULL, fun, ..., output_dims = NULL, List of arrays or matrices or vectors resulting from applying 'fun' to 'data'. } \description{ -This function efficiently applies a given function, which takes N vectors or multi-dimensional arrays as inputs (which may have different numbers of dimensions and dimension lengths), and applies it to a list of N vectors or multi-dimensional arrays with at least as many dimensions as expected by the given function. The user can specify which dimensions of each array the function is to be applied over with the \code{margins} or \code{target_dims} parameters. The function to be applied can receive other helper parameters and return any number of numeric vectors or multidimensional arrays. The target dimensions or margins can be specified by their names, as long as the inputs are provided with dimension names (recommended). This function can also use multi-core in a transparent way if requested via the \code{ncores} parameter.\cr\cr The following steps help to understand how \code{Apply} works:\cr\cr - The function receives N arrays with Dn dimensions each.\cr - The user specifies, for each of the arrays, which of its dimensions are 'target' dimensions (dimensions which the function provided in 'fun' operates with) and which are 'margins' (dimensions to be looped over).\cr - \code{Apply} will generate an array with as many dimensions as margins in all of the input arrays. If a margin is repeated across different inputs, it will appear only once in the resulting array.\cr - For each element of this resulting array, the function provided in the parameter'fun' is applied to the corresponding sub-arrays in 'data'.\cr - If the function returns a vector or a multidimensional array, the additional dimensions will be prepended to the resulting array (in left-most positions).\cr - If the provided function returns more than one vector or array, the process above is carried out for each of the outputs, resulting in a list with multiple arrays, each with the combination of all target dimensions (at the right-most positions) and resulting dimensions (at the left-most positions). +This function efficiently applies a given function, which takes N vectors or multi-dimensional arrays as inputs (which may have different numbers of dimensions and dimension lengths), and applies it to a list of N vectors or multi-dimensional arrays with at least as many dimensions as expected by the given function. The user can specify which dimensions of each array the function is to be applied over with the \code{margins} or \code{target_dims} parameters. The function to be applied can receive other helper parameters and return any number of vectors or multidimensional arrays. The target dimensions or margins can be specified by their names, as long as the inputs are provided with dimension names (recommended). This function can also use multi-core in a transparent way if requested via the \code{ncores} parameter.\cr\cr The following steps help to understand how \code{Apply} works:\cr\cr - The function receives N arrays with Dn dimensions each.\cr - The user specifies, for each of the arrays, which of its dimensions are 'target' dimensions (dimensions which the function provided in 'fun' operates with) and which are 'margins' (dimensions to be looped over).\cr - \code{Apply} will generate an array with as many dimensions as margins in all of the input arrays. If a margin is repeated across different inputs, it will appear only once in the resulting array.\cr - For each element of this resulting array, the function provided in the parameter'fun' is applied to the corresponding sub-arrays in 'data'.\cr - If the function returns a vector or a multidimensional array, the additional dimensions will be prepended to the resulting array (in left-most positions).\cr - If the provided function returns more than one vector or array, the process above is carried out for each of the outputs, resulting in a list with multiple arrays, each with the combination of all target dimensions (at the right-most positions) and resulting dimensions (at the left-most positions). } \details{ When using a single object as input, Apply is almost identical to the apply function (as fast or slightly slower in some cases; with equal or improved -smaller- memory footprint). diff --git a/multiApply-manual.pdf b/multiApply-manual.pdf index 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names are propagated correctly.", { a <- array(1:prod(1:6), dim = c(a = 1, b = 2, c = 3, d = 4, e = 5, f = 6)) b <- array(1:prod(c(1, 2, 3, 5, 6)), dim = c(a = 1, b = 2, c = 3, e = 5, f = 6)) - x <- "" - y <- "" - f <- function(a, b) { - x <<- names(dim(a)) - y <<- names(dim(b)) + stopifnot(identical(names(dim(a)), c('b', 'c', 'd'))) + stopifnot(identical(names(dim(b)), c('b', 'c'))) } r <- multiApply::Apply(list(a, b), list(c('b', 'c', 'd'), c('b', 'c')), f) - - expect_equal(x, c('b', 'c', 'd')) - expect_equal(y, c('b', 'c')) }) # TODOS: -- GitLab