diff --git a/DESCRIPTION b/DESCRIPTION index 6dbf85b..4d7751a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -12,11 +12,17 @@ Authors@R: email = "annsize@upenn.edu")) biocViews: Imports: + boot, data.table, + digest, + Hmisc, microbenchmark, S4Vectors, + SpiecEasi (>= 1.1.1), stringi, purrr +Remotes: + zdk123/SpiecEasi URL: https://github.com/VEuPathDB/veupathUtils BugReports: https://github.com/VEuPathDB/veupathUtils/issues Description: veupathUtils contains various R helper functions intended to be useful across a variety of projects, including the plot.data and microbiomeComputations packages. diff --git a/NAMESPACE b/NAMESPACE index 70ef4cb..4db34fd 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -148,4 +148,3 @@ importFrom(microbenchmark,microbenchmark) importFrom(purrr,map) importFrom(purrr,map_lgl) importFrom(stringi,stri_detect_regex) -useDynLib(microbiomeComputations) diff --git a/R/method-correlation.R b/R/method-correlation.R index 3546a69..2f5ef8a 100644 --- a/R/method-correlation.R +++ b/R/method-correlation.R @@ -58,9 +58,7 @@ setMethod("predicateFactory", signature("character", "numeric"), function(predic #' @param format string defining the desired format of the result. The currently supported values are 'data.table' and 'ComputeResult'. #' @param verbose boolean indicating if timed logging is desired #' @return data.frame with correlation coefficients or a ComputeResult object -#' @import veupathUtils #' @import data.table -#' @useDynLib microbiomeComputations #' @export setGeneric("correlation", function(data1, data2, method, format = c('ComputeResult', 'data.table'), verbose = c(TRUE, FALSE), ...) standardGeneric("correlation"), @@ -261,7 +259,6 @@ buildCorrelationComputeResult <- function(corrResult, data1, data2 = NULL, metho #' @param format string defining the desired format of the result. The currently supported values are 'data.table' and 'ComputeResult'. #' @param verbose boolean indicating if timed logging is desired #' @return ComputeResult object -#' @import veupathUtils #' @export setGeneric("selfCorrelation", function(data, method = c('spearman','pearson','sparcc'), format = c('ComputeResult', 'data.table'), verbose = c(TRUE, FALSE), ...) standardGeneric("selfCorrelation"), @@ -271,14 +268,13 @@ setGeneric("selfCorrelation", #' Self Correlation #' #' This function returns correlation coefficients for variables in one data.table against itself. -#' This is essentially an alias to the microbiomeComputations::correlation function. +#' This is essentially an alias to the veupathUtils::correlation function. #' #' @param data a data.table #' @param method string defining the type of correlation to run. The currently supported values are 'spearman', 'pearson' and 'sparcc' #' @param format string defining the desired format of the result. The currently supported values are 'data.table' and 'ComputeResult'. #' @param verbose boolean indicating if timed logging is desired #' @return ComputeResult object -#' @import veupathUtils #' @export setMethod("selfCorrelation", signature("data.table"), function(data, method = c('spearman','pearson','sparcc'), format = c('ComputeResult', 'data.table'), verbose = c(TRUE, FALSE)) { diff --git a/man/selfCorrelation-data.table-method.Rd b/man/selfCorrelation-data.table-method.Rd index 061c472..07ab971 100644 --- a/man/selfCorrelation-data.table-method.Rd +++ b/man/selfCorrelation-data.table-method.Rd @@ -25,5 +25,5 @@ ComputeResult object } \description{ This function returns correlation coefficients for variables in one data.table against itself. -This is essentially an alias to the microbiomeComputations::correlation function. +This is essentially an alias to the veupathUtils::correlation function. }