Nothing
#' Multidimensional scaling
#' @description perform multidimensional scaling of random forest proximities
#' @param rfModels list containing random forest models as returned by \code{rf()}
#' @param dimensions number of dimensions to scale to
#' @examples
#' library(dplyr)
#'
#' ## Retrieve file paths for example data
#' files <- list.files(system.file('phenotypeDataCollectionSheets',
#' package = 'pdi'),full.names = TRUE)
#'
#' ## Prepare data
#' d <- map(files,readPhenotypeSheet) %>%
#' map(preparePhenotypeData) %>%
#' bind_rows() %>%
#' siteAdjustment() %>%
#' mutate(`Live crown ratio (%)` = liveCrownRatio(`Total height (m)`,
#' `Lower crown height (m)`),
#' `Crown condition (%)` = crownCondition(`Missing crown (%)`,
#' `Crown transparency (%)`),
#' `Crown volume (m^3)` = crownVolume(`Crown radius (m)`,
#' `Total height (m)`,
#' `Lower crown height (m)`,
#' `Crown condition (%)`),
#' `Bleed prevalence (%)` = bleedPrevalence(`Active bleed length (mm)`,
#' `Active bleeds`,
#' `Black staining length (mm)`,
#' `Black staining`,
#' `Diameter at breast height (m)`),
#' `Agrilus exit hole density (m^-2)` = agrilusExitHoleDensity(`Agrilus exit holes`,
#' `Diameter at breast height (m)`)
#' )
#'
#' t <- makeAnalysisTable(d)
#'
#' ## Generate random forest models
#' m <- rf(t,cls = NULL,nreps = 10)
#'
#' mds_data <- mds(m,2)
#' @importFrom tibble as_tibble
#' @importFrom stats cmdscale
#' @importFrom purrr map
#' @importFrom stringr str_remove_all str_c
#' @importFrom dplyr rename_all
#' @export
mds <- function(rfModels,dimensions = 2){
rfModels %>%
map(~{.$proximity %>%
as_tibble(.name_repair = 'minimal') %>%
rowid_to_column(var = 'Sample1') %>%
gather('Sample2','Proximity',-Sample1)}) %>%
bind_rows(.id = 'Iteration') %>%
mutate(Sample2 = as.numeric(Sample2)) %>%
group_by(Sample1,Sample2) %>%
summarise(Proximity = mean(Proximity),.groups = 'drop') %>%
spread(Sample2,Proximity) %>%
ungroup() %>%
select(-Sample1) %>%
as.matrix() %>%
{1 - .} %>%
cmdscale(k = dimensions) %>%
{suppressMessages(as_tibble(.,.name_repair = 'universal'))} %>%
rename_all(str_remove_all,pattern = coll('...')) %>%
rename_all(function(x){str_c('Dimension ',x)})
}
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