#'Compute the anomaly correlation coefficient between the forecast and corresponding observation #' #'Calculate the anomaly correlation coefficient for the ensemble mean of each #'model and the corresponding references over a spatial domain. It can return a #'forecast time series if the data contain forest time dimension, and also the #'start date mean if the data contain start date dimension. #'The domain of interest can be specified by providing the list #'of longitudes/latitudes (lon/lat) of the data together with the corners #'of the domain: lonlatbox = c(lonmin, lonmax, latmin, latmax). #' #'@param exp A numeric array of experimental anomalies with named dimensions. #' It must have at least 'dat_dim' and 'space_dim'. #'@param obs A numeric array of observational anomalies with named dimensions. #' It must have the same dimensions as 'exp' except the length of 'dat_dim' #' and 'memb_dim'. #'@param dat_dim A character string indicating the name of dataset (nobs/nexp) #' dimension. The default value is 'dataset'. #'@param space_dim A character string vector of 2 indicating the name of the #' latitude and longitude dimensions (in order) along which ACC is computed. #' The default value is c('lat', 'lon'). #'@param avg_dim A character string indicating the name of the dimension to be #' averaged. It must be one of 'time_dim'. The mean ACC is calculated along #' averaged. If no need to calculate mean ACC, set as NULL. The default value #' is 'sdate'. #'@param memb_dim A character string indicating the name of the member #' dimension. If the data are not ensemble ones, set as NULL. The default #' value is 'member'. #'@param lat A vector of the latitudes of the exp/obs grids. Only required when #' the domain of interested is specified. The default value is NULL. #'@param lon A vector of the longitudes of the exp/obs grids. Only required when #' the domain of interested is specified. The default value is NULL. #'@param lonlatbox A numeric vector of 4 indicating the corners of the domain of #' interested: c(lonmin, lonmax, latmin, latmax). Only required when the domain #' of interested is specified. The default value is NULL. #'@param conf A logical value indicating whether to retrieve the confidence #' intervals or not. The default value is TRUE. #'@param conftype A charater string of "parametric" or "bootstrap". #' "parametric" provides a confidence interval for the ACC computed by a #' Fisher transformation and a significance level for the ACC from a one-sided #' student-T distribution. "bootstrap" provides a confidence interval for the #' ACC and MACC computed from bootstrapping on the members with 100 drawings #' with replacement. To guarantee the statistical robustness of the result, #' make sure that your experiment and observation always have the same number #' of members. "bootstrap" requires 'memb_dim' has value. The default value is #' 'parametric'. #'@param conf.lev A numeric indicating the confidence level for the #' regression computation. The default value is 0.95. #'@param pval A logical value indicating whether to compute the p-value or not. #' The default value is TRUE. #'@param ncores An integer indicating the number of cores to use for parallel #' computation. The default value is NULL. #' #'@return #'A list containing the numeric arrays:\cr #'\item{acc}{ #' The ACC with the dimensions c(nexp, nobs, the rest of the dimension except #' space_dim and memb_dim). nexp is the number of experiment (i.e., dat_dim in #' exp), and nobs is the number of observation (i.e., dat_dim in obs). #'} #'\item{conf.lower (if conftype = "parametric") or acc_conf.lower (if #' conftype = "bootstrap")}{ #' The lower confidence interval of ACC with the same dimensions as ACC. Only #' present if \code{conf = TRUE}. #'} #'\item{conf.upper (if conftype = "parametric") or acc_conf.upper (if #' conftype = "bootstrap")}{ #' The upper confidence interval of ACC with the same dimensions as ACC. Only #' present if \code{conf = TRUE}. #'} #'\item{p.val}{ #' The p-value with the same dimensions as ACC. Only present if #' \code{pval = TRUE} and code{conftype = "parametric"}. #'} #'\item{macc}{ #' The mean anomaly correlation coefficient with dimensions #' c(nexp, nobs, the rest of the dimension except space_dim, memb_dim, and #' avg_dim). Only present if 'avg_dim' is not NULL. #'} #'\item{macc_conf.lower}{ #' The lower confidence interval of MACC with the same dimensions as MACC. #' Only present if \code{conftype = "bootstrap"}. #'} #'\item{macc_conf.upper}{ #' The upper confidence interval of MACC with the same dimensions as MACC. #' Only present if \code{conftype = "bootstrap"}. #'} #' #'@examples #' \dontshow{ #'startDates <- c('19851101', '19901101', '19951101', '20001101', '20051101') #'sampleData <- s2dv:::.LoadSampleData('tos', c('experiment'), #' c('observation'), startDates, #' leadtimemin = 1, #' leadtimemax = 4, #' output = 'lonlat', #' latmin = 27, latmax = 48, #' lonmin = -12, lonmax = 40) #' } #'sampleData$mod <- Season(sampleData$mod, monini = 11, moninf = 12, monsup = 2) #'sampleData$obs <- Season(sampleData$obs, monini = 11, moninf = 12, monsup = 2) #'clim <- Clim(sampleData$mod, sampleData$obs) #'ano_exp <- Ano(sampleData$mod, clim$clim_exp) #'ano_obs <- Ano(sampleData$obs, clim$clim_obs) #'acc <- ACC(ano_exp, ano_obs) #'acc_bootstrap <- ACC(ano_exp, ano_obs, conftype = 'bootstrap') #'# Combine acc results for PlotACC #'res <- array(c(acc$conf.lower, acc$acc, acc$conf.upper, acc$p.val), #' dim = c(dim(acc$acc), 4)) #'res_bootstrap <- array(c(acc$acc_conf.lower, acc$acc, acc$acc_conf.upper, acc$p.val), #' dim = c(dim(acc$acc), 4)) #' \donttest{ #'PlotACC(res, startDates) #'PlotACC(res_bootstrap, startDates) #' } #'@references Joliffe and Stephenson (2012). Forecast Verification: A #' Practitioner's Guide in Atmospheric Science. Wiley-Blackwell. #'@import multiApply #'@importFrom abind abind #'@importFrom stats qt qnorm quantile #'@importFrom ClimProjDiags Subset #'@export ACC <- function(exp, obs, dat_dim = 'dataset', space_dim = c('lat', 'lon'), avg_dim = 'sdate', memb_dim = 'member', lat = NULL, lon = NULL, lonlatbox = NULL, conf = TRUE, conftype = "parametric", conf.lev = 0.95, pval = TRUE, ncores = NULL) { # Check inputs ## exp and obs (1) if (is.null(exp) | is.null(obs)) { stop("Parameter 'exp' and 'obs' cannot be NULL.") } if (!is.numeric(exp) | !is.numeric(obs)) { stop("Parameter 'exp' and 'obs' must be a numeric array.") } if (is.null(dim(exp)) | is.null(dim(obs))) { stop(paste0("Parameter 'exp' and 'obs' must have at least dimensions ", "dat_dim and space_dim.")) } if(any(is.null(names(dim(exp))))| any(nchar(names(dim(exp))) == 0) | any(is.null(names(dim(obs))))| any(nchar(names(dim(obs))) == 0)) { stop("Parameter 'exp' and 'obs' must have dimension names.") } if(!all(names(dim(exp)) %in% names(dim(obs))) | !all(names(dim(obs)) %in% names(dim(exp)))) { stop("Parameter 'exp' and 'obs' must have same dimension names.") } ## dat_dim if (!is.character(dat_dim) | length(dat_dim) > 1) { stop("Parameter 'dat_dim' must be a character string.") } if (!dat_dim %in% names(dim(exp)) | !dat_dim %in% names(dim(obs))) { stop("Parameter 'dat_dim' is not found in 'exp' or 'obs' dimension.") } ## space_dim if (!is.character(space_dim) | length(space_dim) != 2) { stop("Parameter 'space_dim' must be a character vector of 2.") } if (any(!space_dim %in% names(dim(exp))) | any(!space_dim %in% names(dim(obs)))) { stop("Parameter 'space_dim' is not found in 'exp' or 'obs' dimension.") } ## avg_dim if (!is.null(avg_dim)) { if (!is.character(avg_dim) | length(avg_dim) > 1) { stop("Parameter 'avg_dim' must be a character string.") } if (!avg_dim %in% names(dim(exp)) | !avg_dim %in% names(dim(obs))) { stop("Parameter 'avg_dim' is not found in 'exp' or 'obs' dimension.") } } ## memb_dim if (!is.null(memb_dim)) { if (!is.character(memb_dim) | length(memb_dim) > 1) { stop("Parameter 'memb_dim' must be a character string.") } if (!memb_dim %in% names(dim(exp)) | !memb_dim %in% names(dim(obs))) { stop("Parameter 'memb_dim' is not found in 'exp' or 'obs' dimension.") } } ## lat if (!is.null(lat)) { if (!is.numeric(lat) | length(lat) != dim(exp)[space_dim[1]]) { stop(paste0("Parameter 'lat' must be a numeric vector with the same ", "length as the latitude dimension of 'exp' and 'obs'.")) } } ## lon if (!is.null(lon)) { if (!is.numeric(lon) | length(lon) != dim(exp)[space_dim[2]]) { stop(paste0("Parameter 'lon' must be a numeric vector with the same ", "length as the longitude dimension of 'exp' and 'obs'.")) } } ## lonlatbox if (!is.null(lonlatbox)) { if (!is.numeric(lonlatbox) | length(lonlatbox) != 4) { stop("Parameter 'lonlatbox' must be a numeric vector of 4.") } } ## lat, lon, and lonlatbox if (!is.null(lon) & !is.null(lat) & !is.null(lonlatbox)) { select_lonlat <- TRUE } else if (is.null(lon) & is.null(lat) & is.null(lonlatbox)) { select_lonlat <- FALSE } else { stop(paste0("Parameters 'lon', 'lat', and 'lonlatbox' must be used or be ", "NULL at the same time.")) } ## conf if (!is.logical(conf) | length(conf) > 1) { stop("Parameter 'conf' must be one logical value.") } if (conf) { ## conftype if (!conftype %in% c('parametric', 'bootstrap')) { stop("Parameter 'conftype' must be either 'parametric' or 'bootstrap'.") } if (conftype == 'bootstrap' & is.null(memb_dim)) { stop("Parameter 'memb_dim' cannot be NULL when parameter 'conftype' is 'bootstrap'.") } ## conf.lev if (!is.numeric(conf.lev) | conf.lev < 0 | conf.lev > 1 | length(conf.lev) > 1) { stop("Parameter 'conf.lev' must be a numeric number between 0 and 1.") } } ## pval if (!is.logical(pval) | length(pval) > 1) { stop("Parameter 'pval' must be one logical value.") } ## ncores if (!is.null(ncores)) { if (!is.numeric(ncores) | ncores %% 1 != 0 | ncores < 0 | length(ncores) > 1) { stop("Parameter 'ncores' must be a positive integer.") } } ## exp and obs (2) name_exp <- sort(names(dim(exp))) name_obs <- sort(names(dim(obs))) name_exp <- name_exp[-which(name_exp == dat_dim)] name_obs <- name_obs[-which(name_obs == dat_dim)] if (!is.null(memb_dim)) { name_exp <- name_exp[-which(name_exp == memb_dim)] name_obs <- name_obs[-which(name_obs == memb_dim)] } if(!all(dim(exp)[name_exp] == dim(obs)[name_obs])) { stop(paste0("Parameter 'exp' and 'obs' must have same length of ", "all the dimensions expect 'dat_dim' and 'memb_dim'.")) } #----------------------------------------------------------------- ############################### # Sort dimension name_exp <- names(dim(exp)) name_obs <- names(dim(obs)) order_obs <- match(name_exp, name_obs) obs <- Reorder(obs, order_obs) ############################### # Select the domain if (select_lonlat) { for (jind in 1:2) { while (lonlatbox[jind] < 0) { lonlatbox[jind] <- lonlatbox[jind] + 360 } while (lonlatbox[jind] > 360) { lonlatbox[jind] <- lonlatbox[jind] - 360 } } indlon <- which((lon >= lonlatbox[1] & lon <= lonlatbox[2]) | (lonlatbox[1] > lonlatbox[2] & (lon > lonlatbox[1] | lon < lonlatbox[2]))) indlat <- which(lat >= lonlatbox[3] & lat <= lonlatbox[4]) exp <- ClimProjDiags::Subset(exp, space_dim, list(indlat, indlon), drop = FALSE) obs <- ClimProjDiags::Subset(obs, space_dim, list(indlat, indlon), drop = FALSE) } # Ensemble mean if (!is.null(memb_dim)) { if (conftype == 'bootstrap') { exp_ori <- exp obs_ori <- obs } exp <- MeanDims(exp, memb_dim, na.rm = TRUE, ncores = ncores) obs <- MeanDims(obs, memb_dim, na.rm = TRUE, ncores = ncores) } if (is.null(avg_dim)) { res <- Apply(list(exp, obs), target_dims = list(c(space_dim, dat_dim), c(space_dim, dat_dim)), fun = .ACC, dat_dim = dat_dim, avg_dim = avg_dim, conftype = conftype, pval = pval, conf = conf, conf.lev = conf.lev, ncores_input = ncores, ncores = ncores) if (conftype == 'bootstrap') { res_conf <- Apply(list(exp_ori, obs_ori), target_dims = list(c(memb_dim, dat_dim, space_dim), c(memb_dim, dat_dim, space_dim)), fun = .ACC_bootstrap, dat_dim = dat_dim, memb_dim = memb_dim, avg_dim = avg_dim, conftype = conftype, pval = pval, conf = conf, conf.lev = conf.lev, ncores_input = ncores, ncores = ncores) #NOTE: pval? res <- list(acc = res$acc, acc_conf.lower = res_conf$acc_conf.lower, acc_conf.upper = res_conf$acc_conf.upper, macc = res$macc, macc_conf.lower = res_conf$macc_conf.lower, macc_conf.upper = res_conf$macc_conf.upper) } } else { res <- Apply(list(exp, obs), target_dims = list(c(space_dim, avg_dim, dat_dim), c(space_dim, avg_dim, dat_dim)), fun = .ACC, dat_dim = dat_dim, avg_dim = avg_dim, conftype = conftype, pval = pval, conf = conf, conf.lev = conf.lev, ncores_input = ncores, ncores = ncores) if (conftype == 'bootstrap') { res_conf <- Apply(list(exp_ori, obs_ori), target_dims = list(c(memb_dim, dat_dim, avg_dim, space_dim), c(memb_dim, dat_dim, avg_dim, space_dim)), fun = .ACC_bootstrap, dat_dim = dat_dim, memb_dim = memb_dim, avg_dim = avg_dim, conftype = conftype, pval = pval, conf = conf, conf.lev = conf.lev, ncores_input = ncores, ncores = ncores) res <- list(acc = res$acc, acc_conf.lower = res_conf$acc_conf.lower, acc_conf.upper = res_conf$acc_conf.upper, macc = res$macc, macc_conf.lower = res_conf$macc_conf.lower, macc_conf.upper = res_conf$macc_conf.upper) } } return(res) } .ACC <- function(exp, obs, dat_dim = 'dataset', #space_dim = c('lat', 'lon'), avg_dim = 'sdate', #memb_dim = NULL, lon = NULL, lat = NULL, lonlatbox = NULL, conf = TRUE, conftype = "parametric", conf.lev = 0.95, pval = TRUE, ncores_input = NULL) { # if (is.null(avg_dim)) # exp: [space_dim, dat_exp] # obs: [space_dim, dat_obs] # if (!is.null(avg_dim)) # exp: [space_dim, avg_dim, dat_exp] # obs: [space_dim, avg_dim, dat_obs] # .ACC() should use all the spatial points to calculate ACC. It returns [nexp, nobs]. nexp <- as.numeric(dim(exp)[length(dim(exp))]) nobs <- as.numeric(dim(obs)[length(dim(obs))]) if (is.null(avg_dim)) { acc <- array(dim = c(nexp = nexp, nobs = nobs)) if (pval) p.val <- array(dim = c(nexp = nexp, nobs = nobs)) if (conf) { conf.upper <- array(dim = c(nexp = nexp, nobs = nobs)) conf.lower <- array(dim = c(nexp = nexp, nobs = nobs)) if (conftype == 'bootstrap') { ndraw <- 100 acc_draw <- array(dim = c(nexp = nexp, nobs = nobs, ndraw)) } } } else { acc <- array(dim = c(nexp = nexp, nobs = nobs, dim(exp)[length(dim(exp)) - 1])) names(dim(acc))[3] <- avg_dim macc <- array(dim = c(nexp = nexp, nobs = nobs)) if (pval) p.val <- array(dim = c(nexp = nexp, nobs = nobs, dim(exp)[length(dim(exp)) - 1])) if (conf) { conf.upper <- array(dim = c(nexp = nexp, nobs = nobs, dim(exp)[length(dim(exp)) - 1])) conf.lower <- array(dim = c(nexp = nexp, nobs = nobs, dim(exp)[length(dim(exp)) - 1])) if (conftype == 'bootstrap') { ndraw <- 100 acc_draw <- array(dim = c(nexp = nexp, nobs = nobs, dim(exp)[length(dim(exp)) - 1], ndraw)) macc_draw <- array(dim = c(nexp = nexp, nobs = nobs, ndraw)) } } } # Per-paired exp and obs. NAs should be in the same position in both exp and obs for (iobs in 1:nobs) { for (iexp in 1:nexp) { exp_sub <- ClimProjDiags::Subset(exp, dat_dim, iexp, drop = 'selected') obs_sub <- ClimProjDiags::Subset(obs, dat_dim, iobs, drop = 'selected') # dim: [space_dim] # Variance(iexp) should not take into account any point # that is not available in iobs and therefore not accounted for # in covariance(iexp, iobs) and vice-versa exp_sub[is.na(obs_sub)] <- NA obs_sub[is.na(exp_sub)] <- NA if (is.null(avg_dim)) { # ACC top <- sum(exp_sub*obs_sub, na.rm = TRUE) #a number bottom <- sqrt(sum(exp_sub^2, na.rm = TRUE) * sum(obs_sub^2, na.rm = TRUE)) acc[iexp, iobs] <- top/bottom #a number # handle bottom = 0 if (is.infinite(acc[iexp, iobs])) acc[iexp, iobs] <- NA # pval and conf if (pval | conf) { if (conftype == "parametric") { # calculate effective sample size along space_dim # combine space_dim into one dim first obs_tmp <- array(obs_sub, dim = c(space = length(obs_sub))) eno <- Eno(obs_tmp, 'space', ncores = ncores_input) # a number if (pval) { t <- qt(conf.lev, eno - 2) # a number p.val[iexp, iobs] <- sqrt(t^2 / (t^2 + eno - 2)) } if (conf) { conf.upper[iexp, iobs] <- tanh(atanh(acc[iexp, iobs]) + qnorm(1 - (1 - conf.lev) / 2) / sqrt(eno - 3)) conf.lower[iexp, iobs] <- tanh(atanh(acc[iexp, iobs]) + qnorm((1 - conf.lev) / 2) / sqrt(eno - 3)) } } } } else { #avg_dim is not NULL # MACC top <- sum(exp_sub*obs_sub, na.rm = TRUE) #a number bottom <- sqrt(sum(exp_sub^2, na.rm = TRUE) * sum(obs_sub^2, na.rm = TRUE)) macc[iexp, iobs] <- top/bottom #a number # handle bottom = 0 if (is.infinite(macc[iexp, iobs])) macc[iexp, iobs] <- NA # ACC for (i in 1:dim(acc)[3]) { #NOTE: use sapply!!! exp_sub_i <- ClimProjDiags::Subset(exp_sub, avg_dim, i, drop = 'selected') obs_sub_i <- ClimProjDiags::Subset(obs_sub, avg_dim, i, drop = 'selected') #dim: [space_dim] top <- sum(exp_sub_i*obs_sub_i, na.rm = TRUE) #a number bottom <- sqrt(sum(exp_sub_i^2, na.rm = TRUE) * sum(obs_sub_i^2, na.rm = TRUE)) acc[iexp, iobs, i] <- top/bottom #a number # handle bottom = 0 if (is.infinite(acc[iexp, iobs, i])) acc[iexp, iobs, i] <- NA } # pval and conf if (pval | conf) { if (conftype == "parametric") { # calculate effective sample size along space_dim # combine space_dim into one dim first obs_tmp <- array(obs_sub, dim = c(space = prod(dim(obs_sub)[-length(dim(obs_sub))]), dim(obs_sub)[length(dim(obs_sub))])) eno <- Eno(obs_tmp, 'space', ncores = ncores_input) # a vector of avg_dim if (pval) { t <- qt(conf.lev, eno - 2) # a vector of avg_dim p.val[iexp, iobs, ] <- sqrt(t^2 / (t^2 + eno - 2)) } if (conf) { conf.upper[iexp, iobs, ] <- tanh(atanh(acc[iexp, iobs, ]) + qnorm(1 - (1 - conf.lev) / 2) / sqrt(eno - 3)) conf.lower[iexp, iobs, ] <- tanh(atanh(acc[iexp, iobs, ]) + qnorm((1 - conf.lev) / 2) / sqrt(eno - 3)) } } } } # if avg_dim is not NULL } } #------------------------------------------------ # Return output if (is.null(avg_dim)) { if (conf & pval) { return(list(acc = acc, conf.lower = conf.lower, conf.upper = conf.upper, p.val = p.val)) } else if (conf & !pval) { return(list(acc = acc, conf.lower = conf.lower, conf.upper = conf.upper, macc = macc)) } else if (!conf & pval) { return(list(acc = acc, p.val = p.val)) } else { return(list(acc = acc)) } } else { if (conf & pval) { return(list(acc = acc, conf.lower = conf.lower, conf.upper = conf.upper, p.val = p.val, macc = macc)) } else if (conf & !pval) { return(list(acc = acc, conf.lower = conf.lower, conf.upper = conf.upper, macc = macc)) } else if (!conf & pval) { return(list(acc = acc, p.val = p.val, macc = macc)) } else { return(list(acc = acc, macc = macc)) } } } .ACC_bootstrap <- function(exp, obs, dat_dim = 'dataset', #space_dim = c('lat', 'lon'), avg_dim = 'sdate', memb_dim = NULL, lon = NULL, lat = NULL, lonlatbox = NULL, conf = TRUE, conftype = "parametric", conf.lev = 0.95, pval = TRUE, ncores_input = NULL) { # if (is.null(avg_dim)) # exp: [memb_exp, dat_exp, space_dim] # obs: [memb_obs, dat_obs, space_dim] # if (!is.null(avg_dim)) # exp: [memb_exp, dat_exp, avg_dim, space_dim] # obs: [memb_obs, dat_obs, avg_dim, space_dim] nexp <- as.numeric(dim(exp)[2]) nobs <- as.numeric(dim(obs)[2]) nmembexp <- as.numeric(dim(exp)[1]) nmembobs <- as.numeric(dim(obs)[1]) ndraw <- 100 if (is.null(avg_dim)) { acc_draw <- array(dim = c(nexp = nexp, nobs = nobs, ndraw)) } else { acc_draw <- array(dim = c(nexp = nexp, nobs = nobs, dim(exp)[3], ndraw)) macc_draw <- array(dim = c(nexp = nexp, nobs = nobs, ndraw)) } for (jdraw in 1:ndraw) { #choose a randomly member index for each point of the matrix indexp <- array(sample(nmembexp, size = prod(dim(exp)[-c(length(dim(exp)) - 1, length(dim(exp)))]), replace = TRUE), dim = dim(exp)) indobs <- array(sample(nmembobs, size = prod(dim(obs)[-c(length(dim(obs)) - 1, length(dim(obs)))]), replace = TRUE), dim = dim(obs)) #combine maxtrix of data and random index varindexp <- abind::abind(exp, indexp, along = length(dim(exp)) + 1) varindobs <- abind::abind(obs, indobs, along = length(dim(obs)) + 1) #select randomly the members for each point of the matrix # if (is.null(avg_dim)) { drawexp <- array( apply(varindexp, c(2:length(dim(exp))), function(x) x[,1][x[,2]] ), dim = dim(exp)) drawobs <- array( apply(varindobs, c(2:length(dim(obs))), function(x) x[,1][x[,2]] ), dim = dim(obs)) # ensemble mean before .ACC drawexp <- MeanDims(drawexp, memb_dim, na.rm = TRUE, ncores = ncores_input) drawobs <- MeanDims(drawobs, memb_dim, na.rm = TRUE, ncores = ncores_input) # Reorder if (is.null(avg_dim)) { drawexp <- Reorder(drawexp, c(2, 3, 1)) drawobs <- Reorder(drawobs, c(2, 3, 1)) } else { drawexp <- Reorder(drawexp, c(3, 4, 2, 1)) drawobs <- Reorder(drawobs, c(3, 4, 2, 1)) } #calculate the ACC of the randomized field tmpACC <- .ACC(drawexp, drawobs, conf = FALSE, pval = FALSE, avg_dim = avg_dim, ncores_input = ncores_input) if (is.null(avg_dim)) { acc_draw[, , jdraw] <- tmpACC$acc } else { acc_draw[, , , jdraw] <- tmpACC$acc macc_draw[, , jdraw] <- tmpACC$macc } } #calculate the confidence interval if (is.null(avg_dim)) { acc_conf.upper <- apply(acc_draw, c(1, 2), function (x) { quantile(x, 1 - (1 - conf.lev) / 2, na.rm = TRUE)}) acc_conf.lower <- apply(acc_draw, c(1, 2), function (x) { quantile(x, (1 - conf.lev) / 2, na.rm = TRUE)}) } else { acc_conf.upper <- apply(acc_draw, c(1, 2, 3), function (x) { quantile(x, 1 - (1 - conf.lev) / 2, na.rm = TRUE)}) acc_conf.lower <- apply(acc_draw, c(1, 2, 3), function (x) { quantile(x, (1 - conf.lev) / 2, na.rm = TRUE)}) macc_conf.upper <- apply(macc_draw, c(1, 2), function (x) { quantile(x, 1 - (1 - conf.lev) / 2, na.rm = TRUE)}) macc_conf.lower <- apply(macc_draw, c(1, 2), function (x) { quantile(x, (1 - conf.lev) / 2, na.rm = TRUE)}) } # Return output if (is.null(avg_dim)) { return(list(acc_conf.lower = acc_conf.lower, acc_conf.upper = acc_conf.upper)) } else { return(list(acc_conf.lower = acc_conf.lower, acc_conf.upper = acc_conf.upper, macc_conf.lower = macc_conf.lower, macc_conf.upper = macc_conf.upper)) } }