Created
August 16, 2018 19:21
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How to use a progress bar within a foreach loop to keep an eye on the overall progress of a queue
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#use row-wise iterator to avoid exporting the entire voxels x time matrix to each worker | |
library(tictoc) | |
library(utils) | |
message("Starting voxelwise ARIMA fitting") | |
pb <- txtProgressBar(0, max = nrow(toprocess), style = 3) | |
tic("arima fitting") | |
vox_results <- foreach(v=iter(toprocess, by="row"), .noexport="fmri_ts_data", .packages="forecast", .inorder=TRUE, .multicombine=TRUE, .combine=rbind) %dopar% { | |
it <- as.numeric(row.names(v)[1]) #use row number of matrix to set progress bar | |
if (it %% 100 == 0) { setTxtProgressBar(pb, it) } | |
vfit <- arimafit(v, search_pdq=search_pdq, max.p=max_p, max.d=max_d, max.q=max_q, fit.p=fit_p, fit.d=fit_d, fit.q=fit_q) #fit arima to voxel | |
arima_coef <- base_coef_vector #start with empty vector of max order for each model part | |
arima_coef[names(vfit$arima_coef)] <- vfit$arima_coef #populate non-zero elements of fitted ARMA coefficients | |
c(vfit$resid_ts, vfit$arima_order[c("p", "d", "q")], vfit$white_bg_pvals, arima_coef) #concatenating into a long vector rather than try to get 2+ objects out | |
} | |
toc() | |
close(pb) |
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