diff --git a/multiarea_model/data_multiarea/SLN_logdensities.R b/multiarea_model/data_multiarea/SLN_logdensities.R deleted file mode 100644 index 38fbe8a3e19f9e74bf85d53324c96f160d69a8a3..0000000000000000000000000000000000000000 --- a/multiarea_model/data_multiarea/SLN_logdensities.R +++ /dev/null @@ -1,13 +0,0 @@ -library('aod') -source(paste(Sys.getenv('HOME'),'/model-june/data_multi_area/bbAlt.R', sep="")) -f <- file(paste(Sys.getenv('HOME'),'/model-june/data_multi_area/raw_data/RData_prepared_logdensities.txt', sep=""),'r') -x <- read.table(f) -close(f) - - -dens <- data.matrix(x)[,7] - -m2.bb <- betabin(cbind(S, I) ~ dens , ~ 1, data = x, "probit", control = list(maxit = 100000)) -h2.bb <- c(coef(m2.bb)) - -print(h2.bb) diff --git a/multiarea_model/data_multiarea/VisualCortex_Data.py b/multiarea_model/data_multiarea/VisualCortex_Data.py index 37ef027f82519e5a3083dc0781d91cc3d1842d79..047ca4a4f7791ac4ebf56fd9db8ad5330dfca80c 100644 --- a/multiarea_model/data_multiarea/VisualCortex_Data.py +++ b/multiarea_model/data_multiarea/VisualCortex_Data.py @@ -1328,16 +1328,11 @@ def process_raw_data(): return res # Call R script to perform SLN fit - try: - proc = subprocess.Popen(["Rscript", - os.path.join(basepath, 'SLN_logdensities.R')], - stdout=subprocess.PIPE) - out = proc.communicate()[0].decode('utf-8') - R_fit = [float(out.split('\n')[1].split(' ')[1]), - float(out.split('\n')[1].split(' ')[3])] - except OSError: - print("No R installation, taking hard-coded fit parameters.") - R_fit = [-0.1516142, -1.5343200] + print("We currently cannot publish the R code because of " + "copyright issues, there taking hard-coded fit parameters. " + "See Schmidt et al. (2018) for a full explanation " + "of the procedure.") + R_fit = [-0.1516142, -1.5343200] """ 4. Fill missing data with fitted values.