From b6e39feac9baf8d94345d009e252530b0341e60c Mon Sep 17 00:00:00 2001
From: Maximilian Schmidt <max.schmidt@fz-juelich.de>
Date: Fri, 30 Mar 2018 17:15:29 +0900
Subject: [PATCH] Remove R code for now because of outstanding permission for
bbalt.R script
---
multiarea_model/data_multiarea/SLN_logdensities.R | 13 -------------
.../data_multiarea/VisualCortex_Data.py | 15 +++++----------
2 files changed, 5 insertions(+), 23 deletions(-)
delete mode 100644 multiarea_model/data_multiarea/SLN_logdensities.R
diff --git a/multiarea_model/data_multiarea/SLN_logdensities.R b/multiarea_model/data_multiarea/SLN_logdensities.R
deleted file mode 100644
index 38fbe8a..0000000
--- 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 37ef027..047ca4a 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.
--
GitLab