remove options(mc.cores = parallel::detectCores())

idhx · Oct 20, 2019 · 9697810 · 9697810
1 parent cda486e
commit 9697810
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diff --git a/Arsenic/arsenic_logistic_apc.R b/Arsenic/arsenic_logistic_apc.R
@@ -17,7 +17,6 @@ knitr::opts_chunk$set(message=FALSE, error=FALSE, warning=FALSE, comment=NA)
 library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 library("loo")
 invlogit <- plogis
 

diff --git a/Arsenic/arsenic_logistic_apc.Rmd b/Arsenic/arsenic_logistic_apc.Rmd
@@ -19,7 +19,6 @@ knitr::opts_chunk$set(message=FALSE, error=FALSE, warning=FALSE, comment=NA)
 library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 library("loo")
 invlogit <- plogis
 ```

diff --git a/Arsenic/arsenic_logistic_building.R b/Arsenic/arsenic_logistic_building.R
@@ -19,7 +19,6 @@ savefigs <- FALSE
 library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 library("loo")
 invlogit <- plogis
 

diff --git a/Arsenic/arsenic_logistic_building.Rmd b/Arsenic/arsenic_logistic_building.Rmd
@@ -21,7 +21,6 @@ savefigs <- FALSE
 library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 library("loo")
 invlogit <- plogis
 ```

diff --git a/Arsenic/arsenic_logistic_building_optimizing.R b/Arsenic/arsenic_logistic_building_optimizing.R
@@ -25,7 +25,6 @@ savefigs <- FALSE
 library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 library("loo")
 invlogit <- plogis
 

diff --git a/Arsenic/arsenic_logistic_building_optimizing.Rmd b/Arsenic/arsenic_logistic_building_optimizing.Rmd
@@ -27,7 +27,6 @@ savefigs <- FALSE
 library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 library("loo")
 invlogit <- plogis
 ```

diff --git a/Arsenic/arsenic_logistic_residuals.R b/Arsenic/arsenic_logistic_residuals.R
@@ -19,7 +19,6 @@ savefigs <- FALSE
 library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 library("loo")
 invlogit <- plogis
 

diff --git a/Arsenic/arsenic_logistic_residuals.Rmd b/Arsenic/arsenic_logistic_residuals.Rmd
@@ -21,7 +21,6 @@ savefigs <- FALSE
 library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 library("loo")
 invlogit <- plogis
 ```

diff --git a/Beauty/beauty.R b/Beauty/beauty.R
@@ -19,7 +19,6 @@ knitr::opts_chunk$set(message=FALSE, error=FALSE, warning=FALSE, comment=NA)
 library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 library("ggplot2")
 library("bayesplot")
 theme_set(bayesplot::theme_default(base_family = "sans"))

diff --git a/Beauty/beauty.Rmd b/Beauty/beauty.Rmd
@@ -21,7 +21,6 @@ knitr::opts_chunk$set(message=FALSE, error=FALSE, warning=FALSE, comment=NA)
 library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 library("ggplot2")
 library("bayesplot")
 theme_set(bayesplot::theme_default(base_family = "sans"))

diff --git a/Congress/congress.R b/Congress/congress.R
@@ -17,7 +17,6 @@ knitr::opts_chunk$set(message=FALSE, error=FALSE, warning=FALSE, comment=NA)
 library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 
 #' **Load and pre-process data**
 congress <- vector("list", 49)

diff --git a/Congress/congress.Rmd b/Congress/congress.Rmd
@@ -19,7 +19,6 @@ knitr::opts_chunk$set(message=FALSE, error=FALSE, warning=FALSE, comment=NA)
 library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 ```
 
 **Load and pre-process data**

diff --git a/DifferentSoftware/linear.R b/DifferentSoftware/linear.R
@@ -17,7 +17,6 @@ knitr::opts_chunk$set(message=FALSE, error=FALSE, warning=FALSE, comment=NA)
 #' **Load packages**
 library("arm")
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 library("brms")
 
 #' **Create fake data**

diff --git a/DifferentSoftware/linear.Rmd b/DifferentSoftware/linear.Rmd
@@ -19,7 +19,6 @@ knitr::opts_chunk$set(message=FALSE, error=FALSE, warning=FALSE, comment=NA)
 ```{r }
 library("arm")
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 library("brms")
 ```
 

diff --git a/Earnings/earnings_compound.R b/Earnings/earnings_compound.R
@@ -17,7 +17,6 @@ knitr::opts_chunk$set(message=FALSE, error=FALSE, warning=FALSE, comment=NA)
 library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 library("ggplot2")
 library("bayesplot")
 theme_set(bayesplot::theme_default(base_family = "sans"))
@@ -38,15 +37,15 @@ height_jitter_add <- runif(n, -.2, .2)
 #+ results='hide'
 fit_2a <- stan_glm(positive ~ height + male,
                    family = binomial(link = "logit"),
-                   data = earnings_all)
+                   data = earnings_all, refresh = 0)
 sims_2a <- as.matrix(fit_2a)
 #+
 print(fit_2a, digits=2)
 
 #' **Linear regression on log scale**
 earnings$log_earn <- log(earnings$earn)
 #+ results='hide'
-fit_2b <- stan_glm(log_earn ~ height + male, data = earnings)
+fit_2b <- stan_glm(log_earn ~ height + male, data = earnings, refresh = 0)
 sims_2b <- as.matrix(fit_2b)
 #+
 print(fit_2b, digits=2)

diff --git a/Earnings/earnings_compound.Rmd b/Earnings/earnings_compound.Rmd
@@ -19,7 +19,6 @@ knitr::opts_chunk$set(message=FALSE, error=FALSE, warning=FALSE, comment=NA)
 library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 library("ggplot2")
 library("bayesplot")
 theme_set(bayesplot::theme_default(base_family = "sans"))
@@ -44,7 +43,7 @@ height_jitter_add <- runif(n, -.2, .2)
 ```{r results='hide'}
 fit_2a <- stan_glm(positive ~ height + male,
                    family = binomial(link = "logit"),
-                   data = earnings_all)
+                   data = earnings_all, refresh = 0)
 sims_2a <- as.matrix(fit_2a)
 ```
 ```{r }
@@ -57,7 +56,7 @@ print(fit_2a, digits=2)
 earnings$log_earn <- log(earnings$earn)
 ```
 ```{r results='hide'}
-fit_2b <- stan_glm(log_earn ~ height + male, data = earnings)
+fit_2b <- stan_glm(log_earn ~ height + male, data = earnings, refresh = 0)
 sims_2b <- as.matrix(fit_2b)
 ```
 ```{r }

diff --git a/Earnings/earnings_loo.R b/Earnings/earnings_loo.R
diff --git a/Earnings/earnings_regression.R b/Earnings/earnings_regression.R
@@ -19,7 +19,6 @@ savefigs <- FALSE
 library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 library("ggplot2")
 library("bayesplot")
 theme_set(bayesplot::theme_default(base_family = "sans"))

diff --git a/Earnings/earnings_regression.Rmd b/Earnings/earnings_regression.Rmd
@@ -21,7 +21,6 @@ savefigs <- FALSE
 library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 library("ggplot2")
 library("bayesplot")
 theme_set(bayesplot::theme_default(base_family = "sans"))

diff --git a/ElectionsEconomy/hibbs.R b/ElectionsEconomy/hibbs.R
@@ -19,7 +19,6 @@ savefigs <- FALSE
 library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 library("ggplot2")
 library("bayesplot")
 theme_set(bayesplot::theme_default(base_family = "sans"))

diff --git a/ElectionsEconomy/hibbs.Rmd b/ElectionsEconomy/hibbs.Rmd
@@ -21,7 +21,6 @@ savefigs <- FALSE
 library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 library("ggplot2")
 library("bayesplot")
 theme_set(bayesplot::theme_default(base_family = "sans"))

diff --git a/ElectionsEconomy/hibbs_coverage.R b/ElectionsEconomy/hibbs_coverage.R
@@ -18,7 +18,6 @@ knitr::opts_chunk$set(message=FALSE, error=FALSE, warning=FALSE, comment=NA)
 library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 
 #' **Load data**
 hibbs <- read.table(root("ElectionsEconomy/data","hibbs.dat"), header=TRUE)

diff --git a/ElectionsEconomy/hibbs_coverage.Rmd b/ElectionsEconomy/hibbs_coverage.Rmd
@@ -20,7 +20,6 @@ knitr::opts_chunk$set(message=FALSE, error=FALSE, warning=FALSE, comment=NA)
 library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 ```
 
 **Load data**

diff --git a/ElectionsEconomy/hills.R b/ElectionsEconomy/hills.R
@@ -20,7 +20,6 @@ library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("arm")
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 
 #' **Load data**
 hibbs <- read.table(root("ElectionsEconomy/data","hibbs.dat"), header=TRUE)

diff --git a/ElectionsEconomy/hills.Rmd b/ElectionsEconomy/hills.Rmd
@@ -22,7 +22,6 @@ library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("arm")
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 ```
 
 **Load data**

diff --git a/ElectricCompany/electric.R b/ElectricCompany/electric.R
@@ -19,7 +19,6 @@ savefigs <- FALSE
 library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 invlogit <- plogis
 
 #' **Load data**

diff --git a/ElectricCompany/electric.Rmd b/ElectricCompany/electric.Rmd
@@ -21,7 +21,6 @@ savefigs <- FALSE
 library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 invlogit <- plogis
 ```
 

diff --git a/FakeKCV/fake_kcv.R b/FakeKCV/fake_kcv.R
@@ -17,7 +17,6 @@ knitr::opts_chunk$set(message=FALSE, error=FALSE, warning=FALSE, comment=NA)
 library("MASS")      # needed for mvrnorm()
 library("rstanarm")
 library("loo")
-options(mc.cores = parallel::detectCores())
 #' Set random seed for reproducability
 SEED <- 1754
 

diff --git a/FakeKCV/fake_kcv.Rmd b/FakeKCV/fake_kcv.Rmd
@@ -19,7 +19,6 @@ knitr::opts_chunk$set(message=FALSE, error=FALSE, warning=FALSE, comment=NA)
 library("MASS")      # needed for mvrnorm()
 library("rstanarm")
 library("loo")
-options(mc.cores = parallel::detectCores())
 ```
 
 Set random seed for reproducability

diff --git a/FakeMidtermFinal/FakeMidtermFinal.R b/FakeMidtermFinal/FakeMidtermFinal.R
@@ -17,7 +17,6 @@ savefigs <- FALSE
 
 #' **Load packages**
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 
 #' **Simulate fake data**
 N <- 1000

diff --git a/FakeMidtermFinal/FakeMidtermFinal.Rmd b/FakeMidtermFinal/FakeMidtermFinal.Rmd
@@ -19,7 +19,6 @@ savefigs <- FALSE
 
 ```{r }
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 ```
 
 **Simulate fake data**

diff --git a/Golf/golf.R b/Golf/golf.R
@@ -20,7 +20,6 @@ library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("rstan")
 rstan_options(auto_write = TRUE)
-options(mc.cores = parallel::detectCores())
 library("rstanarm")
 invlogit <- plogis
 

diff --git a/Golf/golf.Rmd b/Golf/golf.Rmd
@@ -22,7 +22,6 @@ library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("rstan")
 rstan_options(auto_write = TRUE)
-options(mc.cores = parallel::detectCores())
 library("rstanarm")
 invlogit <- plogis
 ```

diff --git a/Imputation/imputation.R b/Imputation/imputation.R
@@ -19,7 +19,6 @@ savefigs <- FALSE
 library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 
 #' **Load data**
 source(root("Imputation/data","imputation_setup.R"))

diff --git a/Imputation/imputation.Rmd b/Imputation/imputation.Rmd
@@ -21,7 +21,6 @@ savefigs <- FALSE
 library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 ```
 
 **Load data**

diff --git a/Imputation/imputation_gg.R b/Imputation/imputation_gg.R
@@ -20,7 +20,6 @@ savefigs <- FALSE
 library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 library("dplyr")
 library("ggplot2")
 theme_set(bayesplot::theme_default(base_family = "sans"))

diff --git a/Imputation/imputation_gg.Rmd b/Imputation/imputation_gg.Rmd
@@ -22,7 +22,6 @@ savefigs <- FALSE
 library("rprojroot")
 root<-has_dirname("ROS-Examples")$make_fix_file()
 library("rstanarm")
-options(mc.cores = parallel::detectCores())
 library("dplyr")
 library("ggplot2")
 theme_set(bayesplot::theme_default(base_family = "sans"))
-Original file line number
+Diff line change
@@ Expand Up / @@ -19,7 +19,6 @@ savefigs <- FALSE @@
     ```{r }
     library("rstanarm")
-    options(mc.cores = parallel::detectCores())
     ```
     **Simulate fake data**
@@ Expand Down @@