last state at handover to Liming

openpharma · Jun 26, 2024 · 8fb99ca · 8fb99ca
1 parent b10a061
commit 8fb99ca
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Showing 8 changed files with 119 additions and 119 deletions.
diff --git a/simulations/missing-data-benchmarks/R/meals/meal-extreme-missingness-SAS.R b/simulations/missing-data-benchmarks/R/meals/meal-extreme-missingness-SAS.R
@@ -3,6 +3,8 @@
 ################################################################################
 
 # load required libraries
+library(reticulate)
+use_virtualenv("daniel")
 library(simChef)
 library(mmrm)
 library(glmmTMB)
@@ -19,7 +21,7 @@ library(microbenchmark)
 
 # source the R scripts
 sim_functions_files <- list.files(
-  c("R/dgp", "R/method", "R/eval", "R/viz"),
+  c("R/dgp", "R/method", "R/eval", "R/viz", "R/customizations"),
   pattern = "*.R$", full.names = TRUE, ignore.case = TRUE
 )
 sapply(sim_functions_files, source)
@@ -30,7 +32,7 @@ csh_cov_mat <- compute_csh_matrix()
 toep_cov_mat <- toeplitz(c(1, 0.5, 0.25, 0.125, rep(0, 6)))
 
 # set the sample size
-n_obs <- 600
+n_obs <- 200
 
 # dgps with no treatment effect
 no_effect_us_dgp <- create_dgp(
@@ -157,8 +159,8 @@ type_2_error_rate_eval <- create_evaluator(
 
 # create the experiment
 experiment <- create_experiment(
-  name = "mmrm-benchmark-extreme-missingness-n-600-SAS",
-  save_dir = "results/extreme-miss/n-600-SAS"
+  name = glue::glue("mmrm-benchmark-extreme-missingness-n-{n_obs}-SAS"),
+  save_dir = glue::glue("results/extreme-miss/n-{n_obs}-SAS")
 ) %>%
   add_dgp(no_effect_us_dgp, name = "no_effect_us") %>%
   add_dgp(no_effect_csh_dgp, name = "no_effect_csh") %>%
@@ -188,32 +190,30 @@ experiment <- create_experiment(
   add_evaluator(type_1_error_rate_eval, name = "type_1_error_rate") %>%
   add_evaluator(type_2_error_rate_eval, name = "type_2_error_rate")
 
-# # Determine host name
-# hostname <- "sabanesd-nwpfwh-eu.ocean"
-#
-# # Do this to register host
-# session <- ssh::ssh_connect(hostname)
-# ssh_disconnect(session)
-#
-# # We can also be specific if there are multiple SAS containers we want to connect to.
-# cfg_name <- "~/sascfg_personal.py"
-# sasr.roche::setup_sasr_ocean(hostname, sascfg = cfg_name)
-# options(sascfg = cfg_name)
-#
-# # Test if it works.
-# df <- data.frame(a = 1, b = 2)
-# sasr::df2sd(df)
+# Determine host name
+hostname <- "sabanesd-w2yc52-eu.ocean"
 
-# run the experiment
-# set.seed(713452)
-# results <- experiment$run(
-#   n_reps = 1000,
-#   save = TRUE,
-#   verbose = 2,
-#   checkpoint_n_reps = 10
-# )
+# Do this to register host
+session <- ssh::ssh_connect(hostname)
+ssh_disconnect(session)
 
-source("R/format-replicate-results/helpers.R")
+# We can also be specific if there are multiple SAS containers we want to connect to.
+cfg_name <- "~/sascfg_personal.py"
+sasr.roche::setup_sasr_ocean(hostname, sascfg = cfg_name)
+options(sascfg = cfg_name)
 
-format_fit_and_save(experiment)
+# Test if it works.
+df <- data.frame(a = 1, b = 2)
+sasr::df2sd(df)
 
+# run the experiment
+set.seed(713452)
+results <- experiment$run(
+  n_reps = 1000,
+  save = TRUE,
+  use_cached = TRUE,
+  verbose = 2,
+  checkpoint_n_reps = 100
+)
+
+format_fit_and_save(experiment)
diff --git a/simulations/missing-data-benchmarks/R/meals/meal-high-missingness-SAS.R b/simulations/missing-data-benchmarks/R/meals/meal-high-missingness-SAS.R
@@ -3,6 +3,8 @@
 ################################################################################
 
 # load required libraries
+library(reticulate)
+use_virtualenv("daniel")
 library(simChef)
 library(mmrm)
 library(glmmTMB)
@@ -19,7 +21,7 @@ library(microbenchmark)
 
 # source the R scripts
 sim_functions_files <- list.files(
-  c("R/dgp", "R/method", "R/eval", "R/viz"),
+  c("R/dgp", "R/method", "R/eval", "R/viz", "R/customizations"),
   pattern = "*.R$", full.names = TRUE, ignore.case = TRUE
 )
 sapply(sim_functions_files, source)
@@ -30,7 +32,7 @@ csh_cov_mat <- compute_csh_matrix()
 toep_cov_mat <- toeplitz(c(1, 0.5, 0.25, 0.125, rep(0, 6)))
 
 # set the sample size
-n_obs <- 600
+n_obs <- 200
 
 # dgps with no treatment effect
 no_effect_us_dgp <- create_dgp(
@@ -157,8 +159,8 @@ type_2_error_rate_eval <- create_evaluator(
 
 # create the experiment
 experiment <- create_experiment(
-  name = "mmrm-benchmark-high-missingness-n-600-SAS",
-  save_dir = "results/high-miss/n-600-SAS"
+  name = glue::glue("mmrm-benchmark-high-missingness-n-{n_obs}-SAS"),
+  save_dir = glue::glue("results/high-miss/n-{n_obs}-SAS")
 ) %>%
   add_dgp(no_effect_us_dgp, name = "no_effect_us") %>%
   add_dgp(no_effect_csh_dgp, name = "no_effect_csh") %>%
@@ -188,31 +190,29 @@ experiment <- create_experiment(
   add_evaluator(type_1_error_rate_eval, name = "type_1_error_rate") %>%
   add_evaluator(type_2_error_rate_eval, name = "type_2_error_rate")
 
-# # Input here the name of the SAS container.
-# hostname <- "sabanesd-k2n72p-eu.ocean"
-#
-# # Do this to register host
-# session <- ssh::ssh_connect(hostname)
-# ssh_disconnect(session)
-#
-# # We can also be specific if there are multiple SAS containers we want to connect to.
-# cfg_name <- "sascfg_personal_2.py"
-# sasr.roche::setup_sasr_ocean(hostname, sascfg = cfg_name)
-# options(sascfg = cfg_name)
-#
-# # Test if it works.
-# df <- data.frame(a = 1, b = 2)
-# sasr::df2sd(df)
+# Input here the name of the SAS container.
+hostname <- "sabanesd-k2lza0-eu.ocean"
 
-# run the experiment
-# set.seed(713452)
-# results <- experiment$run(
-#   n_reps = 1000,
-#   save = TRUE,
-#   verbose = 2,
-#   checkpoint_n_reps = 10
-# )
+# Do this to register host
+session <- ssh::ssh_connect(hostname)
+ssh_disconnect(session)
+
+# We can also be specific if there are multiple SAS containers we want to connect to.
+cfg_name <- "sascfg_personal_3.py"
+sasr.roche::setup_sasr_ocean(hostname, sascfg = cfg_name)
+options(sascfg = cfg_name)
 
-source("R/format-replicate-results/helpers.R")
+# Test if it works.
+df <- data.frame(a = 1, b = 2)
+sasr::df2sd(df)
+
+# run the experiment
+set.seed(235234)
+results <- experiment$run(
+  n_reps = 1000,
+  save = TRUE,
+  verbose = 2,
+  checkpoint_n_reps = 100
+)
 
 format_fit_and_save(experiment)
diff --git a/simulations/missing-data-benchmarks/R/meals/meal-low-missingness-SAS.R b/simulations/missing-data-benchmarks/R/meals/meal-low-missingness-SAS.R
@@ -3,6 +3,8 @@
 ################################################################################
 
 # load required libraries
+library(reticulate)
+use_virtualenv("daniel")
 library(simChef)
 library(mmrm)
 library(glmmTMB)
@@ -19,7 +21,7 @@ library(microbenchmark)
 
 # source the R scripts
 sim_functions_files <- list.files(
-  c("R/dgp", "R/method", "R/eval", "R/viz"),
+  c("R/dgp", "R/method", "R/eval", "R/viz", "R/customizations"),
   pattern = "*.R$", full.names = TRUE, ignore.case = TRUE
 )
 sapply(sim_functions_files, source)
@@ -30,7 +32,7 @@ csh_cov_mat <- compute_csh_matrix()
 toep_cov_mat <- toeplitz(c(1, 0.5, 0.25, 0.125, rep(0, 6)))
 
 # set the sample size
-n_obs <- 600
+n_obs <- 200
 
 # dgps with no treatment effect
 no_effect_us_dgp <- create_dgp(
@@ -157,8 +159,8 @@ type_2_error_rate_eval <- create_evaluator(
 
 # create the experiment
 experiment <- create_experiment(
-  name = "mmrm-benchmark-low-missingness-n-600-SAS",
-  save_dir = "results/low-miss/n-600-SAS"
+  name = glue::glue("mmrm-benchmark-low-missingness-n-{n_obs}-SAS"),
+  save_dir = glue::glue("results/low-miss/n-{n_obs}-SAS")
 ) %>%
   add_dgp(no_effect_us_dgp, name = "no_effect_us") %>%
   add_dgp(no_effect_csh_dgp, name = "no_effect_csh") %>%
@@ -188,31 +190,29 @@ experiment <- create_experiment(
   add_evaluator(type_1_error_rate_eval, name = "type_1_error_rate") %>%
   add_evaluator(type_2_error_rate_eval, name = "type_2_error_rate")
 
-# # Input here the name of the SAS container.
-# hostname <- "sabanesd-byknxg-eu.ocean"
-#
-# # Do this to register host
-# session <- ssh::ssh_connect(hostname)
-# ssh_disconnect(session)
-#
-# # We can also be specific if there are multiple SAS containers we want to connect to.
-# cfg_name <- "sascfg_personal_3.py"
-# sasr.roche::setup_sasr_ocean(hostname, sascfg = cfg_name)
-# options(sascfg = cfg_name)
-#
-# # Test if it works.
-# df <- data.frame(a = 1, b = 2)
-# sasr::df2sd(df)
+# Input here the name of the SAS container.
+hostname <- "sabanesd-9nb6cb-eu.ocean"
 
-# run the experiment
-# set.seed(56129)
-# results <- experiment$run(
-#   n_reps = 1000,
-#   save = TRUE,
-#   verbose = 2,
-#   checkpoint_n_reps = 10
-# )
+# Do this to register host
+session <- ssh::ssh_connect(hostname)
+ssh_disconnect(session)
+
+# We can also be specific if there are multiple SAS containers we want to connect to.
+cfg_name <- "sascfg_personal_3.py"
+sasr.roche::setup_sasr_ocean(hostname, sascfg = cfg_name)
+options(sascfg = cfg_name)
 
-source("R/format-replicate-results/helpers.R")
+# Test if it works.
+df <- data.frame(a = 1, b = 2)
+sasr::df2sd(df)
+
+# run the experiment
+set.seed(56129)
+results <- experiment$run(
+  n_reps = 1000,
+  save = TRUE,
+  verbose = 2,
+  checkpoint_n_reps = 100
+)
 
 format_fit_and_save(experiment)
diff --git a/simulations/missing-data-benchmarks/R/meals/meal-no-missingness-SAS.R b/simulations/missing-data-benchmarks/R/meals/meal-no-missingness-SAS.R
@@ -3,6 +3,8 @@
 ################################################################################
 
 # load required libraries
+library(reticulate)
+use_virtualenv("daniel")
 library(simChef)
 library(mmrm)
 library(glmmTMB)
@@ -19,7 +21,7 @@ library(microbenchmark)
 
 # source the R scripts
 sim_functions_files <- list.files(
-  c("R/dgp", "R/method", "R/eval", "R/viz"),
+  c("R/dgp", "R/method", "R/eval", "R/viz", "R/customizations"),
   pattern = "*.R$", full.names = TRUE, ignore.case = TRUE
 )
 sapply(sim_functions_files, source)
@@ -30,7 +32,7 @@ csh_cov_mat <- compute_csh_matrix()
 toep_cov_mat <- toeplitz(c(1, 0.5, 0.25, 0.125, rep(0, 6)))
 
 # set the sample size
-n_obs <- 600
+n_obs <- 200
 
 # dgps with no treatment effect
 no_effect_us_dgp <- create_dgp(
@@ -148,8 +150,8 @@ type_2_error_rate_eval <- create_evaluator(
 
 # create the experiment
 experiment <- create_experiment(
-  name = "mmrm-benchmark-no-missingness-n-600-SAS",
-  save_dir = "results/no-miss/n-600-SAS"
+  name = glue::glue("mmrm-benchmark-no-missingness-n-{n_obs}-SAS"),
+  save_dir = glue::glue("results/no-miss/n-{n_obs}-SAS")
 ) %>%
   add_dgp(no_effect_us_dgp, name = "no_effect_us") %>%
   add_dgp(no_effect_csh_dgp, name = "no_effect_csh") %>%
@@ -178,33 +180,31 @@ experiment <- create_experiment(
   add_evaluator(coverage_eval, name = "coverage_rate") %>%
   add_evaluator(type_1_error_rate_eval, name = "type_1_error_rate") %>%
   add_evaluator(type_2_error_rate_eval, name = "type_2_error_rate")
-#
-# # Input here the name of the SAS container.
-# hostname <- "sabanesd-ddi1zu-eu.ocean"
-#
-# # Do this to register host
-# session <- ssh::ssh_connect(hostname)
-# ssh_disconnect(session)
-#
-# # We can also be specific if there are multiple SAS containers we want to connect to.
-# cfg_name <- "sascfg_personal_4.py"
-# sasr.roche::setup_sasr_ocean(hostname, sascfg = cfg_name)
-# options(sascfg = cfg_name)
-#
-# # Test if it works.
-# df <- data.frame(a = 1, b = 2)
-# sasr::df2sd(df)
-#
-# # run the experiment
-# set.seed(62342)
-# results <- experiment$run(
-#   n_reps = 1000,
-#   save = TRUE,
-#   verbose = 2,
-#   checkpoint_n_reps = 10
-# )
 
-source("R/format-replicate-results/helpers.R")
+# Input here the name of the SAS container.
+hostname <- "sabanesd-m55pe7-eu.ocean"
+
+# Do this to register host
+session <- ssh::ssh_connect(hostname)
+ssh_disconnect(session)
+
+# We can also be specific if there are multiple SAS containers we want to connect to.
+cfg_name <- "sascfg_personal_4.py"
+sasr.roche::setup_sasr_ocean(hostname, sascfg = cfg_name)
+options(sascfg = cfg_name)
+
+# Test if it works.
+df <- data.frame(a = 1, b = 2)
+sasr::df2sd(df)
+
+# run the experiment
+set.seed(62342)
+results <- experiment$run(
+  n_reps = 1000,
+  save = TRUE,
+  verbose = 2,
+  checkpoint_n_reps = 100
+)
 
 format_fit_and_save(experiment)
 
diff --git a/simulations/missing-data-benchmarks/sascfg_personal.py b/simulations/missing-data-benchmarks/sascfg_personal.py
@@ -1,2 +1,2 @@
 SAS_config_names=['default']
-default={'host': 'sabanesd-nwpfwh-eu.ocean', 'saspath': '/opt/sas/SASHome/SASFoundation/9.4/sas', 'ssh': '/usr/bin/ssh', 'encoding': 'latin1', 'options': ['-fullstimer'], 'tunnel': 9991, 'rtunnel': 9992}
+default={'host': 'sabanesd-w2yc52-eu.ocean', 'saspath': '/opt/sas/SASHome/SASFoundation/9.4/sas', 'ssh': '/usr/bin/ssh', 'encoding': 'latin1', 'options': ['-fullstimer'], 'tunnel': 9991, 'rtunnel': 9992}
diff --git a/simulations/missing-data-benchmarks/sascfg_personal_2.py b/simulations/missing-data-benchmarks/sascfg_personal_2.py
@@ -1,2 +1,2 @@
 SAS_config_names=['default']
-default={'host': 'sabanesd-k2n72p-eu.ocean', 'saspath': '/opt/sas/SASHome/SASFoundation/9.4/sas', 'ssh': '/usr/bin/ssh', 'encoding': 'latin1', 'options': ['-fullstimer'], 'tunnel': 9991, 'rtunnel': 9992}
+default={'host': 'sabanesd-n5i2d5-eu.ocean', 'saspath': '/opt/sas/SASHome/SASFoundation/9.4/sas', 'ssh': '/usr/bin/ssh', 'encoding': 'latin1', 'options': ['-fullstimer'], 'tunnel': 9991, 'rtunnel': 9992}
diff --git a/simulations/missing-data-benchmarks/sascfg_personal_3.py b/simulations/missing-data-benchmarks/sascfg_personal_3.py
@@ -1,2 +1,2 @@
 SAS_config_names=['default']
-default={'host': 'sabanesd-byknxg-eu.ocean', 'saspath': '/opt/sas/SASHome/SASFoundation/9.4/sas', 'ssh': '/usr/bin/ssh', 'encoding': 'latin1', 'options': ['-fullstimer'], 'tunnel': 9991, 'rtunnel': 9992}
+default={'host': 'sabanesd-k2lza0-eu.ocean', 'saspath': '/opt/sas/SASHome/SASFoundation/9.4/sas', 'ssh': '/usr/bin/ssh', 'encoding': 'latin1', 'options': ['-fullstimer'], 'tunnel': 9991, 'rtunnel': 9992}
diff --git a/simulations/missing-data-benchmarks/sascfg_personal_4.py b/simulations/missing-data-benchmarks/sascfg_personal_4.py
@@ -1,2 +1,2 @@
 SAS_config_names=['default']
-default={'host': 'sabanesd-ddi1zu-eu.ocean', 'saspath': '/opt/sas/SASHome/SASFoundation/9.4/sas', 'ssh': '/usr/bin/ssh', 'encoding': 'latin1', 'options': ['-fullstimer'], 'tunnel': 9991, 'rtunnel': 9992}
+default={'host': 'sabanesd-m55pe7-eu.ocean', 'saspath': '/opt/sas/SASHome/SASFoundation/9.4/sas', 'ssh': '/usr/bin/ssh', 'encoding': 'latin1', 'options': ['-fullstimer'], 'tunnel': 9991, 'rtunnel': 9992}