In stemangiola/RNAseq-noise-model:

#devtools::install(quick = TRUE,build_vignettes = FALSE)
devtools::load_all()

library(rstan)
rstan_options(auto_write = TRUE)
library(tidyverse)
library(RNASeqNoiseModel)
library(here)

simple_model_code = "
data {
  real x[5];
}

parameters {
  real mu;
}

model {
  x ~ normal(mu, 1);
}
"
simple_model = stan_model(model_code = simple_model_code)

second_simple_model = stan_model(model_code = "
data {
  real x[7];
}

parameters {
  real<lower=0> sigma;
}

model {
  x ~ normal(0, sigma);
}
")

num_data = 10
data_list = list()
for(i in 1:num_data) {
  data_list[[i]] = list(x = rnorm(5, i, 1))
}

res = sampling_multi(simple_model, data_list)
res[[1]]
res[[10]]

num_data = 5
data_list_mixed = list()
models = list()
for(i in 1:num_data) {
  data_list_mixed[[i]] = list(x = rnorm(5, i, 1))
  models[[i]] = simple_model
}

for(i in 1:num_data) {
  data_list_mixed[[i + num_data]] = list(x = rnorm(7, 0, i))
  models[[i + num_data]] = second_simple_model
}

res = sampling_multi(models, data_list_mixed)
res[[1]]
res[[5]]
res[[6]]
res[[10]]

Storing to files

num_data = 10
data_list = list()
for(i in 1:num_data) {
  data_list[[i]] = list(x = rnorm(5, i, 1))
}

if(!dir.exists(here("local_temp_data"))) {
  dir.create(here("local_temp_data"))
}


res = sampling_multi(simple_model, data_list, 
                     map_fun = sampling_multi_store_file_generator(here("local_temp_data"),"simple_fit"), 
                     combine_fun = c)

res[[1]]
res[[1]] %>% map(readRDS) %>% sflist2stanfit()
res[[10]]
res[[10]] %>% map(readRDS) %>% sflist2stanfit()

Control arguments

res = sampling_multi(simple_model, data_list, control = list(adapt_delta = 0.95))
res[[1]]@stan_args[[1]]$control$adapt_delta

Caching

cache_dir <- here("local_temp_data","test_cache")
if(!dir.exists(cache_dir)){
  dir.create(cache_dir)
}
res = sampling_multi(simple_model, data_list, cache_dir = cache_dir)
#Expect all read from cache
res_cached = sampling_multi(simple_model, data_list, cache_dir = cache_dir)

#Expect not read from cache - half data, half model
res_cached_cached_changed = sampling_multi(models, data_list_mixed, cache_dir = cache_dir)

stemangiola/RNAseq-noise-model documentation built on Oct. 18, 2019, 1:47 p.m.