update stevebronder from ctb to auth

DESCRIPTION

@@ -17,7 +17,7 @@ Authors@R:
            email = "[email protected]", comment = c(ORCID = "0000-0003-1878-3253")),
       person(given = "Jacob", family = "Socolar", role = "ctb"),
       person(given = "Martin", family = "Modrák", role = "ctb"),
-      person(given = "Steve", family = "Bronder", role = "ctb"))
+      person(given = "Steve", family = "Bronder", role = "aut"))
 Description: A lightweight interface to 'Stan' <https://mc-stan.org>.
     The 'CmdStanR' interface is an alternative to 'RStan' that calls the command
     line interface for compilation and running algorithms instead of interfacing

doc/cmdstanr-internals.R

@@ -0,0 +1,214 @@
+params <-
+list(EVAL = FALSE)
+
+## ----settings-knitr, include=FALSE--------------------------------------------
+stopifnot(require(knitr))
+opts_chunk$set(
+  # collapse = TRUE,
+  dev = "png",
+  dpi = 150,
+  fig.asp = 0.618,
+  fig.width = 5,
+  out.width = "60%",
+  fig.align = "center",
+  comment = NA,
+  eval = if (isTRUE(exists("params"))) params$EVAL else FALSE
+)
+
+## ----setup, message=FALSE-----------------------------------------------------
+#  library(cmdstanr)
+#  check_cmdstan_toolchain(fix = TRUE, quiet = TRUE)
+
+## ----start-clean, include=FALSE-----------------------------------------------
+#  exe <- file.path(cmdstan_path(), "examples", "bernoulli", "bernoulli")
+#  unlink(exe)
+
+## ----compile------------------------------------------------------------------
+#  stan_file <- file.path(cmdstan_path(), "examples", "bernoulli", "bernoulli.stan")
+#  mod <- cmdstan_model(stan_file)
+#  mod$print()
+#  mod$stan_file()
+#  mod$exe_file()
+
+## ----already-compiled---------------------------------------------------------
+#  mod <- cmdstan_model(stan_file)
+
+## ----compile-options, eval=FALSE----------------------------------------------
+#  mod <- cmdstan_model(
+#    stan_file,
+#    force_recompile = TRUE,
+#    include_paths = "paths/to/directories/with/included/files",
+#    cpp_options = list(stan_threads = TRUE, STANC2 = TRUE)
+#  )
+
+## ----compile-method-----------------------------------------------------------
+#  unlink(mod$exe_file())
+#  mod <- cmdstan_model(stan_file, compile = FALSE)
+#  mod$exe_file() # not yet created
+#  mod$compile()
+#  mod$exe_file()
+
+## ----stan_file_pedantic-------------------------------------------------------
+#  stan_file_pedantic <- write_stan_file("
+#  data {
+#    int N;
+#    array[N] int y;
+#  }
+#  parameters {
+#    // should have <lower=0> but omitting to demonstrate pedantic mode
+#    real lambda;
+#  }
+#  model {
+#    y ~ poisson(lambda);
+#  }
+#  ")
+
+## ----pedantic-compile, collapse = TRUE----------------------------------------
+#  mod_pedantic <- cmdstan_model(stan_file_pedantic, pedantic = TRUE)
+
+## ----pedantic-check_syntax, collapse=TRUE-------------------------------------
+#  mod_pedantic$check_syntax(pedantic = TRUE)
+
+## ----pedantic-check_syntax-2, collapse=TRUE-----------------------------------
+#  file.remove(mod_pedantic$exe_file()) # delete compiled executable
+#  rm(mod_pedantic)
+#  
+#  mod_pedantic <- cmdstan_model(stan_file_pedantic, compile = FALSE)
+#  mod_pedantic$check_syntax(pedantic = TRUE)
+
+## ----stan_file_variables------------------------------------------------------
+#  stan_file_variables <- write_stan_file("
+#  data {
+#    int<lower=1> J;
+#    vector<lower=0>[J] sigma;
+#    vector[J] y;
+#  }
+#  parameters {
+#    real mu;
+#    real<lower=0> tau;
+#    vector[J] theta_raw;
+#  }
+#  transformed parameters {
+#    vector[J] theta = mu + tau * theta_raw;
+#  }
+#  model {
+#    target += normal_lpdf(tau | 0, 10);
+#    target += normal_lpdf(mu | 0, 10);
+#    target += normal_lpdf(theta_raw | 0, 1);
+#    target += normal_lpdf(y | theta, sigma);
+#  }
+#  ")
+#  mod_v <- cmdstan_model(stan_file_variables)
+#  variables <- mod_v$variables()
+
+## ----variables-list-names-----------------------------------------------------
+#  names(variables)
+#  names(variables$data)
+#  names(variables$parameters)
+#  names(variables$transformed_parameters)
+#  names(variables$generated_quantities)
+
+## ----variable-type-dims-------------------------------------------------------
+#  variables$data$J
+#  variables$data$sigma
+#  variables$parameters$tau
+#  variables$transformed_parameters$theta
+
+## ----compile-with-dir, eval = FALSE-------------------------------------------
+#  mod <- cmdstan_model(stan_file, dir = "path/to/directory/for/executable")
+
+## ----print-program-again------------------------------------------------------
+#  mod$print()
+
+## ----data-list, eval=FALSE----------------------------------------------------
+#  # data block has 'N' and 'y'
+#  data_list <- list(N = 10, y = c(0,1,0,0,0,0,0,0,0,1))
+#  fit <- mod$sample(data = data_list)
+
+## ----write_stan_json----------------------------------------------------------
+#  data_list <- list(N = 10, y = c(0,1,0,0,0,0,0,0,0,1))
+#  json_file <- tempfile(fileext = ".json")
+#  write_stan_json(data_list, json_file)
+#  cat(readLines(json_file), sep = "\n")
+
+## ----data-json, eval=FALSE----------------------------------------------------
+#  fit <- mod$sample(data = json_file)
+
+## ----data-rdump, eval=FALSE---------------------------------------------------
+#  rdump_file <- tempfile(fileext = ".data.R")
+#  rstan::stan_rdump(names(data_list), file = rdump_file, envir = list2env(data_list))
+#  cat(readLines(rdump_file), sep = "\n")
+#  fit <- mod$sample(data = rdump_file)
+
+## ----sample-tempdir, results = "hide"-----------------------------------------
+#  data_list <- list(N = 10, y = c(0,1,0,0,0,0,0,0,0,1))
+#  fit <- mod$sample(data = data_list)
+
+## ----output_files-------------------------------------------------------------
+#  fit$output_files()
+
+## ----gc-----------------------------------------------------------------------
+#  files <- fit$output_files()
+#  file.exists(files)
+#  
+#  rm(fit)
+#  gc()
+#  
+#  file.exists(files)
+
+## ----save_output_files, eval=FALSE--------------------------------------------
+#  # see ?save_output_files for info on optional arguments
+#  fit$save_output_files(dir = "path/to/directory")
+
+## ----output_dir, eval = FALSE-------------------------------------------------
+#  fit <- mod$sample(
+#    data = data_list,
+#    output_dir = "path/to/directory"
+#  )
+
+## ----refit, include=FALSE-----------------------------------------------------
+#  fit <- mod$sample(data = data_list)
+
+## ----csv-not-read-------------------------------------------------------------
+#  str(fit)
+
+## ----for-csv-reading----------------------------------------------------------
+#  draws <- fit$draws() # force CSVs to be read into R
+#  str(fit)
+
+## ----read_cmdstan_csv---------------------------------------------------------
+#  # see ?read_cmdstan_csv for info on optional arguments controlling
+#  # what information is read in
+#  csv_contents <- read_cmdstan_csv(fit$output_files())
+#  str(csv_contents)
+
+## ----as_cmdstan_fit-----------------------------------------------------------
+#  fit2 <- as_cmdstan_fit(fit$output_files())
+
+## ----save_latent_dynamics, results = "hide"-----------------------------------
+#  fit <- mod$sample(data = data_list, save_latent_dynamics = TRUE)
+
+## ----read-latent-dynamics-----------------------------------------------------
+#  fit$latent_dynamics_files()
+#  
+#  # read one of the files in
+#  x <- utils::read.csv(fit$latent_dynamics_files()[1], comment.char = "#")
+#  head(x)
+
+## ----explore-latent-dynamics--------------------------------------------------
+#  head(x[, c("theta", "p_theta", "g_theta")])
+
+## ----verbose-mode-------------------------------------------------------------
+#  options("cmdstanr_verbose"=TRUE)
+#  
+#  mod <- cmdstan_model(stan_file, force_recompile = TRUE)
+#  fit <- mod$sample(
+#    data = data_list,
+#    chains = 1,
+#    iter_warmup = 100,
+#    iter_sampling = 100
+#  )
+
+## ----include=FALSE------------------------------------------------------------
+#  options("cmdstanr_verbose" = FALSE)
+