Merge pull request #84 from MangiolaLaboratory/cmdstanr

Cmdstanr

Author: stemangiola

.Rbuildignore

@@ -1,6 +1,19 @@
+^\.github$
+^LICENSE\.md$
+^README\.md$
+^README\.rmd$
+^\.gitignore$
 ^sccomp\.Rproj$
+^README_files$
 ^\.Rproj\.user$
-^\.github
+^NOTICE$
+^\.Rhistory$
+^\.Rbuildignore$
+^\.RData$
+^dev$
+sccomp_draws_files*
+src/stanExport*
+src/Rcpp*
 ^\.git
 ^README*
 ^dev
@@ -13,3 +26,4 @@ model_glm_dirichlet_multinomial_imputation.rds
 ^doc$
 ^Meta$
 sccomp_draws_files
+

.gitignore

@@ -2,8 +2,8 @@
 .Rhistory
 .RData
 .Ruserdata
-README_cache/*
-vignettes/introduction_cache*
+.Rapp.history
+inst/doc
 sccomp.Rproj
 Meta
 doc

DESCRIPTION

@@ -1,24 +1,22 @@
 Package: sccomp
 Title: Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data
-Version: 1.7.15
+Version: 1.7.16
 Authors@R: c(person("Stefano", "Mangiola", email = "mangiolastefano@gmail.com",
                   role = c("aut", "cre"))
                   )
 Description: A robust and outlier-aware method for testing differential tissue composition from single-cell data. This model can infer changes in tissue composition and heterogeneity, and can produce realistic data simulations based on any existing dataset. This model can also transfer knowledge from a large set of integrated datasets to increase accuracy further.
 License: GPL-3 
+URL: https://github.com/MangiolaLaboratory/sccomp
+BugReports: https://github.com/MangiolaLaboratory/sccomp/issues
 Encoding: UTF-8
-LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
-Biarch: true
-Depends: 
-    R (>= 4.2.0)
-Imports: 
-    methods,
-    Rcpp (>= 0.12.0),
-    RcppParallel (>= 5.0.1),
-    rstantools (>= 2.1.1),
-    rstan (>= 2.26.0),
+RoxygenNote: 7.3.2
+Depends: R (>= 4.2.0)
+Imports:
+    instantiate (>= 0.2.3),
+    callr,
+    fs,
+    stats,
     SeuratObject,
     SingleCellExperiment,
     parallel,
@@ -40,44 +38,27 @@ Imports:
     readr,
     scales,
     stringr,
-    glue
+    glue,
+    withr
 Suggests:
+    cmdstanr (>= 0.6.0),
+    knitr,
+    rmarkdown,
     BiocStyle,
     testthat (>= 3.0.0),
     markdown,
     knitr,
     loo,
+    prettydoc,
     tidyseurat,
     tidySingleCellExperiment,
-    prettydoc
-Enhances:
-    furrr,
-    extraDistr
-LinkingTo: 
-    BH (>= 1.66.0),
-    Rcpp (>= 0.12.0),
-    RcppEigen (>= 0.3.3.3.0),
-    RcppParallel (>= 5.0.1),
-    rstan (>= 2.26.0),
-    StanHeaders (>= 2.26.0)
-SystemRequirements: GNU make
-VignetteBuilder: 
-    knitr
-RdMacros:
-    lifecycle
-biocViews: 
-    ImmunoOncology, 
-    Normalization, 
-    Sequencing, 
-    RNASeq, 
-    Software, 
-    GeneExpression,
-    Transcriptomics, 
-    SingleCell, 
-    Clustering
-LazyDataCompression: xz
-Config/testthat/edition: 3
-URL: https://github.com/stemangiola/sccomp
-BugReports: https://github.com/stemangiola/sccomp/issues
+    bayesplot,
+    posterior
+Remotes:
+    wlandau/instantiate
 Additional_repositories:
     https://mc-stan.org/r-packages/
+SystemRequirements: CmdStan (https://mc-stan.org/users/interfaces/cmdstan)
+biocViews: Bayesian, Regression, DifferentialExpression, SingleCell
+LazyData: true
+VignetteBuilder: knitr

NAMESPACE

@@ -16,43 +16,40 @@ S3method(sccomp_remove_unwanted_variation,sccomp_tbl)
 S3method(sccomp_replicate,sccomp_tbl)
 S3method(sccomp_test,sccomp_tbl)
 S3method(simulate_data,tbl)
+export(get_output_samples)
 export(plot_1D_intervals)
 export(plot_2D_intervals)
-export(plot_summary)
 export(sccomp_boxplot)
 export(sccomp_estimate)
-export(sccomp_glm)
 export(sccomp_predict)
 export(sccomp_proportional_fold_change)
 export(sccomp_remove_outliers)
 export(sccomp_remove_unwanted_variation)
 export(sccomp_replicate)
 export(sccomp_test)
 export(simulate_data)
-export(test_contrasts)
-import(Rcpp)
-import(SeuratObject)
 import(dplyr)
 import(ggplot2)
-import(lifecycle)
-import(methods)
-import(rstantools)
-importFrom(RcppParallel,CxxFlags)
-importFrom(RcppParallel,RcppParallelLibs)
 importFrom(SingleCellExperiment,colData)
 importFrom(SingleCellExperiment,counts)
-importFrom(boot,logit)
 importFrom(dplyr,any_of)
 importFrom(dplyr,arrange)
+importFrom(dplyr,as_tibble)
 importFrom(dplyr,cummean)
+importFrom(dplyr,distinct)
 importFrom(dplyr,distinct_at)
 importFrom(dplyr,enquo)
 importFrom(dplyr,filter)
+importFrom(dplyr,group_by)
 importFrom(dplyr,if_else)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
+importFrom(dplyr,mutate_all)
+importFrom(dplyr,mutate_if)
+importFrom(dplyr,pull)
 importFrom(dplyr,row_number)
 importFrom(dplyr,select)
+importFrom(dplyr,summarise)
 importFrom(dplyr,with_groups)
 importFrom(forcats,fct_relevel)
 importFrom(forcats,fct_reorder)
@@ -66,6 +63,11 @@ importFrom(ggplot2,geom_vline)
 importFrom(ggplot2,ggplot)
 importFrom(ggrepel,geom_text_repel)
 importFrom(glue,glue)
+importFrom(instantiate,stan_cmdstan_exists)
+importFrom(instantiate,stan_package_compile)
+importFrom(instantiate,stan_package_model)
+importFrom(lifecycle,deprecate_warn)
+importFrom(lifecycle,is_present)
 importFrom(magrittr,"%$%")
 importFrom(magrittr,divide_by)
 importFrom(magrittr,equals)
@@ -89,6 +91,8 @@ importFrom(purrr,pmap)
 importFrom(purrr,reduce)
 importFrom(purrr,when)
 importFrom(readr,read_file)
+importFrom(readr,type_convert)
+importFrom(readr,write_file)
 importFrom(rlang,":=")
 importFrom(rlang,enquo)
 importFrom(rlang,ensym)
@@ -98,13 +102,6 @@ importFrom(rlang,quo_is_symbolic)
 importFrom(rlang,quo_name)
 importFrom(rlang,quo_squash)
 importFrom(rlang,set_names)
-importFrom(rstan,Rhat)
-importFrom(rstan,extract)
-importFrom(rstan,sampling)
-importFrom(rstan,sflist2stanfit)
-importFrom(rstan,stan_model)
-importFrom(rstan,summary)
-importFrom(rstan,vb)
 importFrom(scales,trans_new)
 importFrom(stats,C)
 importFrom(stats,as.formula)
@@ -119,10 +116,8 @@ importFrom(stringr,str_split)
 importFrom(stringr,str_subset)
 importFrom(stringr,str_trim)
 importFrom(tibble,add_column)
-importFrom(tibble,as_tibble)
 importFrom(tibble,deframe)
 importFrom(tibble,enframe)
-importFrom(tibble,rowid_to_column)
 importFrom(tidyr,complete)
 importFrom(tidyr,drop_na)
 importFrom(tidyr,expand_grid)
@@ -136,7 +131,9 @@ importFrom(tidyr,separate)
 importFrom(tidyr,spread)
 importFrom(tidyr,unite)
 importFrom(tidyr,unnest)
+importFrom(tidyselect,all_of)
 importFrom(tidyselect,eval_select)
 importFrom(tidyselect,last_col)
 importFrom(utils,data)
-useDynLib(sccomp, .registration = TRUE)
+importFrom(utils,install.packages)
+importFrom(utils,menu)

R/cmdstanr_safe.R

@@ -0,0 +1,42 @@
+
+
+sample_safe <- function(model, fx, ...) {
+  tryCatch(
+    {
+      # Attempt to run the arbitrary fx with additional arguments
+      result <- fx(model, ...)
+      return(result)
+    },
+    error = function(e) {
+      # Check if the error message is "model not compiled"
+      if (grepl("Model not compiled", e$message)) {
+        message("Model not compiled. Compiling.")
+        # Load the model with force=TRUE
+        model <- model$compile(cpp_options = list(stan_threads = TRUE)) # load_model("glm_multi_beta_binomial_generate_data", force = TRUE)
+        # Retry the arbitrary fx with additional arguments
+        result <- fx(model, ...)
+        return(result)
+      } else {
+        # If a different error, rethrow the error
+        stop(e)
+      }
+    }
+  )
+}
+
+
+sample_fx <- function(model, ...) {
+  model$sample(...)
+}
+
+pathfinder_fx <- function(model, ...) {
+  model$pathfinder(...)
+}
+
+variational_fx <- function(model, ...) {
+  model$variational(...)
+}
+
+generate_quantities_fx <- function(model, ...) {
+  model$generate_quantities(...)
+}