rebase

Merge branch 'master' into cmdstanr

Conflicts:
	.gitignore
	R/functions_multi_beta_binomial.R
	R/methods.R
	README.md
	inst/figures/unnamed-chunk-11-1.png
	inst/figures/unnamed-chunk-12-1.png
	inst/figures/unnamed-chunk-14-1.png
	inst/figures/unnamed-chunk-15-1.png
	inst/stan/glm_multi_beta_binomial.stan

.Rbuildignore

@@ -1,11 +1,15 @@
 ^sccomp\.Rproj$
 ^\.Rproj\.user$
 ^\.github
+^\.git
 ^README*
 ^dev$
-^dev*
 ^dev/*
 ^rsconnect
 model_glm_dirichlet_multinomial.rds
 model_glm_dirichlet_multinomial_generate_quantities.rds
 model_glm_dirichlet_multinomial_imputation.rds
+^sccode_env
+^sccomp_draws_files
+^glm_multi*
+^model_glm*

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,12 @@
+Thanks for submitting an issue.
+
+Please add the following information to the issue
+
+1. Describe the issue/bug
+2. Print out the input dataset immediately before the bug occurs
+3. Paste the code immediately leading to the bug
+4. Print out of the output, if any
+5. Print out of the complete error/warning message, if any
+6. sessionInfo()
+
+Thanks!

.gitignore

@@ -38,3 +38,6 @@ glm_multi_beta_binomial_cmdstanr
 glm_multi_beta_binomial_cmdstanr.rds
 glm_multi_beta_binomial_cmdstanr.stan
 sccomp_draws_files
+glm_multi_beta_binomial_generate_cmdstanr
+glm_multi_beta_binomial_generate_cmdstanr.rds
+glm_multi_beta_binomial_generate_cmdstanr.stan

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: sccomp
 Title: Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data
-Version: 0.99.18
+Version: 0.99.30
 Authors@R: c(person("Stefano", "Mangiola", email = "mangiolastefano@gmail.com",
                   role = c("aut", "cre"))
                   )
@@ -9,7 +9,7 @@ License: GPL-3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.0
 Biarch: true
 Depends: 
     R (>= 4.1.0)
@@ -36,7 +36,10 @@ Imports:
     ggplot2,
     ggrepel,
     patchwork,
-    forcats
+    forcats,
+    readr,
+    scales,
+    stringr
 Suggests:
     BiocStyle,
     testthat (>= 3.0.0),

NAMESPACE

@@ -27,6 +27,7 @@ importFrom(dplyr,case_when)
 importFrom(dplyr,cummean)
 importFrom(dplyr,distinct_at)
 importFrom(dplyr,enquo)
+importFrom(dplyr,last_col)
 importFrom(dplyr,left_join)
 importFrom(dplyr,select)
 importFrom(dplyr,with_groups)
@@ -45,10 +46,12 @@ importFrom(purrr,map)
 importFrom(purrr,map2)
 importFrom(purrr,map2_lgl)
 importFrom(purrr,map_dbl)
+importFrom(purrr,map_dfc)
 importFrom(purrr,map_int)
 importFrom(purrr,map_lgl)
 importFrom(purrr,pmap)
 importFrom(purrr,when)
+importFrom(readr,read_file)
 importFrom(rlang,":=")
 importFrom(rlang,enquo)
 importFrom(rlang,ensym)
@@ -63,12 +66,17 @@ importFrom(rstan,sflist2stanfit)
 importFrom(rstan,stan_model)
 importFrom(rstan,summary)
 importFrom(rstan,vb)
+importFrom(scales,trans_new)
 importFrom(stats,C)
 importFrom(stats,model.matrix)
+importFrom(stats,quantile)
 importFrom(stats,rnorm)
 importFrom(stats,sd)
 importFrom(stats,setNames)
 importFrom(stats,terms)
+importFrom(stringr,str_detect)
+importFrom(stringr,str_replace)
+importFrom(tibble,add_column)
 importFrom(tibble,as_tibble)
 importFrom(tibble,enframe)
 importFrom(tibble,rowid_to_column)