update package

src/htrsim/DESCRIPTION

@@ -24,4 +24,8 @@ Imports:
     data.table,
     plyr,
     reshape2,
-    tidyr
+    tidyr,
+    S4Vectors,
+    readr,
+    testthat
+Config/testthat/edition: 3

src/htrsim/NAMESPACE

@@ -2,6 +2,7 @@
 
 export(estim.alpha)
 export(estim.mu)
+export(estim.mu_beta)
 export(generate_counts)
 export(handle_except)
 export(htrsim)
@@ -11,10 +12,12 @@ export(run.deseq)
 export(setup_countGener)
 import(BiocGenerics)
 import(DESeq2)
+import(S4Vectors)
 import(data.table)
 import(dplyr)
 import(plyr)
 import(purrr)
+import(readr)
 import(reshape2)
 import(stats)
 import(stringr)

src/htrsim/devtools_history.R

@@ -11,4 +11,8 @@ usethis::use_package("data.table")
 usethis::use_package("plyr")
 usethis::use_package("reshape2")
 usethis::use_package("tidyr")
+usethis::use_package("S4Vectors")
+usethis::use_package("readr")
+usethis::use_package("testthat")
+usethis::use_test("name")
 devtools::load_all()

src/htrsim/inst/extdata/public_bioDesign.csv

-sample;env;mutant;mutant_env
-Msn2D_KCl_rep1;kcl;msn2D;msn2D_kcl
-Msn2D_KCl_rep2;kcl;msn2D;msn2D_kcl
-Msn4D_KCl_rep1;kcl;msn4D;msn4D_kcl
-Msn4D_KCl_rep2;kcl;msn4D;msn4D_kcl
-Msn2D_control_rep1;control;msn2D;msn2D_control
-Msn2D_control_rep1;control;msn2D;msn2D_control
-Msn4D_control_rep1;control;msn4D;msn4D_control
-Msn4D_control_rep2;control;msn4D;msn4D_control
-WT_control_rep1;control;wt;wt_control
-WT_control_rep2;control;wt;wt_control
-WT_KCl_rep1;kcl;wt;wt_kcl
-WT_KCl_rep2;kcl;wt;wt_kcl
+sample;env;genotype
+WT_control_rep1;control;wt
+WT_control_rep2;control;wt
+WT_KCl_rep1;kcl;wt
+WT_KCl_rep2;kcl;wt
+Msn4D_control_rep1;control;msn4D
+Msn4D_control_rep2;control;msn4D
+Msn4D_KCl_rep1;kcl;msn4D
+Msn4D_KCl_rep2;kcl;msn4D
+Msn2D_control_rep1;control;msn2D
+Msn2D_control_rep2;control;msn2D
+Msn2D_KCl_rep1;kcl;msn2D
+Msn2D_KCl_rep2;kcl;msn2D