Merge pull request #72 from microbiome/case2

Case2

.github/workflows/check-bioc-devel.yml

@@ -171,6 +171,7 @@ jobs:
 
           # rspm is out of date
           install.packages("matrixStats", repos = "https://cran.rstudio.com/")
+          install.packages("foreach", repos = "https://cran.rstudio.com/")
 
           ## Pass #1 at installing dependencies
           message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: miaSim
 Type: Package
-Version: 1.5.4
+Version: 1.5.5
 Authors@R:
      c(person(given = "Yagmur", family = "Simsek", role = c("cre", "aut"),
               email = "[email protected]"),
@@ -18,7 +18,7 @@ Authors@R:
        person(given = "Leo", family = "Lahti", role = c("aut"),
               email = "[email protected]",
               comment = c(ORCID = "0000-0001-5537-637X"))
-	      )
+      )
 Title: Microbiome Data Simulation
 Description:
     Microbiome time series simulation with generalized Lotka-Volterra model,
@@ -41,6 +41,8 @@ Imports:
 Suggests:
     ape,
     cluster,
+    foreach,
+    doParallel,
     dplyr,
     GGally,
     ggplot2,

NAMESPACE

@@ -2,9 +2,9 @@
 
 export(.estimateAFromSimulations)
 export(.eventTimes)
-export(.generateSimulations)
 export(.rdirichlet)
 export(.simulationTimes)
+export(generateSimulations)
 export(powerlawA)
 export(randomA)
 export(randomE)

R/utils.R

@@ -295,7 +295,7 @@
 #'
 #'
 #' @export
-.generateSimulations <- function(model,
+generateSimulations <- function(model,
     params_list,
     param_iter = NULL,
     n_instances = 1,
@@ -331,7 +331,7 @@
                 params_list,
                 lapply(param_iter, "[[", i)
             )
-            simulations_local <- .generateSimulations(
+            simulations_local <- generateSimulations(
                 model,
                 params_list_local,
                 param_iter = NULL,