bringing updates to dev

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: gen3sis
 Type: Package
 Title: General Engine for Eco-Evolutionary Simulations
-Version: 1.5.11
+Version: 1.5.15
 Date: 2023-11-21
 Authors@R: c(
   person("ETH Zürich", role=c("cph")),

R/simulation.R

@@ -312,7 +312,7 @@ setup_distance_matrix <- function(config, data, vars) {
 update_extinction_times <- function(config, data, vars) {
   for (sp in data$all_species) {
     if(length(sp[["abundance"]])) {
-      data$phy$"Extinction.Time"[as.integer(sp[["id"]])] <- vars$ti
+      data$phy$"Extinction.Time"[as.integer(sp[["id"]])] <- vars$ti - 1
     }
   }
   return(list(config = config, data = data, vars = vars))

R/skeleton_config.R

@@ -5,8 +5,13 @@
 # empty skeleton config
 # internal helper: returns a single compiled string used by write_config_skeleton()
 
+#' create a skeleton config string from scratch
+#' @details create a skeleton config string from scratch
+#'
+#' @return a string containing the skeleton config
+#' @noRd
 skeleton_config <- function(){
-paste0(c('
+  paste0(c('
 ######################################
 ###            METADATA            ###
 ######################################
@@ -15,7 +20,7 @@ paste0(c('
 # Version: 1.0
 #
 # Author:
-#', paste0("# Date: ", format(Sys.Date(), format="%d.%m.%Y")),                          
+# ', paste0("# Date: ", format(Sys.Date(), format="%d.%m.%Y")),                          
 '#
 # Landscape:
 #

inst/extdata/CaseStudy1/reference_saves/phy.nex

@@ -1,5 +1,5 @@
 #NEXUS
 begin trees;
-Tree tree = (((species1:5,species4:1):0,species3:5):0,species2:2):0;
+Tree tree = (((species1:5,species4:2):0,species3:5):0,species2:3):0;
 end;
 [!Tree generated with the gen3sis R package, following convention of TreeSim and TreeSimGM r-packages]

tests/testthat/test-gen3sis_main.R

@@ -17,4 +17,5 @@ test_that("run_simulation works", {
   ref_summary <- readRDS(file.path(datapath, "reference_saves", "sgen3sis_summary.rds"))
   expect_true(all.equal(ref_summary, s$summary))
   expect_true(tools::md5sum(file.path(s$parameters$directories$output, "phy.nex")) == tools::md5sum(file.path(datapath, "reference_saves", "phy.nex")))
+  expect_true(tools::md5sum(file.path(s$parameters$directories$output, "phy.txt")) == tools::md5sum(file.path(datapath, "reference_saves", "phy.txt")))
 })