Merge pull request #9 from IsabelMarleen/dev

Correctly parse all valid test cases

.gitmodules

@@ -1,3 +0,0 @@
-[submodule "demes-spec"]
- path = tools/demes-spec
- url = https://github.com/popsim-consortium/demes-spec.git

R/helper.R

@@ -13,21 +13,23 @@ order_demes <- function(deme) {
 
  ordered_deme$demes[[i]]$name <- deme$demes[[i]]$name
  ordered_deme$demes[[i]]$description <- deme$demes[[i]]$description
+ ordered_deme$demes[[i]]$ancestors <- deme$demes[[i]]$ancestors
+ ordered_deme$demes[[i]]$proportions <- deme$demes[[i]]$proportions
  ordered_deme$demes[[i]]$start_time <- deme$demes[[i]]$start_time
 
  ordered_deme$demes[[i]]$epochs <- list()
- for (j in 1:length(deme$demes[[i]]$epochs)){
- ordered_deme$demes[[i]]$epochs[j][[1]] <- list()
-
- ordered_deme$demes[[i]]$epochs[[j]]$end_time <- deme$demes[[i]]$epochs[[j]]$end_time
- ordered_deme$demes[[i]]$epochs[[j]]$start_size <- deme$demes[[i]]$epochs[[j]]$start_size
- ordered_deme$demes[[i]]$epochs[[j]]$end_size <- deme$demes[[i]]$epochs[[j]]$end_size
- ordered_deme$demes[[i]]$epochs[[j]]$size_function <- deme$demes[[i]]$epochs[[j]]$size_function
- ordered_deme$demes[[i]]$epochs[[j]]$selfing_rate <- deme$demes[[i]]$epochs[[j]]$selfing_rate
- ordered_deme$demes[[i]]$epochs[[j]]$cloning_rate <- deme$demes[[i]]$epochs[[j]]$cloning_rate
+ if (length(deme$demes[[i]]$epochs) > 0){
+ for (j in 1:length(deme$demes[[i]]$epochs)){
+ ordered_deme$demes[[i]]$epochs[j][[1]] <- list()
+
+ ordered_deme$demes[[i]]$epochs[[j]]$end_time <- deme$demes[[i]]$epochs[[j]]$end_time
+ ordered_deme$demes[[i]]$epochs[[j]]$start_size <- deme$demes[[i]]$epochs[[j]]$start_size
+ ordered_deme$demes[[i]]$epochs[[j]]$end_size <- deme$demes[[i]]$epochs[[j]]$end_size
+ ordered_deme$demes[[i]]$epochs[[j]]$size_function <- deme$demes[[i]]$epochs[[j]]$size_function
+ ordered_deme$demes[[i]]$epochs[[j]]$selfing_rate <- deme$demes[[i]]$epochs[[j]]$selfing_rate
+ ordered_deme$demes[[i]]$epochs[[j]]$cloning_rate <- deme$demes[[i]]$epochs[[j]]$cloning_rate
+ }
  }
- ordered_deme$demes[[i]]$proportions <- deme$demes[[i]]$proportions
- ordered_deme$demes[[i]]$ancestors <- deme$demes[[i]]$ancestors
  }
 
  ordered_deme$migrations <- list()
@@ -58,22 +60,40 @@ order_demes <- function(deme) {
  return(ordered_deme)
 }
 
-conv_prop_vec <- function(demes){
+conv_prop_anc_vec <- function(demes){
  for (i in 1:length(demes$demes)){
  if (length(demes$demes[[i]]$proportions) > 0){
- demes$demes[[i]]$proportions <- as.double(unlist(demes$demes[[i]]$proportions))
+ demes$demes[[i]]$proportions <- as.double(demes$demes[[i]]$proportions)
  } else{
  demes$demes[[i]]$proportions <- vector(mode="double")
  }
+
+ if (length(demes$demes[[i]]$ancestors) > 0){
+ demes$demes[[i]]$ancestors <- unlist(demes$demes[[i]]$ancestors)
+ } else{
+ demes$demes[[i]]$ancestors <- vector(mode="character")
+ }
  }
 
  return(demes)
 }
 
+conv_migr <- function(demes){
+ if (length(demes$migrations) > 0){
+ for (j in 1:length(demes$migrations)){
+ if (length(demes$migrations[[j]]) > 0){
+ demes$migrations[[j]]$rate <- as.double(demes$migrations[[j]]$rate)
+ }
+ }
+ }
+ return(demes)
+}
+
 post_process_expected <- function(exp){
  exp <- order_demes(exp)
  exp <- convert_infinity(exp)
- exp <- conv_prop_vec(exp)
+ exp <- conv_prop_anc_vec(exp)
+ exp <- conv_migr(exp)
 
  return(exp)
 }

R/name_demes.R

@@ -3,7 +3,7 @@
 name_demes <- function(demes){
  deme_names <- c()
  for (i in 1:length(demes$demes)){
- deme_names[i] <- demes$demes[[1]]$name
+ deme_names[i] <- demes$demes[[i]]$name
  }
  names(demes$demes) <- deme_names
  return(demes)