Update ts_load/ts_save

bodkan · Oct 28, 2024 · a32be78 · a32be78
1 parent 6a35b87
commit a32be78
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Showing 4 changed files with 17 additions and 17 deletions.
diff --git a/tests/testthat/test-simulate-model.R b/tests/testthat/test-simulate-model.R
@@ -45,7 +45,7 @@ test_that("basic simulate_model() runs produce a tree-sequence file (SLiM)", {
     format = "files",
     data = data_list
   )
-  expect_s3_class(ts_load(norm_path(file.path(result$path, "slim.trees"))), "slendr_ts")
+  expect_s3_class(ts_read(norm_path(file.path(result$path, "slim.trees"))), "slendr_ts")
 })
 
 test_that("basic simulate_model() runs produce a tree-sequence file (msprime)", {
@@ -57,7 +57,7 @@ test_that("basic simulate_model() runs produce a tree-sequence file (msprime)",
     format = "files",
     data = data_list
   )
-  expect_s3_class(ts_load(norm_path(file.path(result$path, "msprime.trees"))), "slendr_ts")
+  expect_s3_class(ts_read(norm_path(file.path(result$path, "msprime.trees"))), "slendr_ts")
 })
 
 test_that("for customized files, data-generating functions must be provided", {
@@ -76,8 +76,8 @@ test_that("format = 'ts' allows only 'ts' and 'model' to be available in data fu
       engine = "slim",
       format = "ts",
       data = list(
-        ts = function(path, model) file.path(path, "slim.trees") %>% ts_load(model),
-        gt = function(path, model) file.path(path, "slim.trees") %>% ts_load(model) %>% ts_mutate(1e-8) %>% ts_genotypes()
+        ts = function(path, model) file.path(path, "slim.trees") %>% ts_read(model),
+        gt = function(path, model) file.path(path, "slim.trees") %>% ts_read(model) %>% ts_mutate(1e-8) %>% ts_genotypes()
       )
     ),
     "The following function arguments are not valid: \"path\"."
@@ -89,8 +89,8 @@ test_that("format = 'ts' allows only 'ts' and 'model' to be available in data fu
       sequence_length = 1e6, recombination_rate = 1e-8,
       engine = "slim",
       format = "files", data = list(
-        ts = function(path, model) file.path(path, "slim.trees") %>% ts_load(model),
-        gt = function(path, model) file.path(path, "slim.trees") %>% ts_load(model) %>% ts_mutate(1e-8) %>% ts_genotypes()
+        ts = function(path, model) file.path(path, "slim.trees") %>% ts_read(model),
+        gt = function(path, model) file.path(path, "slim.trees") %>% ts_read(model) %>% ts_mutate(1e-8) %>% ts_genotypes()
       )
     ))
   )
@@ -107,8 +107,8 @@ test_that("format = 'ts' allows only 'ts' and 'model' to be available in data fu
       engine = "msprime",
       format = "ts",
       data = list(
-        ts = function(path, model) file.path(path, "slim.trees") %>% ts_load(model),
-        gt = function(path, model) file.path(path, "slim.trees") %>% ts_load(model) %>% ts_mutate(1e-8) %>% ts_genotypes()
+        ts = function(path, model) file.path(path, "slim.trees") %>% ts_read(model),
+        gt = function(path, model) file.path(path, "slim.trees") %>% ts_read(model) %>% ts_mutate(1e-8) %>% ts_genotypes()
       )
     ),
     "The following function arguments are not valid: \"path\"."
@@ -120,8 +120,8 @@ test_that("format = 'ts' allows only 'ts' and 'model' to be available in data fu
       sequence_length = 1e6, recombination_rate = 1e-8,
       engine = "msprime",
       format = "files", data = list(
-        ts = function(path, model) file.path(path, "msprime.trees") %>% ts_load(model),
-        gt = function(path, model) file.path(path, "msprime.trees") %>% ts_load(model) %>% ts_mutate(1e-8) %>% ts_genotypes()
+        ts = function(path, model) file.path(path, "msprime.trees") %>% ts_read(model),
+        gt = function(path, model) file.path(path, "msprime.trees") %>% ts_read(model) %>% ts_mutate(1e-8) %>% ts_genotypes()
       )
     ))
   )
@@ -151,7 +151,7 @@ test_that("format = 'custom' allows only 'path' and 'model' to be available", {
       engine = "slim",
       format = "files",
       data = list(
-        gt = function(path, model) file.path(path, "slim.trees") %>% ts_load(model) %>% ts_mutate(1e-8) %>% ts_genotypes()
+        gt = function(path, model) file.path(path, "slim.trees") %>% ts_read(model) %>% ts_mutate(1e-8) %>% ts_genotypes()
       )
     )$gt,
     "data.frame"

diff --git a/tests/testthat/test-summarise-data.R b/tests/testthat/test-summarise-data.R
@@ -61,8 +61,8 @@ data <- simulate_model(
   engine = "slim",
   format = "files",
   data = list(
-    ts = function(path, model) file.path(path, "slim.trees") %>% ts_load(model),
-    samples = function(path, model) file.path(path, "slim.trees") %>% ts_load(model) %>% ts_names(split = "pop"),
+    ts = function(path, model) file.path(path, "slim.trees") %>% ts_read(model),
+    samples = function(path, model) file.path(path, "slim.trees") %>% ts_read(model) %>% ts_names(split = "pop"),
     stats = function(path) file.path(path, "stats.tsv") %>% read.table(header = TRUE)
   )
 )
@@ -90,7 +90,7 @@ test_that("summarise_data produces data frames for every summary function", {
 test_that("summarise_data can utilize pre-computed statistics as data (pre-defined data functions)", {
   data_functions <- list(
     ts_pi = function(path, model) {
-      ts <- file.path(path, "slim.trees") %>% ts_load(model)
+      ts <- file.path(path, "slim.trees") %>% ts_read(model)
       ts_diversity(ts, ts_names(ts, split = "pop"))
     },
     slim_pi = function(path) file.path(path, "stats.tsv") %>%
@@ -118,7 +118,7 @@ test_that("summarise_data can utilize pre-computed statistics as data (inline da
     format = "files",
     data = list(
       ts_pi = function(path, model) {
-        ts <- file.path(path, "slim.trees") %>% ts_load(model)
+        ts <- file.path(path, "slim.trees") %>% ts_read(model)
         ts_diversity(ts, ts_names(ts, split = "pop"))
       },
       slim_pi = function(path) file.path(path, "stats.tsv") %>%

diff --git a/vignettes/vignette-05-custom-engines.Rmd b/vignettes/vignette-05-custom-engines.Rmd
@@ -162,7 +162,7 @@ functions <- list(
 
 # data-generating functions for computing summary statistics
 data <- list(
-  ts = function(path) ts_load(file.path(path, "result.trees"))
+  ts = function(path) ts_read(file.path(path, "result.trees"))
 )
 ```
 

diff --git a/vignettes/vignette-07-selection.Rmd b/vignettes/vignette-07-selection.Rmd
@@ -148,7 +148,7 @@ simulate_model(
   model, priors,
   model_args = list(origin_pop = "EUR", target_pop = "EUR"),
   outputs = list(
-    ts = function(paths, model) ts_load(paths[1], model) %>% ts_mutate(1e-8),
+    ts = function(paths, model) ts_read(paths[1], model) %>% ts_mutate(1e-8),
     freq = function(paths) readr::read_tsv(paths[2]),
     paths
   )