Make seed optional argument, random if NULL resolves #8

duke-malaria-collaboratory · Nov 20, 2023 · 319a4a8 · 319a4a8
1 parent c6ed007
commit 319a4a8
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Showing 12 changed files with 62 additions and 28 deletions.
diff --git a/R/bistro.R b/R/bistro.R
@@ -53,7 +53,7 @@
 #' @param threads Number of threads to use when calculating log10_lrs.
 #'   [euroformix::contLikSearch()] argument. Default: 4
 #' @param seed Seed when calculating log10_lrs. [euroformix::contLikSearch()]
-#'   argument. Default: 1
+#'   argument. Default: NULL (no seed)
 #' @param time_limit Time limit in minutes to run the
 #'   [euroformix::contLikSearch()] function on 1 bloodmeal-human pair. Default:
 #'   3
@@ -102,7 +102,7 @@ bistro <-
            model_fw_stutt = FALSE,
            difftol = 1,
            threads = 4,
-           seed = 1,
+           seed = NULL,
            time_limit = 3,
            return_lrs = FALSE) {
     check_pkg_version("tidyr", utils::packageVersion("tidyr"), "1.3.0")

diff --git a/R/calc_log10_lrs.R b/R/calc_log10_lrs.R
@@ -25,7 +25,7 @@ calc_one_log10_lr <-
            model_fw_stutt = FALSE,
            difftol = 1,
            threads = 4,
-           seed = 1,
+           seed = NULL,
            time_limit = 3) {
     bloodmeal_profile <- bloodmeal_profiles |>
       dplyr::filter(SampleName == bloodmeal_id)
@@ -154,7 +154,7 @@ calc_log10_lrs <-
            model_fw_stutt = FALSE,
            difftol = 1,
            threads = 4,
-           seed = 1,
+           seed = NULL,
            time_limit = 3,
            check_inputs = TRUE) {
     if (check_inputs) {
@@ -197,7 +197,9 @@ calc_log10_lrs <-
       check_is_bool(model_fw_stutt, "model_fw_stutt")
       check_is_numeric(difftol, "difftol", pos = TRUE)
       check_is_numeric(threads, "threads", pos = TRUE)
-      check_is_numeric(seed, "seed")
+      if(!is.null(seed)){
+        check_is_numeric(seed, "seed")
+      }
       check_is_numeric(time_limit, "time_limit", pos = TRUE)
     }
 

diff --git a/R/checks.R b/R/checks.R
@@ -75,7 +75,9 @@ check_bistro_inputs <-
     check_is_bool(return_lrs, "return_lrs")
     check_is_numeric(difftol, "difftol", pos = TRUE)
     check_is_numeric(threads, "threads", pos = TRUE)
-    check_is_numeric(seed, "seed")
+    if(!is.null(seed)){
+      check_is_numeric(seed, "seed")
+    }
     check_is_numeric(time_limit, "time_limit", pos = TRUE)
   }
 

diff --git a/man/bistro.Rd b/man/bistro.Rd
diff --git a/man/calc_log10_lrs.Rd b/man/calc_log10_lrs.Rd
diff --git a/man/calc_one_log10_lr.Rd b/man/calc_one_log10_lr.Rd
diff --git a/man/check_bistro_inputs.Rd b/man/check_bistro_inputs.Rd
diff --git a/tests/testthat/_snaps/bistro.md b/tests/testthat/_snaps/bistro.md
@@ -2,7 +2,7 @@
 
     Code
       bistro(data.frame(bm_evid1), data.frame(hu_p1), pop_allele_freqs = pop_allele_freqs,
-      kit = "ESX17", peak_thresh = 200)
+      kit = "ESX17", peak_thresh = 200, seed = 1)
     Message
       1/17 markers in kit but not in pop_allele_freqs: AMEL
       Formatting bloodmeal profiles
@@ -24,7 +24,8 @@
 ---
 
     Code
-      bistro(bm_evid1, hu_p1, calc_allele_freqs = TRUE, kit = "ESX17", peak_thresh = 200)
+      bistro(bm_evid1, hu_p1, calc_allele_freqs = TRUE, kit = "ESX17", peak_thresh = 200,
+        seed = 1)
     Message
       Formatting bloodmeal profiles
       Removing 4 peaks under the threshold of 200 RFU.
@@ -46,7 +47,7 @@
 
     Code
       bistro(bm_evid1, human_profiles, pop_allele_freqs = pop_allele_freqs, kit = "ESX17",
-        peak_thresh = 200, return_lrs = TRUE)
+        peak_thresh = 200, seed = 1, return_lrs = TRUE)
     Message
       1/17 markers in kit but not in pop_allele_freqs: AMEL
       Formatting bloodmeal profiles

diff --git a/tests/testthat/_snaps/calc_log10_lrs.md b/tests/testthat/_snaps/calc_log10_lrs.md
@@ -3,7 +3,7 @@
     Code
       calc_one_log10_lr(bloodmeal_profiles_sub, "evid1", human_profiles,
         "00-JP0001-14_20142342311_NO-3241", pop_allele_freqs = pop_allele_freqs, kit = "ESX17",
-        peak_thresh = 200)
+        peak_thresh = 200, seed = 1)
     Output
       # A tibble: 1 x 7
         bloodmeal_id human_id               locus_count est_noc efm_noc log10_lr notes
@@ -15,7 +15,7 @@
     Code
       calc_one_log10_lr(bloodmeal_profiles_sub, "evid2", human_profiles,
         "00-JP0001-14_20142342311_NO-3241", pop_allele_freqs = pop_allele_freqs, kit = "ESX17",
-        peak_thresh = 200)
+        peak_thresh = 200, seed = 1)
     Output
       # A tibble: 1 x 7
         bloodmeal_id human_id               locus_count est_noc efm_noc log10_lr notes
@@ -27,7 +27,7 @@
     Code
       calc_one_log10_lr(bloodmeal_profiles_sub, "evid4", human_profiles,
         "00-JP0001-14_20142342311_NO-3241", pop_allele_freqs = pop_allele_freqs, kit = "ESX17",
-        peak_thresh = 200)
+        peak_thresh = 200, seed = 1)
     Output
       # A tibble: 1 x 7
         bloodmeal_id human_id               locus_count est_noc efm_noc log10_lr notes
@@ -38,7 +38,7 @@
 
     Code
       calc_one_log10_lr(bloodmeal_profiles_sub, "evid2", human_profiles, "P1",
-        pop_allele_freqs = pop_allele_freqs, kit = "ESX17", peak_thresh = 200)
+        pop_allele_freqs = pop_allele_freqs, kit = "ESX17", peak_thresh = 200, seed = 1)
     Output
       # A tibble: 1 x 7
         bloodmeal_id human_id locus_count est_noc efm_noc log10_lr notes           
@@ -61,7 +61,7 @@
 
     Code
       calc_log10_lrs(bm_profs, hu_profs, pop_allele_freqs = pop_allele_freqs, kit = "ESX17",
-        peak_thresh = 200, check_inputs = FALSE)
+        peak_thresh = 200, seed = 1, check_inputs = FALSE)
     Message
       # bloodmeal ids: 2
       # human ids: 1

diff --git a/tests/testthat/test-bistro.R b/tests/testthat/test-bistro.R
@@ -10,16 +10,26 @@ test_that("bistro works", {
       data.frame(hu_p1),
       pop_allele_freqs = pop_allele_freqs,
       kit = "ESX17",
-      peak_thresh = 200
+      peak_thresh = 200,
+      seed = 1
     )
   )
 
+  suppressMessages(expect_no_error(bistro(
+    data.frame(bm_evid1),
+    data.frame(hu_p1),
+    pop_allele_freqs = pop_allele_freqs,
+    kit = "ESX17",
+    peak_thresh = 200
+  )))
+
   expect_snapshot(bistro(
     bm_evid1,
     hu_p1,
     calc_allele_freqs = TRUE,
     kit = "ESX17",
-    peak_thresh = 200
+    peak_thresh = 200,
+    seed = 1
   ))
 
   expect_error(
@@ -38,6 +48,7 @@ test_that("bistro works", {
     pop_allele_freqs = pop_allele_freqs,
     kit = "ESX17",
     peak_thresh = 200,
+    seed = 1,
     return_lrs = TRUE
   ))
 })
diff --git a/tests/testthat/test-calc_log10_lrs.R b/tests/testthat/test-calc_log10_lrs.R
@@ -17,7 +17,8 @@ test_that("calc_log10_lrs works", {
       "00-JP0001-14_20142342311_NO-3241",
       pop_allele_freqs = pop_allele_freqs,
       kit = "ESX17",
-      peak_thresh = 200
+      peak_thresh = 200,
+      seed = 1
     )
   )
 
@@ -29,7 +30,8 @@ test_that("calc_log10_lrs works", {
       "00-JP0001-14_20142342311_NO-3241",
       pop_allele_freqs = pop_allele_freqs,
       kit = "ESX17",
-      peak_thresh = 200
+      peak_thresh = 200,
+      seed = 1
     )
   )
 
@@ -41,7 +43,8 @@ test_that("calc_log10_lrs works", {
       "00-JP0001-14_20142342311_NO-3241",
       pop_allele_freqs = pop_allele_freqs,
       kit = "ESX17",
-      peak_thresh = 200
+      peak_thresh = 200,
+      seed = 1
     )
   )
 
@@ -53,7 +56,8 @@ test_that("calc_log10_lrs works", {
       "P1",
       pop_allele_freqs = pop_allele_freqs,
       kit = "ESX17",
-      peak_thresh = 200
+      peak_thresh = 200,
+      seed = 1
     )
   )
 
@@ -77,7 +81,20 @@ test_that("calc_log10_lrs works", {
       pop_allele_freqs = pop_allele_freqs,
       kit = "ESX17",
       peak_thresh = 200,
+      seed = 1,
       check_inputs = FALSE
     )
   )
+
+  suppressMessages(expect_no_error(calc_log10_lrs(
+    bm_profs,
+    hu_profs,
+    pop_allele_freqs = pop_allele_freqs,
+    kit = "ESX17",
+    peak_thresh = 200,
+    # seed = 1,
+    check_inputs = TRUE
+  )))
+
+
 })
diff --git a/tests/testthat/test-identify_matches.R b/tests/testthat/test-identify_matches.R
@@ -11,7 +11,8 @@ test_that("identify_matches works", {
         human_profiles,
         pop_allele_freqs = pop_allele_freqs,
         kit = "ESX17",
-        peak_thresh = 200
+        peak_thresh = 200,
+        seed = 1
       )
     )