rename to yeast

smskim · Jun 21, 2024 · 3f5e50e · 3f5e50e
1 parent def6dc1
commit 3f5e50e
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Showing 4 changed files with 32 additions and 32 deletions.
diff --git a/evaluate_on_real_world_data.R b/evaluate_on_real_world_data.R
@@ -20,8 +20,8 @@ source("methods/caa.R")
 source("methods/gavi.R")
 source("methods/gst.R")
 source("methods/msprt.R")
-source("methods/psst.R")
-source("methods/sst.R")
+source("methods/yeast.R")
+source("methods/pyeast.R")
 source("utils.R")
 
 
@@ -42,29 +42,29 @@ initialise_continuous_methods = function(robust_increment_std,
                                          expected_num_observations,
                                          actual_num_observations) {
   return(list(
-    # -- SST
-    SST = SST$new(
-      "SST",
+    # -- YEAST
+    YEAST = YEAST$new(
+      "YEAST",
       SIGNIFICANCE_LEVEL,
       sum(expected_num_observations),
       robust_increment_std
     ),
-    SSTnr = SST$new(
-      "SST-non-robust",
+    YEASTnr = YEAST$new(
+      "YEAST-non-robust",
       SIGNIFICANCE_LEVEL,
       sum(expected_num_observations),
       non_robust_increment_std
     ),
-    # -- pSST
-    pSST14 = pSST$new(
-      "pSST14",
+    # -- pYEAST
+    pYEAST14 = pYEAST$new(
+      "pYEAST14",
       SIGNIFICANCE_LEVEL,
       cumsum(expected_num_observations),
       robust_increment_std,
       cumsum(actual_num_observations)
     ),
-    pSST14nr = pSST$new(
-      "pSST14-non-robust",
+    pYEAST14nr = pYEAST$new(
+      "pYEAST14-non-robust",
       SIGNIFICANCE_LEVEL,
       cumsum(expected_num_observations),
       non_robust_increment_std,
@@ -197,12 +197,12 @@ clusterExport(
     "initialise_continuous_methods",
     "SequentialTest",
     "Bonferroni",
-    "SST",
+    "YEAST",
     "ell",
     "compute_convolution",
     "estimate_false_detection_rate_bound",
-    "compute_pSST_thresholds",
-    "pSST",
+    "compute_pYEAST_thresholds",
+    "pYEAST",
     "GAVI",
     "mSPRT",
     "CAA",
@@ -322,7 +322,7 @@ result_dt[, `:=`(
 )]
 
 methods = c(
-  "SST", "pSST14", "GAVI250", "GAVI500", "GAVI750",
+  "YEAST", "pYEAST14", "GAVI250", "GAVI500", "GAVI750",
   "mSPRT100", "mSPRT011", "mSPRT025",
   "GAVI250", "GAVI500", "GAVI750",
   "CAA", "Classical"

diff --git a/methods/psst.R → methods/pyeast.R b/methods/psst.R → methods/pyeast.R
@@ -61,7 +61,7 @@ estimate_false_detection_rate_bound = function(cumulative_num_observations_by_pe
 }
 
 
-compute_pSST_thresholds = function(expected_cumulative_num_observations_by_period,
+compute_pYEAST_thresholds = function(expected_cumulative_num_observations_by_period,
                                    increment_std,
                                    significance_level) {
   thresholds = (
@@ -82,8 +82,8 @@ compute_pSST_thresholds = function(expected_cumulative_num_observations_by_perio
 }
 
 
-pSST = R6Class(
-  "pSST",
+pYEAST = R6Class(
+  "pYEAST",
   inherit = SequentialTest,
   public = list(
     significance_level = NULL,
@@ -102,7 +102,7 @@ pSST = R6Class(
       super$initialize(name)
       self$significance_level = significance_level
       self$increment_std = increment_std
-      self$thresholds = compute_pSST_thresholds(
+      self$thresholds = compute_pYEAST_thresholds(
         expected_cumulative_num_observations_by_period,
         increment_std,
         significance_level
@@ -142,10 +142,10 @@ pSST = R6Class(
 
 # set.seed(2024)
 # print(round(measure_fdr(
-#   pSST$new("pSST7", 0.05, round((1:7) * (500 / 7)), 10), 10, 500, 1000
+#   pYEAST$new("pYEAST7", 0.05, round((1:7) * (500 / 7)), 10), 10, 500, 1000
 # ), 2))
 # 
 # set.seed(2024)
 # print(round(measure_fdr(
-#   pSST$new("pSST14", 0.05, round((1:14) * (500 / 14)), 10), 10, 500, 1000
+#   pYEAST$new("pYEAST14", 0.05, round((1:14) * (500 / 14)), 10), 10, 500, 1000
 # ), 2))
diff --git a/methods/sst.R → methods/yeast.R b/methods/sst.R → methods/yeast.R
@@ -2,8 +2,8 @@ source("methods/sequential_test.R")
 source("utils.R")
 
 
-SST = R6Class(
-  "SST",
+YEAST = R6Class(
+  "YEAST",
   inherit = SequentialTest,
   public = list(
     significance_level = NULL,
@@ -32,4 +32,4 @@ SST = R6Class(
 
 
 # set.seed(2024)
-# print(round(measure_fdr(SST$new("SST", 0.05, 500, 10), 10, 500, 1000), 2))
+# print(round(measure_fdr(YEAST$new("YEAST", 0.05, 500, 10), 10, 500, 1000), 2))
diff --git a/run_simulations.R b/run_simulations.R
@@ -4,8 +4,8 @@ source("methods/caa.R")
 source("methods/gavi.R")
 source("methods/gst.R")
 source("methods/msprt.R")
-source("methods/psst.R")
-source("methods/sst.R")
+source("methods/pyeast.R")
+source("methods/yeast")
 source("utils.R")
 
 
@@ -25,11 +25,11 @@ EFFECT_SIZES = c(0.0, 0.1, 0.2, 0.3, 0.4)
 
 increment_std = sqrt(2) * EVENT_VALUE_STD
 continuous_methods = list(
-  # -- SST
-  SST = SST$new("SST", SIGNIFICANCE_LEVEL, NUM_OBSERVATIONS, increment_std),
-  # -- pSST
-  pSST07 = pSST$new("pSST07", SIGNIFICANCE_LEVEL, round((1:7) * (NUM_OBSERVATIONS /  7)), increment_std),
-  pSST14 = pSST$new("pSST14", SIGNIFICANCE_LEVEL, round((1:14) * (
+  # -- YEAST
+  YEAST = YEAST$new("YEAST", SIGNIFICANCE_LEVEL, NUM_OBSERVATIONS, increment_std),
+  # -- pYEAST
+  pYEAST07 = pYEAST$new("pYEAST07", SIGNIFICANCE_LEVEL, round((1:7) * (NUM_OBSERVATIONS /  7)), increment_std),
+  pYEAST14 = pYEAST$new("pYEAST14", SIGNIFICANCE_LEVEL, round((1:14) * (
     NUM_OBSERVATIONS / 14
   )), increment_std),
   # -- mSPRT