Feature Complete + Tests

Genentech · Mar 27, 2024 · a959bd5 · a959bd5
1 parent 7abe6e2
commit a959bd5
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Showing 11 changed files with 438 additions and 79 deletions.
diff --git a/R/GridGrouped.R b/R/GridGrouped.R
@@ -13,14 +13,31 @@ NULL
 )
 
 #' @export
-GridGrouped <- function(groups = NULL, times = NULL) {
+GridGrouped <- function(groups, times = NULL) {
     .GridGrouped(
         groups = groups,
         times = times
     )
 }
 
 
+setValidity(
+    "GridGrouped",
+    function(object) {
+        if (!all(vapply(object@groups, is.character, logical(1)))) {
+            return("Each element of `groups` must be a character vector")
+        }
+        gnames <- names(object@groups)
+        gnames <- gnames[!is.na(gnames) & gnames != ""]
+        if (length(gnames) != length(object@groups)) {
+            return("Each element of `groups` must be named")
+        }
+        return(TRUE)
+    }
+)
+
+
+
 #' @export
 as.QuantityGenerator.GridGrouped <- function(object, data) {
     assert_class(data, "DataJoint")
@@ -76,6 +93,6 @@ as.QuantityCollapser.GridGrouped <- function(object, data) {
 }
 
 #' @export
-as.list.GridGrouped <- function(x) {
+as.list.GridGrouped <- function(x, ...) {
     x@groups
 }
diff --git a/R/SurvivalQuantities.R b/R/SurvivalQuantities.R
@@ -179,7 +179,7 @@ autoplot.SurvivalQuantities <- function(
     kmdf <- if (add_km) {
         subset(
             object@data,
-            as.list(object@grid, object@data)
+            as.list(object@grid, data = object@data)
         )
     } else {
         NULL
@@ -305,12 +305,14 @@ setMethod(
         template <- c(
             "SurvivalQuantities Object:",
             "    # of samples    = %d",
-            "    # of quantities = %d"
+            "    # of quantities = %d",
+            "    Type            = %s"
         )
         string <- sprintf(
             paste(template, collapse = "\n"),
             nrow(object@quantities),
-            ncol(object@quantities)
+            ncol(object@quantities),
+            object@type
         )
         cat("\n", string, "\n\n")
     }

diff --git a/inst/stan/lm-gsf/functions.stan b/inst/stan/lm-gsf/functions.stan
@@ -22,15 +22,14 @@ functions {
         return result;
     }
 
-    row_vector lm_predict_individual_patient(vector time, row_vector long_gq_parameters) {
-        int nrow = rows(time);
+    vector lm_predict_individual_patient(vector time, matrix long_gq_parameters) {
         return sld(
             time,
-            rep_vector(long_gq_parameters[1], nrow),
-            rep_vector(long_gq_parameters[2], nrow),
-            rep_vector(long_gq_parameters[3], nrow),
-            rep_vector(long_gq_parameters[4], nrow)
-        )';
+            long_gq_parameters[,1],
+            long_gq_parameters[,2],
+            long_gq_parameters[,3],
+            long_gq_parameters[,4]
+        );
     }
 }
 
diff --git a/inst/stan/lm-stein-fojo/functions.stan b/inst/stan/lm-stein-fojo/functions.stan
@@ -22,14 +22,13 @@ functions {
         );
         return result;
     }
-    row_vector lm_predict_individual_patient(vector time, row_vector long_gq_parameters) {
-        int nrow = rows(time);
+    vector lm_predict_individual_patient(vector time, matrix long_gq_parameters) {
         return sld(
             time,
-            rep_vector(long_gq_parameters[1], nrow),
-            rep_vector(long_gq_parameters[2], nrow),
-            rep_vector(long_gq_parameters[3], nrow)
-         )';
+            long_gq_parameters[,1],
+            long_gq_parameters[,2],
+            long_gq_parameters[,3]
+        );
     }
 }
 
diff --git a/tests/testthat/_snaps/LongitudinalQuantiles.md b/tests/testthat/_snaps/LongitudinalQuantiles.md
@@ -1,27 +1,29 @@
 # LongitudinalQuantities print method works as expected
 
     Code
-      ptgroups <- c("pt_011", "pt_061", "pt_001", "pt_002")
+      ptgroups <- c("pt_0011", "pt_0061", "pt_0001", "pt_0002")
       times <- seq(0, 100, by = 10)
-      samps_p1 <- LongitudinalQuantities(test_data_1$jsamples, ptgroups, times)
+      samps_p1 <- LongitudinalQuantities(test_data_1$jsamples, grid = GridFixed(
+        subjects = ptgroups, times = times))
       print(samps_p1)
     Output
       
-         LongitudinalQuantities Object:
-            # of Subjects     = 4
-            # of Time Points  = 11 
+       LongitudinalQuantities Object:
+          # of samples    = 100
+          # of quantities = 44 
       
 
 ---
 
     Code
-      ptgroups <- c("pt_011", "pt_061")
-      samps_p2 <- LongitudinalQuantities(test_data_1$jsamples, ptgroups)
+      ptgroups <- c("pt_0011", "pt_0061")
+      samps_p2 <- LongitudinalQuantities(test_data_1$jsamples, grid = GridFixed(
+        subjects = ptgroups))
       print(samps_p2)
     Output
       
-         LongitudinalQuantities Object:
-            # of Subjects     = 2
-            # of Time Points  = 201 
+       LongitudinalQuantities Object:
+          # of samples    = 100
+          # of quantities = 402 
       
 
diff --git a/tests/testthat/_snaps/Quantities.md b/tests/testthat/_snaps/Quantities.md
@@ -1,15 +1,13 @@
 # Quantities print method works as expected
 
     Code
-      raw_x1 <- matrix(1:12, ncol = 3)
-      raw_x2 <- matrix(21:32, ncol = 3)
-      pobj <- Quantities(list(raw_x1, raw_x2))
-      print(pobj)
+      raw_x <- matrix(1:10, ncol = 2)
+      x <- Quantities(quantities = raw_x, groups = c("a", "b"), times = c(10, 20))
+      print(x)
     Output
       
          Quantities Object:
-            # of Elements  = 2
-            # of Rows      = 4
-            # of Columns   = 3 
+            # of samples    = 5
+            # of quantities = 2 
       
 
diff --git a/tests/testthat/_snaps/SurvivalQuantities.md b/tests/testthat/_snaps/SurvivalQuantities.md
@@ -5,27 +5,29 @@
       ptgroups <- list(gtpt1 = sample(test_data_1$dat_os$pt, 20), gtpt2 = sample(
         test_data_1$dat_os$pt, 20), gtpt3 = sample(test_data_1$dat_os$pt, 20))
       times <- seq(0, 100, by = 10)
-      samps_p1 <- SurvivalQuantities(test_data_1$jsamples, ptgroups, times, type = "surv")
+      samps_p1 <- SurvivalQuantities(test_data_1$jsamples, grid = GridGrouped(groups = ptgroups,
+        times = times), type = "surv")
       print(samps_p1)
     Output
       
-         SurvivalQuantities Object:
-            Type              = surv
-            # of Groups       = 3
-            # of Time Points  = 11 
+       SurvivalQuantities Object:
+          # of samples    = 100
+          # of quantities = 33
+          Type            = surv 
       
 
 ---
 
     Code
       times <- seq(0, 100, by = 10)
-      samps_p2 <- SurvivalQuantities(test_data_1$jsamples, time_grid = times, type = "loghaz")
+      samps_p2 <- SurvivalQuantities(test_data_1$jsamples, grid = GridFixed(times = times),
+      type = "loghaz")
       print(samps_p2)
     Output
       
-         SurvivalQuantities Object:
-            Type              = loghaz
-            # of Groups       = 400
-            # of Time Points  = 11 
+       SurvivalQuantities Object:
+          # of samples    = 100
+          # of quantities = 4400
+          Type            = loghaz