Merge branch 'main' into vectorise-spectral-density

NEWS.md

@@ -17,6 +17,8 @@
 - The default stan control options have been updated from `list(adapt_delta = 0.95, max_treedepth = 15)` to `list(adapt_delta = 0.9, max_treedepth = 12)` due to improved performance and to reduce the runtime of the default parameterisations. By @seabbs in #742 and reviewed by @jamesmbaazam.
 - Initialisation has been simplified by sampling directly from the priors, where possible, rather than from a constrained space. By @seabbs in #742 and reviewed by @jamesmbaazam.
 - Unnecessary normalisation of delay priors has been removed. By @seabbs in #742 and reviewed by @jamesmbaazam.
+- Ornstein-Uhlenbeck and 5 / 2 Matérn kernels have been added. By @sbfnk in # and reviewed by @.
+- Optimised convolution code to take into account the relative length of the vectors being convolved. See #745 by @seabbs and reviewed by @jamesmbaazam.
 - Switch to broadcasting the day of the week effect. By @seabbs in #746 and reviewed by @jamesmbaazam.
 - A warning is now thrown if nonparametric PMFs passed to delay options have consecutive tail values that are below a certain low threshold as these lead to loss in speed with little gain in accuracy. By @jamesmbaazam in #752 and reviewed by @seabbs.
 

inst/stan/functions/convolve.stan

@@ -1,36 +1,100 @@
-// convolve two vectors as a backwards dot product
-// y vector should be reversed
-// limited to the length of x and backwards looking for x indexes
+/**
+ * Calculate convolution indices for the case where s <= xlen
+ *
+ * @param s Current position in the output vector
+ * @param xlen Length of the x vector
+ * @param ylen Length of the y vector
+ * @return An array of integers: {start_x, end_x, start_y, end_y}
+ */
+array[] int calc_conv_indices_xlen(int s, int xlen, int ylen) {
+  int s_minus_ylen = s - ylen;
+  int start_x = max(1, s_minus_ylen + 1);
+  int end_x = s;
+  int start_y = max(1, 1 - s_minus_ylen);
+  int end_y = ylen;
+  return {start_x, end_x, start_y, end_y};
+}
+
+/**
+ * Calculate convolution indices for the case where s > xlen
+ *
+ * @param s Current position in the output vector
+ * @param xlen Length of the x vector
+ * @param ylen Length of the y vector
+ * @return An array of integers: {start_x, end_x, start_y, end_y}
+ */
+array[] int calc_conv_indices_len(int s, int xlen, int ylen) {
+  int s_minus_ylen = s - ylen;
+  int start_x = max(1, s_minus_ylen + 1);
+  int end_x = xlen;
+  int start_y = max(1, 1 - s_minus_ylen);;
+  int end_y = ylen + xlen - s;
+  return {start_x, end_x, start_y, end_y};
+}
+
+/**
+ * Convolve a vector with a reversed probability mass function.
+ *
+ * This function performs a discrete convolution of two vectors, where the second vector
+ * is assumed to be an already reversed probability mass function.
+ *
+ * @param x The input vector to be convolved.
+ * @param y The already reversed probability mass function vector.
+ * @param len The desired length of the output vector.
+ * @return A vector of length `len` containing the convolution result.
+ * @throws If `len` is not of equal length to the sum of the lengths of `x` and `y`.
+ */
 vector convolve_with_rev_pmf(vector x, vector y, int len) {
-    int xlen = num_elements(x);
-    int ylen = num_elements(y);
-    vector[len] z;
-    if (xlen + ylen <= len) {
-      reject("convolve_with_rev_pmf: len is longer then x and y combined");
-    }
-    for (s in 1:len) {
-      z[s] = dot_product(
-        x[max(1, (s - ylen + 1)):min(s, xlen)],
-        y[max(1, ylen - s + 1):min(ylen, ylen + xlen - s)]
-      );
+  int xlen = num_elements(x);
+  int ylen = num_elements(y);
+  vector[len] z;
+
+  if (xlen + ylen - 1 < len) {
+    reject("convolve_with_rev_pmf: len is longer than x and y convolved");
+  }
+
+  if (xlen > len) {
+    reject("convolve_with_rev_pmf: len is shorter than x");
+  }
+
+  for (s in 1:xlen) {
+    array[4] int indices = calc_conv_indices_xlen(s, xlen, ylen);
+    z[s] = dot_product(x[indices[1]:indices[2]], y[indices[3]:indices[4]]);
+  }
+
+  if (len > xlen) {
+    for (s in (xlen + 1):len) {
+      array[4] int indices = calc_conv_indices_len(s, xlen, ylen);
+      z[s] = dot_product(x[indices[1]:indices[2]], y[indices[3]:indices[4]]);
     }
-   return(z);
   }
+
+  return z;
+}
 
-
-// convolve latent infections to reported (but still unobserved) cases
+/**
+ * Convolve infections to reported cases.
+ *
+ * This function convolves a vector of infections with a reversed delay
+ * distribution to produce a vector of reported cases.
+ *
+ * @param infections A vector of infection counts.
+ * @param delay_rev_pmf A vector representing the reversed probability mass
+ * function of the delay distribution.
+ * @param seeding_time The number of initial time steps to exclude from the
+ * output.
+ * @return A vector of reported cases, starting from `seeding_time + 1`.
+ */
 vector convolve_to_report(vector infections,
                           vector delay_rev_pmf,
                           int seeding_time) {
   int t = num_elements(infections);
-  vector[t - seeding_time] reports;
-  vector[t] unobs_reports = infections;
   int delays = num_elements(delay_rev_pmf);
-  if (delays) {
-    unobs_reports = convolve_with_rev_pmf(unobs_reports, delay_rev_pmf, t);
-    reports = unobs_reports[(seeding_time + 1):t];
-  } else {
-    reports = infections[(seeding_time + 1):t];
+
+  if (delays == 0) {
+    return infections[(seeding_time + 1):t];
   }
-  return(reports);
+
+  vector[t] unobs_reports = convolve_with_rev_pmf(infections, delay_rev_pmf, t);
+  return unobs_reports[(seeding_time + 1):t];
 }

inst/stan/functions/delays.stan

@@ -43,7 +43,7 @@ vector get_delay_rev_pmf(
         pmf[1:new_len] = new_variable_pmf;
       } else { // subsequent delay to be convolved
         pmf[1:new_len] = convolve_with_rev_pmf(
-          pmf[1:current_len], reverse_mf(new_variable_pmf), new_len
+          pmf[1:current_len], reverse(new_variable_pmf), new_len
         );
       }
     } else { // nonparametric
@@ -54,7 +54,7 @@ vector get_delay_rev_pmf(
         pmf[1:new_len] = delay_np_pmf[start:end];
       } else { // subsequent delay to be convolved
         pmf[1:new_len] = convolve_with_rev_pmf(
-          pmf[1:current_len], reverse_mf(delay_np_pmf[start:end]), new_len
+          pmf[1:current_len], reverse(delay_np_pmf[start:end]), new_len
         );
       }
     }
@@ -70,7 +70,7 @@ vector get_delay_rev_pmf(
     pmf = cumulative_sum(pmf);
   }
   if (reverse_pmf) {
-    pmf = reverse_mf(pmf);
+    pmf = reverse(pmf);
   }
   return pmf;
 }

inst/stan/functions/pmfs.stan

@@ -30,36 +30,3 @@ vector discretised_pmf(vector params, int n, int dist) {
   }
   return(exp(lpmf));
 }
-
-// reverse a mf
-vector reverse_mf(vector pmf) {
-  int pmf_length = num_elements(pmf);
-  vector[pmf_length] rev_pmf;
-  for (d in 1:pmf_length) {
-    rev_pmf[d] = pmf[pmf_length - d + 1];
-  }
-  return rev_pmf;
-}
-
-vector rev_seq(int base, int len) {
-  vector[len] seq;
-  for (i in 1:len) {
-    seq[i] = len + base - i;
-  }
-  return(seq);
-}
-
-real rev_pmf_mean(vector rev_pmf, int base) {
-  int len = num_elements(rev_pmf);
-  vector[len] rev_pmf_seq = rev_seq(base, len);
-  return(dot_product(rev_pmf_seq, rev_pmf));
-}
-
-real rev_pmf_var(vector rev_pmf, int base, real mean) {
-  int len = num_elements(rev_pmf);
-  vector[len] rev_pmf_seq = rev_seq(base, len);
-  for (i in 1:len) {
-    rev_pmf_seq[i] = pow(rev_pmf_seq[i], 2);
-  }
-  return(dot_product(rev_pmf_seq, rev_pmf) - pow(mean, 2));
-}

tests/testthat/test-stan-convole.R

@@ -1,7 +1,21 @@
 skip_on_cran()
 skip_on_os("windows")
 
-test_that("convolve can combine two pmfs as expected", {
+# Test calc_conv_indices_xlen function
+test_that("calc_conv_indices_xlen calculates correct indices", {
+  expect_equal(calc_conv_indices_xlen(1, 5, 3), c(1, 1, 3, 3))
+  expect_equal(calc_conv_indices_xlen(3, 5, 3), c(1, 3, 1, 3))
+  expect_equal(calc_conv_indices_xlen(5, 5, 3), c(3, 5, 1, 3))
+})
+
+# Test calc_conv_indices_len function
+test_that("calc_conv_indices_len calculates correct indices", {
+  expect_equal(calc_conv_indices_len(6, 5, 3), c(4, 5, 1, 2))
+  expect_equal(calc_conv_indices_len(7, 5, 3), c(5, 5, 1, 1))
+  expect_equal(calc_conv_indices_len(8, 5, 3), c(6, 5, 1, 0))
+})
+
+test_that("convolve_with_rev_pmf can combine two pmfs as expected", {
   expect_equal(
     convolve_with_rev_pmf(c(0.1, 0.2, 0.7), rev(c(0.1, 0.2, 0.7)), 5),
     c(0.01, 0.04, 0.18, 0.28, 0.49),
@@ -14,7 +28,7 @@ test_that("convolve can combine two pmfs as expected", {
   )
 })
 
-test_that("convolve performs the same as a numerical convolution", {
+test_that("convolve_with_rev_pmf performs the same as a numerical convolution", {
   # Sample and analytical PMFs for two Poisson distributions
   x <- rpois(100000, 3)
   xpmf <- dpois(0:20, 3)
@@ -32,7 +46,7 @@ test_that("convolve performs the same as a numerical convolution", {
   expect_lte(sum(abs(conv_cdf - cdf)), 0.1)
 })
 
-test_that("convolve_dot_product can combine vectors as we expect", {
+test_that("convolve_with_rev_pmf can combine vectors as we expect", {
   expect_equal(
     convolve_with_rev_pmf(c(0.1, 0.2, 0.7), rev(c(0.1, 0.2, 0.7)), 3),
     c(0.01, 0.04, 0.18),
@@ -54,3 +68,12 @@ test_that("convolve_dot_product can combine vectors as we expect", {
     x
   )
 })
+
+test_that("convolve_dot_product can combine two vectors where x > y and len = x", {
+  x <- c(1, 2, 3, 4, 5)
+  y <- c(1, 2, 3)
+  expect_equal(
+    convolve_with_rev_pmf(x, rev(y), 5),
+    c(1, 4, 10, 16, 22)
+  )
+})

tests/testthat/test-stan-secondary.R

@@ -4,7 +4,7 @@ skip_on_os("windows")
 # test primary reports and observations
 reports <- rep(10, 20)
 obs <- rep(4, 20)
-delay_rev_pmf <- reverse_mf(discretised_pmf(c(log(3), 0.1), 5, 0))
+delay_rev_pmf <- rev(discretised_pmf(c(log(3), 0.1), 5, 0))
 scaled <- reports * 0.1
 convolved <- rep(1e-5, 20) + convolve_to_report(scaled, delay_rev_pmf, 0)