Streamline time wording in in-model doc

epinowcast · seabbs · Sep 20, 2022 · Jul 31, 2022 · Jul 31, 2022 · Jul 31, 2022
commit a68bf807a2f059cfa8b3b9099a3650a45b044f64
diff --git a/inst/stan/chunks/debug.stan b/inst/stan/chunks/debug.stan
@@ -24,7 +24,7 @@
         if (model_refp > 1) {
           print(refp_sd[i]);
         }
-        print("Unique report day hazards");
+        print("Unique reporting time hazards");
         print(srdlh);
         if (model_obs) {
           print("Overdispersion");
@@ -38,6 +38,6 @@
       j += is_inf(abs(srdlh[k])) ? 1 : 0;
     }
     if (j) {
-      print("Hazard effects on report date");
+      print("Hazard effects on reporting time");
       print(srdlh);
     }
diff --git a/inst/stan/epinowcast.stan b/inst/stan/epinowcast.stan
@@ -38,7 +38,7 @@ data {
   // Expectation model
   array[2] real eobs_lsd_p; // standard deviation for expected final obs
 
-  // Reference day model
+  // Reference time model
   int model_refp;
   int refp_fnrow;
   array[s] int refp_findex;
@@ -51,7 +51,7 @@ data {
   array[2] real refp_mean_beta_sd_p;
   array[2] real refp_sd_beta_sd_p; 
 
-  // Reporting day model
+  // Reporting time model
   int model_rep;
   int rep_t; // total number of reporting times (t + dmax - 1)
   int rep_fnrow; 
@@ -62,7 +62,7 @@ data {
   matrix[rep_fncol, rep_rncol + 1] rep_rdesign; 
   array[2] real rep_beta_sd_p;
 
-  // Missing reference date model
+  // Missing reference time model
   int model_miss;
   int miss_obs;
   int miss_fnindex;
@@ -100,7 +100,7 @@ transformed data{
   real logdmax = 5*log(dmax); // scaled maxmimum delay to log for crude bounds
   // prior mean of cases based on thoose observed
   vector[g] eobs_init = log(to_vector(latest_obs[1, 1:g]) + 1);
-  // if no reporting day effects use native probability for reference day
+  // if no reporting time effects use native probability for reference time
   // effects, i.e. do not convert to logit hazard
   int ref_as_p = (model_rep > 0 || model_refp == 0) ? 0 : 1; 
   // Type of likelihood aggregation to use
@@ -125,7 +125,7 @@ parameters {
   vector[rep_fncol] rep_beta;
   vector<lower=0>[rep_rncol] rep_beta_sd; 
 
-  // Missing reference date model
+  // Missing reference time model
   array[model_miss] real miss_int;
   vector[miss_fncol] miss_beta; 
   vector<lower=0>[miss_rncol] miss_beta_sd; 
@@ -142,7 +142,7 @@ transformed parameters{
   vector[refp_fnrow] refp_sd;
   matrix[dmax, refp_fnrow] ref_lh; // sparse report logit hazards
   // Report model
-  vector[rep_fnrow] srdlh; // sparse report day logit hazards
+  vector[rep_fnrow] srdlh; // sparse reporting time logit hazards
   // Missing model
   vector[miss_fnindex] miss_ref_lprop;
 
@@ -160,10 +160,10 @@ transformed parameters{
   }
 
   // Reference model
-  profile("transformed_delay_reference_date_total") {
+  profile("transformed_delay_reference_time_total") {
   if (model_refp) {
-    // calculate sparse reference date effects
-    profile("transformed_delay_reference_date_effects") {
+    // calculate sparse reference time effects
+    profile("transformed_delay_reference_time_effects") {
     refp_mean = combine_effects(refp_mean_int[1], refp_mean_beta, refp_fdesign,
                                 refp_mean_beta_sd, refp_rdesign, 1);
     if (model_refp > 1) {
@@ -172,8 +172,8 @@ transformed parameters{
       refp_sd = exp(refp_sd);
     }
     }
-    // calculate reference date logit hazards (unless no reporting effects)
-    profile("transformed_delay_reference_date_hazards") {
+    // calculate reference time logit hazards (unless no reporting effects)
+    profile("transformed_delay_reference_time_hazards") {
     for (i in 1:refp_fnrow) {
       ref_lh[, i] = discretised_logit_hazard(
         refp_mean[i], refp_sd[i], dmax, model_refp, 2, ref_as_p
@@ -184,7 +184,7 @@ transformed parameters{
   }
 
   // Report model
-  profile("transformed_delay_reporting_date_effects") {
+  profile("transformed_delay_reporting_time_effects") {
   srdlh =
     combine_effects(0, rep_beta, rep_fdesign, rep_beta_sd, rep_rdesign, 1);
   }
@@ -234,10 +234,10 @@ model {
       );
     }
   }
-  // priors and scaling for date of report effects
+  // priors and scaling for time of report effects
   effect_priors_lp(rep_beta, rep_beta_sd, rep_beta_sd_p, rep_fncol, rep_rncol);
 
-  // priors for missing reference date effects
+  // priors for missing reference time effects
   if (model_miss) {
     miss_int ~ normal(miss_int_p[1], miss_int_p[2]);
     effect_priors_lp(
@@ -351,7 +351,7 @@ generated quantities {
       // from a temporary object to a permanent one
       // drop predictions without linked observations
       pp_obs = allocate_observed_obs(1, s, pp_obs_tmp, sl, csl, sdmax, csdmax);
-      // Posterior predictions for observations missing reference dates
+      // Posterior predictions for observations missing reference times
       if (miss_obs) {
         pp_miss_ref = obs_rng(log_exp_miss_ref, phi, model_obs);
       }

diff --git a/inst/stan/functions/combine_logit_hazards.stan b/inst/stan/functions/combine_logit_hazards.stan
@@ -2,13 +2,13 @@ vector combine_logit_hazards(int i, array[,] int rdlurd, vector srdlh,
                              matrix ref_lh, array[] int dpmfs, int ref_p,
                              int rep_h, int g, int t, int l) {
   vector[l] lh;
-  // allocate reference day effects
+  // allocate reference time effects
   if (ref_p) {
     lh = ref_lh[1:l, dpmfs[i]];
   }else{
     lh = rep_vector(0, l);
   }
-  // allocate report day effects
+  // allocate reporting time effects
   if (rep_h) {
     vector[l] rlh = srdlh[rdlurd[g, t:(t + l - 1)]];
     lh = lh + rlh;

diff --git a/inst/stan/functions/delay_lpmf.stan b/inst/stan/functions/delay_lpmf.stan
@@ -8,7 +8,7 @@ real delay_snap_lpmf(array[] int dummy, int start, int end, array[] int obs,
   array[n[3]] int filt_obs = segment(obs, n[1], n[3]);
   vector[n[3]] log_exp_obs;
 
-  // combine expected final obs and date effects to get expected obs
+  // combine expected final obs and time effects to get expected obs
   log_exp_obs = expected_obs_from_snaps(
     start, end, imp_obs, rdlurd, srdlh, ref_lh, dpmfs, ref_p, rep_h, ref_as_p,
     sl, csl, sg, st, n[3]
@@ -40,8 +40,8 @@ real delay_group_lpmf(array[] int groups, int start, int end, array[] int obs,
   vector[n[3]] log_exp_obs;
   vector[model_miss ? miss_obs : 0]  log_exp_miss_ref;
 
-  // Combine expected final obs and date effects to get expected obs
-  // If missing reference module in place calculated all expected obs vs 
+  // Combine expected final obs and time effects to get expected obs
+  // If missing reference module in place calculate all expected obs vs 
   // just those observed and allocate if missing or not.
   if (model_miss) {
     array[3] int f = filt_obs_indexes(i_start, i_end, csdmax, sdmax);
@@ -60,7 +60,7 @@ real delay_group_lpmf(array[] int groups, int start, int end, array[] int obs,
       i_start, i_end, log_exp_obs, sl, csl, log1m_exp(miss_ref_lprop)
     );
 
-    // Allocate expected cases by report date
+    // Allocate expected cases by reporting time
     if (miss_obs) {
       log_exp_complete = apply_missing_reference_effects(
         i_start, i_end, log_exp_complete, sdmax, csdmax, miss_ref_lprop

diff --git a/inst/stan/functions/expected_obs.stan b/inst/stan/functions/expected_obs.stan
@@ -2,18 +2,19 @@
 // 
 // Calculate expected observations (on the log scale) over time from a
 // combination of final expected observations, the probability of reporting
-// on a given day (or alternatively the logit hazard of this). 
+// at a given point in time (or alternatively the logit hazard of this). 
 // 
 // @param tar_obs The log of final expected observations that will be reported
-// for a given date on the log scale.
+// for a given time on the log scale.
 // 
 // @param lh A vector of conditional log probabilities a report occurs on a
-// given day. Optionally when ref_as_p = 0 this should be transformed first
-// into the logit hazard.
+// given point in time. Optionally when ref_as_p = 0 this should be transformed
+// first into the logit hazard.
 // 
-// @param ref_as_p Logical (0/1), should the reference date input be treatsd as 
-// a probability. Useful when no report date effects are present.
-// @return A vector of expected observations for a given date by date of report
+// @param ref_as_p Logical (0/1), should the reference time input be treated as 
+// a probability? Useful when no reporting time effects are present.
+// @return A vector of expected observations for a given reference time, by
+// reporting time
 // 
 // @examples
 // # compile function for use in R
@@ -27,17 +28,17 @@
 // )
 // rep_lh <- rep(0, 30)
 //
-// Example with no reporting day effect
+// Example with no reporting time effect
 // eobs <- exp(expected_obs(tar_obs, date_p + rep(0, 30), 1))
 // all.equal(eobs, date_p)
 //
-// Example with hazard effect only on last day of report
+// Example with hazard effect only on largest reporting delay
 // ref_lh <- logit(hazard_to_log_prob(date_p))
 // eobs <- exp(expected_obs(tar_obs, ref_lh, c(rep(0, 29), 0.1), 0))
 // all.equal(eobs, date_p)
 //
-// Example with a single day of additional reporting hazard and
-// no differential probability due to the reference date.
+// Example with a single time point of additional reporting hazard and
+// no differential probability due to the reference time.
 // rep_lh <- rep(0, 30); rep_lh[7] = 2
 // equal_lh <- logit(hazard_to_log_prob(rep(1/30, 30)))
 // round(exp(expected_obs(tar_obs, equal_lh + rep_lh, 0)), 3)
@@ -46,7 +47,7 @@
 // # 0.026 0.026 0.026 0.026 0.026 0.026
 //
 // Example combining multiple hazards and no differential prob due to reference
-// date
+// time
 // rep_lh <- rep(0, 30)
 // rep_lh[c(6, 12, 16)] = 2
 // rep_lh[c(2, 20)] = -2
@@ -55,7 +56,7 @@
 // # 0.021 0.021 0.021 0.106 0.014 0.014 0.014 0.002 0.016 0.016 0.016 0.016
 // # 0.016 0.016 0.016 0.016 0.016 0.016
 //
-// Example combining both date of reference and date of report effects
+// Example combining both reference time and reporting time effects
 // eobs <- exp(expected_obs(tar_obs, ref_lh + rep_lh, 0))
 // round(sum(eobs - 1e-4), 5) == 1
 // round(eobs, 3)

diff --git a/inst/stan/functions/expected_obs_from.stan b/inst/stan/functions/expected_obs_from.stan
@@ -15,7 +15,7 @@ vector expected_obs_from_index(int i, array[] vector imp_obs,
       i, rdlurd, srdlh, ref_lh, dpmfs, ref_p, rep_h, g, t, l
     );
   }
-  // combine expected final obs and date effects to get expected obs
+  // combine expected final obs and time effects to get expected obs
   profile("model_likelihood_expected_obs") {
   log_exp_obs = expected_obs(tar_obs, lh, ref_as_p);
   }
@@ -42,7 +42,7 @@ vector expected_obs_from_snaps(int start, int end, array[] vector imp_obs,
     t = st[i];
     l = sl[i];
     }
-    // combine expected final obs and date effects to get expected obs
+    // combine expected final obs and time effects to get expected obs
     profile("expected_obs_from_index") {
     esnap += l;
     log_exp_obs[ssnap:esnap] = expected_obs_from_index(