diff --git a/inst/starter_models/ww/calibration_example.R b/inst/starter_models/ww/calibration_example.R
index 6be76f58f..9c9594b93 100644
--- a/inst/starter_models/ww/calibration_example.R
+++ b/inst/starter_models/ww/calibration_example.R
@@ -37,12 +37,11 @@ obs_data = (covid_on
burn_in_period = 15 ## number of days before the data start to begin the simulations
forecast_period = 30 ## number of days after the data end to make forecasts
-time_bounds = mp_sim_bounds(
- sim_start = min(obs_data$time) - lubridate::days(burn_in_period)
- , sim_end = max(obs_data$time) + lubridate::days(forecast_period)
- , "daily"
+time_bounds = mp_sim_offset(
+ sim_start_offset = 15
+ , sim_end_offset = 30
+ , time_scale = "daily"
)
-steps = time_bounds$time_id_engine ## function to convert dates to time-steps
## -------------------------
## Model Specification
diff --git a/inst/starter_models/ww/figures/plot_fits-1.png b/inst/starter_models/ww/figures/plot_fits-1.png
index be9d0abff..2e9c5599d 100644
Binary files a/inst/starter_models/ww/figures/plot_fits-1.png and b/inst/starter_models/ww/figures/plot_fits-1.png differ
diff --git a/man/TMBTV.RBFArg.Rd b/man/TMBTV.RBFArg.Rd
new file mode 100644
index 000000000..53304b027
--- /dev/null
+++ b/man/TMBTV.RBFArg.Rd
@@ -0,0 +1,135 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mp_tmb_calibrator.R
+\name{TMBTV.RBFArg}
+\alias{TMBTV.RBFArg}
+\title{TMBTV.TVArg = function(
+tv
+, struc
+, spec
+, existing_global_names = character()
+) {
+self = TMBTVAbstract()
+self$existing_global_names = existing_global_names
+self$spec = spec
+
+self$before_loop = function() list()
+self$after_loop = function() list()
+\subsection{List with the values of each}{
+}
+
+\subsection{time varying parameter at the change points. The}{
+}
+
+\subsection{names of the list are the time-varying matrices}{
+}
+
+\subsection{in the spec.}{
+
+self$time_var = function() list()
+}
+
+\subsection{List of the integers}{
+}
+
+\subsection{giving the time-steps of the changepoints with}{
+}
+
+\subsection{the first time-step always being 0 (the initial)}{
+}
+
+\subsection{The names of the list are the time-varying}{
+}
+
+\subsection{matrices in the spec.}{
+
+self$change_points = function() list()
+self$change_pointer = function() list()
+}
+
+\subsection{List of expressions that update parameters that}{
+}
+
+\subsection{are time-varying}{
+
+self$var_update_exprs = function() list()
+}
+
+\subsection{data frames describing the fixed and random effects corresponding}{
+}
+
+\subsection{to time-varying parameters}{
+
+self$tv_params_frame = function(tv_pars) self$empty_params_frame
+self$tv_random_frame = function() self$empty_params_frame
+
+return_object(self, "TMBTV")
+}
+}}
+\usage{
+\method{TMBTV}{RBFArg}(tv, struc, spec, existing_global_names = character())
+}
+\description{
+TMBTV.TVArg = function(
+tv
+, struc
+, spec
+, existing_global_names = character()
+) {
+self = TMBTVAbstract()
+self$existing_global_names = existing_global_names
+self$spec = spec
+
+self$before_loop = function() list()
+self$after_loop = function() list()
+\subsection{List with the values of each}{
+}
+
+\subsection{time varying parameter at the change points. The}{
+}
+
+\subsection{names of the list are the time-varying matrices}{
+}
+
+\subsection{in the spec.}{
+
+self$time_var = function() list()
+}
+
+\subsection{List of the integers}{
+}
+
+\subsection{giving the time-steps of the changepoints with}{
+}
+
+\subsection{the first time-step always being 0 (the initial)}{
+}
+
+\subsection{The names of the list are the time-varying}{
+}
+
+\subsection{matrices in the spec.}{
+
+self$change_points = function() list()
+self$change_pointer = function() list()
+}
+
+\subsection{List of expressions that update parameters that}{
+}
+
+\subsection{are time-varying}{
+
+self$var_update_exprs = function() list()
+}
+
+\subsection{data frames describing the fixed and random effects corresponding}{
+}
+
+\subsection{to time-varying parameters}{
+
+self$tv_params_frame = function(tv_pars) self$empty_params_frame
+self$tv_random_frame = function() self$empty_params_frame
+
+return_object(self, "TMBTV")
+}
+}
+}
diff --git a/man/mp_par.Rd b/man/mp_par.Rd
index a7699a149..c4bc90819 100644
--- a/man/mp_par.Rd
+++ b/man/mp_par.Rd
@@ -4,7 +4,7 @@
\alias{mp_par}
\title{Fit Parameters}
\usage{
-mp_par(params, random)
+mp_par(params = empty_named_list(), random = empty_named_list())
}
\arguments{
\item{params}{Named list of distributional specifications for the
diff --git a/man/mp_tmb_profile.Rd b/man/mp_tmb_profile.Rd
new file mode 100644
index 000000000..6a2ca3c13
--- /dev/null
+++ b/man/mp_tmb_profile.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/surfplot.R
+\name{mp_tmb_profile}
+\alias{mp_tmb_profile}
+\title{TMB Likelihood Profiling}
+\usage{
+mp_tmb_profile(model, param, ...)
+}
+\arguments{
+\item{model}{A TMB model probably produced using
+\code{\link{mp_tmb_calibrator}}.}
+
+\item{param}{The name of a fixed effect parameter set through the \code{par}
+argument of the call to \code{\link{mp_tmb_calibrator}} used to create
+\code{model}.}
+
+\item{...}{Arguments to pass to \code{\link{TMB::tmbprofile}}.}
+}
+\value{
+The output of \code{\link{TMB::tmbprofile}}.
+}
+\description{
+Use \code{\link{TMB::tmbprofile}} to compute the profile likelihood
+of a calibrator produced using \code{\link{mp_tmb_calibrator}}.
+}
diff --git a/tests/testthat/test-calibrator-time.R b/tests/testthat/test-calibrator-time.R
index 294b12a71..df8868a8f 100644
--- a/tests/testthat/test-calibrator-time.R
+++ b/tests/testthat/test-calibrator-time.R
@@ -73,4 +73,5 @@ test_that("start-date offsets work", {
cal_dates = make_cal("daily")
cc_dates = mp_tmb_coef(cal)
expect_identical(cc, cc_dates)
+>>>>>>> main
})
diff --git a/tests/testthat/test-distributions.R b/tests/testthat/test-distributions.R
index 3f8148751..5c57e2cf0 100644
--- a/tests/testthat/test-distributions.R
+++ b/tests/testthat/test-distributions.R
@@ -1,4 +1,13 @@
library(macpan2); library(testthat); library(dplyr); library(tidyr); library(ggplot2)
+
+norm = mp_normal(location = "texas", sd = "fred")
+norm$likelihood("obs", "exp")
+norm$prior("beta")
+norm$distr_param_objs$location$expr_ref()
+norm$distr_param_objs$sd$expr_ref()
+
+
+
test_that("distributions give appropriate variable assumption warnings", {
# At this time the only distribution with variable assumptions is the
@@ -49,14 +58,16 @@ test_that("distributions give appropriate variable assumption warnings", {
)
# The variable assumption is violated here. For the log-normal distribution,
# the variable cannot be zero.
+ # TODO: be careful! it didn't look like this test made sense,
+ # but it was working before so what changed?
expect_warning(mp_tmb_calibrator(sir_spec
- , data = bind_rows(sir_prevalence, sir_beta)
- , traj = "I"
- , par = list(beta = mp_log_normal(location = 1, sd = 1))
- , tv = "beta"
- , default = list(N = 300)
- )
- , regexp = "contains zeros at the beginning of the simulation"
+ , data = bind_rows(sir_prevalence, sir_beta)
+ , traj = "I"
+ , par = list(beta = mp_log_normal(location = 1, sd = 1))
+ , tv = "beta"
+ , default = list(N = 300)
+ )
+ , regexp = "contains zeros at the beginning of the simulation"
)
data = "TRAJ-sir_50_infection.rds" |> test_cache_read()