diff --git a/docs/source/tutorials/basic_renewal_model.qmd b/docs/source/tutorials/basic_renewal_model.qmd index 2b108a7b..2545aee1 100644 --- a/docs/source/tutorials/basic_renewal_model.qmd +++ b/docs/source/tutorials/basic_renewal_model.qmd @@ -121,7 +121,7 @@ To initialize these five components within the renewal modeling framework, we es # | label: creating-elements # (1) The generation interval (deterministic) pmf_array = jnp.array([0.4, 0.3, 0.2, 0.1]) -gen_int = DeterministicPMF(name="gen_int", vars=pmf_array) +gen_int = DeterministicPMF(name="gen_int", value=pmf_array) # (2) Initial infections (inferred with a prior) I0 = InfectionInitializationProcess( diff --git a/docs/source/tutorials/extending_pyrenew.qmd b/docs/source/tutorials/extending_pyrenew.qmd index 8a525ffd..48e1f80e 100644 --- a/docs/source/tutorials/extending_pyrenew.qmd +++ b/docs/source/tutorials/extending_pyrenew.qmd @@ -42,15 +42,15 @@ The following code-chunk defines the model components. Notice that for both the ```{python} # | label: model-components gen_int_array = jnp.array([0.25, 0.5, 0.15, 0.1]) -gen_int = DeterministicPMF(name="gen_int", vars=gen_int_array) -feedback_strength = DeterministicVariable(name="feedback_strength", vars=0.05) +gen_int = DeterministicPMF(name="gen_int", value=gen_int_array) +feedback_strength = DeterministicVariable(name="feedback_strength", value=0.05) I0 = InfectionInitializationProcess( "I0_initialization", DistributionalRV(name="I0", dist=dist.LogNormal(0, 1)), InitializeInfectionsExponentialGrowth( gen_int_array.size, - DeterministicVariable(name="rate", vars=0.5), + DeterministicVariable(name="rate", value=0.5), ), t_unit=1, ) diff --git a/docs/source/tutorials/hospital_admissions_model.qmd b/docs/source/tutorials/hospital_admissions_model.qmd index 31feec99..478f00f2 100644 --- a/docs/source/tutorials/hospital_admissions_model.qmd +++ b/docs/source/tutorials/hospital_admissions_model.qmd @@ -142,7 +142,7 @@ import jax.numpy as jnp import numpyro.distributions as dist inf_hosp_int = deterministic.DeterministicPMF( - name="inf_hosp_int", vars=inf_hosp_int + name="inf_hosp_int", value=inf_hosp_int ) hosp_rate = metaclass.DistributionalRV( @@ -175,13 +175,13 @@ I0 = InfectionInitializationProcess( ), InitializeInfectionsExponentialGrowth( gen_int_array.size, - deterministic.DeterministicVariable(name="rate", vars=0.05), + deterministic.DeterministicVariable(name="rate", value=0.05), ), t_unit=1, ) # Generation interval and Rt -gen_int = deterministic.DeterministicPMF(name="gen_int", vars=gen_int) +gen_int = deterministic.DeterministicPMF(name="gen_int", value=gen_int) class MyRt(metaclass.RandomVariable): diff --git a/docs/source/tutorials/periodic_effects.qmd b/docs/source/tutorials/periodic_effects.qmd index 8683e976..84702ac2 100644 --- a/docs/source/tutorials/periodic_effects.qmd +++ b/docs/source/tutorials/periodic_effects.qmd @@ -28,13 +28,13 @@ rt_proc = process.RtWeeklyDiffProcess( name="rt_weekly_diff", offset=0, log_rt_prior=deterministic.DeterministicVariable( - name="log_rt_prior", vars=jnp.array([0.1, 0.2]) + name="log_rt_prior", value=jnp.array([0.1, 0.2]) ), autoreg=deterministic.DeterministicVariable( - name="autoreg", vars=jnp.array([0.7]) + name="autoreg", value=jnp.array([0.7]) ), periodic_diff_sd=deterministic.DeterministicVariable( - name="periodic_diff_sd", vars=jnp.array([0.1]) + name="periodic_diff_sd", value=jnp.array([0.1]) ), ) ``` diff --git a/model/src/pyrenew/deterministic/deterministic.py b/model/src/pyrenew/deterministic/deterministic.py index 66a77029..c9ff9d8f 100644 --- a/model/src/pyrenew/deterministic/deterministic.py +++ b/model/src/pyrenew/deterministic/deterministic.py @@ -18,7 +18,7 @@ class DeterministicVariable(RandomVariable): def __init__( self, name: str, - vars: ArrayLike, + value: ArrayLike, ) -> None: """Default constructor @@ -26,7 +26,7 @@ def __init__( ---------- name : str A name to assign to the process. - vars : ArrayLike + value : ArrayLike An ArrayLike object. Returns @@ -35,19 +35,19 @@ def __init__( """ self.name = name - self.vars = jnp.atleast_1d(vars) - self.validate(vars) + self.value = jnp.atleast_1d(value) + self.validate(value) return None @staticmethod - def validate(vars: ArrayLike) -> None: + def validate(value: ArrayLike) -> None: """ Validates input to DeterministicPMF Parameters ---------- - vars : ArrayLike + value : ArrayLike An ArrayLike object. Returns @@ -57,10 +57,10 @@ def validate(vars: ArrayLike) -> None: Raises ------ Exception - If the input vars object is not a ArrayLike. + If the input value object is not a ArrayLike. """ - if not isinstance(vars, ArrayLike): - raise Exception("vars is not a ArrayLike") + if not isinstance(value, ArrayLike): + raise Exception("value is not a ArrayLike") return None @@ -86,5 +86,5 @@ def sample( Containing the stored values during construction. """ if record: - numpyro.deterministic(self.name, self.vars) - return (self.vars,) + numpyro.deterministic(self.name, self.value) + return (self.value,) diff --git a/model/src/pyrenew/deterministic/deterministicpmf.py b/model/src/pyrenew/deterministic/deterministicpmf.py index c7342bdc..04fdb009 100644 --- a/model/src/pyrenew/deterministic/deterministicpmf.py +++ b/model/src/pyrenew/deterministic/deterministicpmf.py @@ -16,13 +16,13 @@ class DeterministicPMF(RandomVariable): def __init__( self, name: str, - vars: ArrayLike, + value: ArrayLike, tol: float = 1e-5, ) -> None: """ Default constructor - Automatically checks that the elements in `vars` can be indeed + Automatically checks that the elements in `value` can be indeed considered to be a PMF by calling pyrenew.distutil.validate_discrete_dist_vector on each one of its entries. @@ -31,7 +31,7 @@ def __init__( ---------- name : str A name to assign to the variable. - vars : tuple + value : tuple An ArrayLike object. tol : float, optional Passed to pyrenew.distutil.validate_discrete_dist_vector. Defaults @@ -41,23 +41,23 @@ def __init__( ------- None """ - vars = validate_discrete_dist_vector( - discrete_dist=vars, + value = validate_discrete_dist_vector( + discrete_dist=value, tol=tol, ) - self.basevar = DeterministicVariable(name=name, vars=vars) + self.basevar = DeterministicVariable(name=name, value=value) return None @staticmethod - def validate(vars: ArrayLike) -> None: + def validate(value: ArrayLike) -> None: """ Validates input to DeterministicPMF Parameters ---------- - vars : ArrayLike + value : ArrayLike An ArrayLike object. Returns @@ -97,4 +97,4 @@ def size(self) -> int: The size of the PMF """ - return self.basevar.vars.size + return self.basevar.value.size diff --git a/model/src/pyrenew/latent/hospitaladmissions.py b/model/src/pyrenew/latent/hospitaladmissions.py index f92c5c90..a7f5dbb1 100644 --- a/model/src/pyrenew/latent/hospitaladmissions.py +++ b/model/src/pyrenew/latent/hospitaladmissions.py @@ -91,11 +91,11 @@ def __init__( if day_of_week_effect_rv is None: day_of_week_effect_rv = DeterministicVariable( - name="weekday_effect", vars=1 + name="weekday_effect", value=1 ) if hosp_report_prob_rv is None: hosp_report_prob_rv = DeterministicVariable( - name="hosp_report_prob", vars=1 + name="hosp_report_prob", value=1 ) HospitalAdmissions.validate( diff --git a/model/src/test/test_deterministic.py b/model/src/test/test_deterministic.py index b20d7da4..243eba39 100644 --- a/model/src/test/test_deterministic.py +++ b/model/src/test/test_deterministic.py @@ -19,16 +19,16 @@ def test_deterministic(): var1 = DeterministicVariable( name="var1", - vars=jnp.array( + value=jnp.array( [ 1, ] ), ) var2 = DeterministicPMF( - name="var2", vars=jnp.array([0.25, 0.25, 0.2, 0.3]) + name="var2", value=jnp.array([0.25, 0.25, 0.2, 0.3]) ) - var3 = DeterministicProcess(name="var3", vars=jnp.array([1, 2, 3, 4])) + var3 = DeterministicProcess(name="var3", value=jnp.array([1, 2, 3, 4])) var4 = NullVariable() var5 = NullProcess() diff --git a/model/src/test/test_forecast.py b/model/src/test/test_forecast.py index 259fdff7..5de2c1a4 100644 --- a/model/src/test/test_forecast.py +++ b/model/src/test/test_forecast.py @@ -21,7 +21,7 @@ def test_forecast(): """Check that forecasts are the right length and match the posterior up until forecast begins.""" pmf_array = jnp.array([0.25, 0.25, 0.25, 0.25]) - gen_int = DeterministicPMF(name="gen_int", vars=pmf_array) + gen_int = DeterministicPMF(name="gen_int", value=pmf_array) I0 = InfectionInitializationProcess( "I0_initialization", DistributionalRV(name="I0", dist=dist.LogNormal(0, 1)), diff --git a/model/src/test/test_infection_seeding_method.py b/model/src/test/test_infection_seeding_method.py index 29abcce6..7eb40a20 100644 --- a/model/src/test/test_infection_seeding_method.py +++ b/model/src/test/test_infection_seeding_method.py @@ -13,8 +13,8 @@ def test_initialize_infections_exponential(): """Check that the InitializeInfectionsExponentialGrowth class generates the correct number of infections at each time point.""" n_timepoints = 10 - rate_RV = DeterministicVariable(name="rate_RV", vars=0.5) - I_pre_init_RV = DeterministicVariable(name="I_pre_init_RV", vars=10.0) + rate_RV = DeterministicVariable(name="rate_RV", value=0.5) + I_pre_init_RV = DeterministicVariable(name="I_pre_init_RV", value=10.0) default_t_pre_init = n_timepoints - 1 (I_pre_init,) = I_pre_init_RV() @@ -36,7 +36,7 @@ def test_initialize_infections_exponential(): # test for failure with non-scalar rate or I_pre_init rate_RV_2 = DeterministicVariable( - name="rate_RV", vars=np.array([0.5, 0.5]) + name="rate_RV", value=np.array([0.5, 0.5]) ) with pytest.raises(ValueError): InitializeInfectionsExponentialGrowth( @@ -45,7 +45,7 @@ def test_initialize_infections_exponential(): I_pre_init_RV_2 = DeterministicVariable( name="I_pre_init_RV", - vars=np.array([10.0, 10.0]), + value=np.array([10.0, 10.0]), ) (I_pre_init_2,) = I_pre_init_RV_2() @@ -75,7 +75,7 @@ def test_initialize_infections_zero_pad(): """Check that the InitializeInfectionsZeroPad class generates the correct number of infections at each time point.""" n_timepoints = 10 - I_pre_init_RV = DeterministicVariable(name="I_pre_init_RV", vars=10.0) + I_pre_init_RV = DeterministicVariable(name="I_pre_init_RV", value=10.0) (I_pre_init,) = I_pre_init_RV() infections = InitializeInfectionsZeroPad( @@ -86,7 +86,7 @@ def test_initialize_infections_zero_pad(): ) I_pre_init_RV_2 = DeterministicVariable( - name="I_pre_init_RV", vars=np.array([10.0, 10.0]) + name="I_pre_init_RV", value=np.array([10.0, 10.0]) ) (I_pre_init_2,) = I_pre_init_RV_2() diff --git a/model/src/test/test_infection_seeding_process.py b/model/src/test/test_infection_seeding_process.py index 685ba61f..b7fa6ef7 100644 --- a/model/src/test/test_infection_seeding_process.py +++ b/model/src/test/test_infection_seeding_process.py @@ -28,14 +28,14 @@ def test_infection_initialization_process(): "exp_model", DistributionalRV(name="I0", dist=dist.LogNormal(0, 1)), InitializeInfectionsExponentialGrowth( - n_timepoints, DeterministicVariable(name="rate", vars=0.5) + n_timepoints, DeterministicVariable(name="rate", value=0.5) ), t_unit=1, ) vec_model = InfectionInitializationProcess( "vec_model", - DeterministicVariable(name="I0", vars=jnp.arange(n_timepoints)), + DeterministicVariable(name="I0", value=jnp.arange(n_timepoints)), InitializeInfectionsFromVec(n_timepoints), t_unit=1, ) @@ -56,7 +56,7 @@ def test_infection_initialization_process(): with pytest.raises(TypeError): InfectionInitializationProcess( "vec_model", - DeterministicVariable(name="I0", vars=jnp.arange(n_timepoints)), + DeterministicVariable(name="I0", value=jnp.arange(n_timepoints)), 3, t_unit=1, ) diff --git a/model/src/test/test_infectionsrtfeedback.py b/model/src/test/test_infectionsrtfeedback.py index e602a3a3..bd15f5cd 100644 --- a/model/src/test/test_infectionsrtfeedback.py +++ b/model/src/test/test_infectionsrtfeedback.py @@ -69,9 +69,9 @@ def test_infectionsrtfeedback(): # By doing the infection feedback strength 0, Rt = Rt_adjusted # So infection should be equal in both inf_feed_strength = DeterministicVariable( - name="inf_feed_strength", vars=jnp.zeros_like(Rt) + name="inf_feed_strength", value=jnp.zeros_like(Rt) ) - inf_feedback_pmf = DeterministicPMF(name="inf_feedback_pmf", vars=gen_int) + inf_feedback_pmf = DeterministicPMF(name="inf_feedback_pmf", value=gen_int) # Test the InfectionsWithFeedback class InfectionsWithFeedback = latent.InfectionsWithFeedback( @@ -113,9 +113,9 @@ def test_infectionsrtfeedback_feedback(): gen_int = jnp.array([0.4, 0.25, 0.25, 0.1, 0.0, 0.0, 0.0]) inf_feed_strength = DeterministicVariable( - name="inf_feed_strength", vars=jnp.repeat(0.5, len(Rt)) + name="inf_feed_strength", value=jnp.repeat(0.5, len(Rt)) ) - inf_feedback_pmf = DeterministicPMF(name="inf_feedback_pmf", vars=gen_int) + inf_feedback_pmf = DeterministicPMF(name="inf_feedback_pmf", value=gen_int) # Test the InfectionsWithFeedback class InfectionsWithFeedback = latent.InfectionsWithFeedback( diff --git a/model/src/test/test_latent_admissions.py b/model/src/test/test_latent_admissions.py index 6b211b7c..ca49acb6 100644 --- a/model/src/test/test_latent_admissions.py +++ b/model/src/test/test_latent_admissions.py @@ -48,7 +48,7 @@ def test_admissions_sample(): # Testing the hospital admissions inf_hosp = DeterministicPMF( name="inf_hosp", - vars=jnp.array( + value=jnp.array( [ 0, 0, diff --git a/model/src/test/test_model_basic_renewal.py b/model/src/test/test_model_basic_renewal.py index d0330ae0..83702b47 100644 --- a/model/src/test/test_model_basic_renewal.py +++ b/model/src/test/test_model_basic_renewal.py @@ -56,7 +56,7 @@ def test_model_basicrenewal_no_timepoints_or_observations(): """ gen_int = DeterministicPMF( - name="gen_int", vars=jnp.array([0.25, 0.25, 0.25, 0.25]) + name="gen_int", value=jnp.array([0.25, 0.25, 0.25, 0.25]) ) I0 = DistributionalRV(name="I0", dist=dist.LogNormal(0, 1)) @@ -87,7 +87,7 @@ def test_model_basicrenewal_both_timepoints_and_observations(): gen_int = DeterministicPMF( name="gen_int", - vars=jnp.array([0.25, 0.25, 0.25, 0.25]), + value=jnp.array([0.25, 0.25, 0.25, 0.25]), ) I0 = DistributionalRV(name="I0", dist=dist.LogNormal(0, 1)) @@ -122,7 +122,7 @@ def test_model_basicrenewal_no_obs_model(): gen_int = DeterministicPMF( name="gen_int", - vars=jnp.array([0.25, 0.25, 0.25, 0.25]), + value=jnp.array([0.25, 0.25, 0.25, 0.25]), ) with pytest.raises(ValueError): @@ -195,7 +195,7 @@ def test_model_basicrenewal_with_obs_model(): """ gen_int = DeterministicPMF( - name="gen_int", vars=jnp.array([0.25, 0.25, 0.25, 0.25]) + name="gen_int", value=jnp.array([0.25, 0.25, 0.25, 0.25]) ) I0 = InfectionInitializationProcess( @@ -244,7 +244,7 @@ def test_model_basicrenewal_with_obs_model(): def test_model_basicrenewal_padding() -> None: # numpydoc ignore=GL08 gen_int = DeterministicPMF( - name="gen_int", vars=jnp.array([0.25, 0.25, 0.25, 0.25]) + name="gen_int", value=jnp.array([0.25, 0.25, 0.25, 0.25]) ) I0 = InfectionInitializationProcess( diff --git a/model/src/test/test_model_hosp_admissions.py b/model/src/test/test_model_hosp_admissions.py index 632e5e9c..2b8d113e 100644 --- a/model/src/test/test_model_hosp_admissions.py +++ b/model/src/test/test_model_hosp_admissions.py @@ -82,7 +82,7 @@ def test_model_hosp_no_timepoints_or_observations(): """ gen_int = DeterministicPMF( - name="gen_int", vars=jnp.array([0.25, 0.25, 0.25, 0.25]) + name="gen_int", value=jnp.array([0.25, 0.25, 0.25, 0.25]) ) I0 = DistributionalRV(name="I0", dist=dist.LogNormal(0, 1)) @@ -94,7 +94,7 @@ def test_model_hosp_no_timepoints_or_observations(): inf_hosp = DeterministicPMF( name="inf_hosp", - vars=jnp.array( + value=jnp.array( [ 0, 0, @@ -147,7 +147,7 @@ def test_model_hosp_both_timepoints_and_observations(): gen_int = DeterministicPMF( name="gen_int", - vars=jnp.array([0.25, 0.25, 0.25, 0.25]), + value=jnp.array([0.25, 0.25, 0.25, 0.25]), ) I0 = DistributionalRV(name="I0", dist=dist.LogNormal(0, 1)) @@ -159,7 +159,7 @@ def test_model_hosp_both_timepoints_and_observations(): inf_hosp = DeterministicPMF( name="inf_hosp", - vars=jnp.array( + value=jnp.array( [ 0, 0, @@ -215,7 +215,7 @@ def test_model_hosp_no_obs_model(): gen_int = DeterministicPMF( name="gen_int", - vars=jnp.array([0.25, 0.25, 0.25, 0.25]), + value=jnp.array([0.25, 0.25, 0.25, 0.25]), ) I0 = InfectionInitializationProcess( @@ -230,7 +230,7 @@ def test_model_hosp_no_obs_model(): inf_hosp = DeterministicPMF( name="inf_hosp", - vars=jnp.array( + value=jnp.array( [ 0, 0, @@ -320,7 +320,7 @@ def test_model_hosp_with_obs_model(): """ gen_int = DeterministicPMF( - name="gen_int", vars=jnp.array([0.25, 0.25, 0.25, 0.25]) + name="gen_int", value=jnp.array([0.25, 0.25, 0.25, 0.25]) ) I0 = InfectionInitializationProcess( @@ -336,7 +336,7 @@ def test_model_hosp_with_obs_model(): inf_hosp = DeterministicPMF( name="inf_hosp", - vars=jnp.array( + value=jnp.array( [ 0, 0, @@ -407,7 +407,7 @@ def test_model_hosp_with_obs_model_weekday_phosp_2(): gen_int = DeterministicPMF( name="gen_int", - vars=jnp.array([0.25, 0.25, 0.25, 0.25]), + value=jnp.array([0.25, 0.25, 0.25, 0.25]), ) I0 = InfectionInitializationProcess( @@ -423,7 +423,7 @@ def test_model_hosp_with_obs_model_weekday_phosp_2(): inf_hosp = DeterministicPMF( name="inf_hosp", - vars=jnp.array( + value=jnp.array( [ 0, 0, @@ -504,7 +504,7 @@ def test_model_hosp_with_obs_model_weekday_phosp(): gen_int = DeterministicPMF( name="gen_int", - vars=jnp.array([0.25, 0.25, 0.25, 0.25]), + value=jnp.array([0.25, 0.25, 0.25, 0.25]), ) n_obs_to_generate = 30 pad_size = 5 @@ -523,7 +523,7 @@ def test_model_hosp_with_obs_model_weekday_phosp(): inf_hosp = DeterministicPMF( name="inf_hosp", - vars=jnp.array( + value=jnp.array( [ 0, 0, @@ -554,7 +554,7 @@ def test_model_hosp_with_obs_model_weekday_phosp(): weekday = jnp.tile(weekday, 10) weekday = weekday[:total_length] - weekday = DeterministicVariable(name="weekday", vars=weekday) + weekday = DeterministicVariable(name="weekday", value=weekday) hosp_report_prob_dist = jnp.array([0.9, 0.8, 0.7, 0.7, 0.6, 0.4]) hosp_report_prob_dist = jnp.tile(hosp_report_prob_dist, 10) @@ -563,7 +563,7 @@ def test_model_hosp_with_obs_model_weekday_phosp(): hosp_report_prob_dist = DeterministicVariable( name="hosp_report_prob_dist", - vars=hosp_report_prob_dist, + value=hosp_report_prob_dist, ) latent_admissions = HospitalAdmissions( diff --git a/model/src/test/test_observation_negativebinom.py b/model/src/test/test_observation_negativebinom.py index 9e17e73b..80507c7b 100644 --- a/model/src/test/test_observation_negativebinom.py +++ b/model/src/test/test_observation_negativebinom.py @@ -16,7 +16,7 @@ def test_negativebinom_deterministic_obs(): negb = NegativeBinomialObservation( "negbinom_rv", - concentration_rv=DeterministicVariable(name="concentration", vars=10), + concentration_rv=DeterministicVariable(name="concentration", value=10), ) rates = np.random.randint(1, 5, size=10) @@ -42,7 +42,7 @@ def test_negativebinom_random_obs(): negb = NegativeBinomialObservation( "negbinom_rv", - concentration_rv=DeterministicVariable(name="concentration", vars=10), + concentration_rv=DeterministicVariable(name="concentration", value=10), ) rates = np.repeat(5, 20000) diff --git a/model/src/test/test_periodiceffect.py b/model/src/test/test_periodiceffect.py index 9712911a..85fbcfb8 100644 --- a/model/src/test/test_periodiceffect.py +++ b/model/src/test/test_periodiceffect.py @@ -13,7 +13,7 @@ def test_periodiceffect() -> None: """Checks basic functionality of the process""" x = jnp.array([1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0]) - rv = DeterministicVariable(name="weekly-sample", vars=x) + rv = DeterministicVariable(name="weekly-sample", value=x) params = { "offset": 0, @@ -58,7 +58,7 @@ def test_weeklyeffect() -> None: """Checks basic functionality of the process""" x = jnp.array([1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0]) - rv = DeterministicVariable(name="weekly-sample", vars=x) + rv = DeterministicVariable(name="weekly-sample", value=x) params = { "offset": 2, diff --git a/model/src/test/test_predictive.py b/model/src/test/test_predictive.py index 2bc1995c..9c53521d 100644 --- a/model/src/test/test_predictive.py +++ b/model/src/test/test_predictive.py @@ -20,7 +20,7 @@ from pyrenew.process import SimpleRandomWalkProcess pmf_array = jnp.array([0.25, 0.1, 0.2, 0.45]) -gen_int = DeterministicPMF(name="gen_int", vars=pmf_array) +gen_int = DeterministicPMF(name="gen_int", value=pmf_array) I0 = InfectionInitializationProcess( "I0_initialization", DistributionalRV(name="I0", dist=dist.LogNormal(0, 1)), diff --git a/model/src/test/test_random_key.py b/model/src/test/test_random_key.py index b75b999a..81565f8e 100644 --- a/model/src/test/test_random_key.py +++ b/model/src/test/test_random_key.py @@ -25,7 +25,7 @@ def create_test_model(): # numpydoc ignore=GL08 pmf_array = jnp.array([0.25, 0.25, 0.25, 0.25]) - gen_int = DeterministicPMF(name="gen_int", vars=pmf_array) + gen_int = DeterministicPMF(name="gen_int", value=pmf_array) I0 = InfectionInitializationProcess( "I0_initialization", DistributionalRV(name="I0", dist=dist.LogNormal(0, 1)), diff --git a/model/src/test/test_random_walk.py b/model/src/test/test_random_walk.py index 1ca04bc5..76ea3c73 100755 --- a/model/src/test/test_random_walk.py +++ b/model/src/test/test_random_walk.py @@ -18,7 +18,7 @@ def test_rw_can_be_sampled(): name="init_rv_rand", dist=dist.Normal(1, 0.5), ) - init_rv_fixed = DeterministicVariable(name="init_rv_fixed", vars=50.0) + init_rv_fixed = DeterministicVariable(name="init_rv_fixed", value=50.0) step_rv = DistributionalRV( name="rw_step", @@ -44,8 +44,8 @@ def test_rw_can_be_sampled(): assert ans_fixed[0].shape == (5023,) # check that fixing inits works - assert_almost_equal(ans_fixed[0][0], init_rv_fixed.vars) - assert ans_rand[0][0] != init_rv_fixed.vars + assert_almost_equal(ans_fixed[0][0], init_rv_fixed.value) + assert ans_rand[0][0] != init_rv_fixed.value def test_rw_samples_correctly_distributed(): @@ -66,7 +66,7 @@ def test_rw_samples_correctly_distributed(): dist=dist.Normal(loc=step_mean, scale=step_sd), ), init_rv=DeterministicVariable( - name="init_rv_fixed", vars=rw_init_val + name="init_rv_fixed", value=rw_init_val ), ) diff --git a/model/src/test/test_rtperiodicdiff.py b/model/src/test/test_rtperiodicdiff.py index 4184a763..be6e0d0a 100644 --- a/model/src/test/test_rtperiodicdiff.py +++ b/model/src/test/test_rtperiodicdiff.py @@ -53,13 +53,13 @@ def test_rtweeklydiff() -> None: "name": "test", "offset": 0, "log_rt_prior": DeterministicVariable( - name="log_rt_prior", vars=jnp.array([0.1, 0.2]) + name="log_rt_prior", value=jnp.array([0.1, 0.2]) ), "autoreg": DeterministicVariable( - name="autoreg", vars=jnp.array([0.7]) + name="autoreg", value=jnp.array([0.7]) ), "periodic_diff_sd": DeterministicVariable( - name="periodic_diff_sd", vars=jnp.array([0.1]) + name="periodic_diff_sd", value=jnp.array([0.1]) ), } duration = 30 @@ -100,15 +100,15 @@ def test_rtweeklydiff_no_autoregressive() -> None: "name": "test", "offset": 0, "log_rt_prior": DeterministicVariable( - name="log_rt_prior", vars=jnp.array([0.0, 0.0]) + name="log_rt_prior", value=jnp.array([0.0, 0.0]) ), # No autoregression! "autoreg": DeterministicVariable( - name="autoreg", vars=jnp.array([0.0]) + name="autoreg", value=jnp.array([0.0]) ), "periodic_diff_sd": DeterministicVariable( name="periodic_diff_sd", - vars=jnp.array([0.1]), + value=jnp.array([0.1]), ), } @@ -141,14 +141,14 @@ def test_rtweeklydiff_manual_reconstruction() -> None: "offset": 0, "log_rt_prior": DeterministicVariable( name="log_rt_prior", - vars=jnp.array([0.1, 0.2]), + value=jnp.array([0.1, 0.2]), ), "autoreg": DeterministicVariable( - name="autoreg", vars=jnp.array([0.7]) + name="autoreg", value=jnp.array([0.7]) ), "periodic_diff_sd": DeterministicVariable( name="periodic_diff_sd", - vars=jnp.array([0.1]), + value=jnp.array([0.1]), ), } @@ -180,14 +180,14 @@ def test_rtperiodicdiff_smallsample(): "offset": 0, "log_rt_prior": DeterministicVariable( name="log_rt_prior", - vars=jnp.array([0.1, 0.2]), + value=jnp.array([0.1, 0.2]), ), "autoreg": DeterministicVariable( - name="autoreg", vars=jnp.array([0.7]) + name="autoreg", value=jnp.array([0.7]) ), "periodic_diff_sd": DeterministicVariable( name="periodic_diff_sd", - vars=jnp.array([0.1]), + value=jnp.array([0.1]), ), }