Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Removed redundant global error parameter from affine model. #52

Merged
merged 8 commits into from
Jan 13, 2025
Merged

Removed redundant global error parameter from affine model. #52

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
1d8ad2c
Removed redundant global error parameter from affine model.
Tess-LaCoil Jan 6, 2025
6f7d5c7
Simplified affine DE.
Tess-LaCoil Jan 6, 2025
0112570
Revert "Removed redundant global error parameter from affine model."
Tess-LaCoil Jan 7, 2025
ce7f5bb
Changed parameter name in comment to reflect parameterisation.
Tess-LaCoil Jan 7, 2025
8c2e066
Fixed merge I hope.
Tess-LaCoil Jan 7, 2025
2e7964b
Put y_bar back in.
Tess-LaCoil Jan 7, 2025
b1b23ff
Returned y_bar to test.
Tess-LaCoil Jan 7, 2025
3435682
Removed constraint on ind_const to be non-negative in order to permit…
Tess-LaCoil Jan 7, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion R/hmde_models.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -116,8 +116,8 @@ hmde_affine_single_ind <- function(){
y_obs = NULL,
obs_index = NULL,
time = NULL,
y_bar = NULL,
int_method = NULL,
y_bar = NULL,
prior_means = c(1,1),
prior_sds = c(2,2),
model = "affine_single_ind")
Expand Down
9 changes: 3 additions & 6 deletions inst/stan/affine_single_ind.stan
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
//Growth function
functions{
//Growth function for use with Runge-Kutta method
//pars = (beta_0, beta_1, y_bar)
//pars = (const, beta_1, y_bar)
real DE_rk4(real y, array[] real pars){ //change number of pars
return pars[1] - (pars[2] * (y-pars[3])); //growth function
}
Expand Down Expand Up @@ -74,11 +74,8 @@ data {
parameters {
//Individual level
real<lower=0> ind_y_0;
real<lower=0> ind_const;
real ind_const;
real<lower=0> ind_beta_1;

//Global level
real<lower=0> global_error_sigma;
}

// The model to be estimated.
Expand Down Expand Up @@ -125,7 +122,7 @@ model {

//Priors
//Individual level
ind_const ~lognormal(log(prior_means[1]), prior_sds[1]);
ind_const ~normal(prior_means[1], prior_sds[1]);
ind_beta_1 ~lognormal(log(prior_means[2]), prior_sds[2]);
}

Expand Down
2 changes: 1 addition & 1 deletion tests/testthat/test-hmde_models_affine.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ test_that("Model structures: affine", {
# Single individual
single_model <- hmde_model("affine_single_ind")
expect_named(single_model, c("step_size", "n_obs", "y_obs", "obs_index",
"time", "y_bar", "int_method", "prior_means",
"time", "int_method", "y_bar", "prior_means",
"prior_sds", "model"))
expect_type(single_model, "list")
expect_visible(single_model)
Expand Down
Loading