Comments (4)
hyunjimoon
commented on August 26, 2024
Plot design for S > 1 is needed.
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hyunjimoon
commented on August 26, 2024
idata for sbc looks like the following but prior_draws need to be added to every data variables. I think currently two prior_draw and draw are the same.
<xarray.Dataset>
Dimensions: (chain: 1, draw: 2, initial_outcome_dim_0: 3,
integrated_result_dim_0: 20,
integrated_result_dim_1: 3, predator_dim_0: 20,
prey_dim_0: 20, process_noise_dim_0: 20,
prey_obs_dim_0: 20, predator_obs_dim_0: 20,
prior_draw: 2)
Coordinates:
* chain (chain) int64 1
* draw (draw) int64 0 1
* prior_draw (prior_draw) int64 1 2
Dimensions without coordinates: initial_outcome_dim_0, integrated_result_dim_0,
integrated_result_dim_1, predator_dim_0,
prey_dim_0, process_noise_dim_0,
prey_obs_dim_0, predator_obs_dim_0
Data variables: (12/13)
prey_birth_frac (chain, draw) float64 ...
pred_birth_frac (chain, draw) float64 ...
m_noise_scale (chain, draw) float64 ...
predator__init (chain, draw) float64 ...
prey__init (chain, draw) float64 ...
process_noise__init (chain, draw) float64 ...
... ...
integrated_result (chain, draw, integrated_result_dim_0, integrated_result_dim_1) float64 ...
predator (chain, draw, predator_dim_0) float64 ...
prey (chain, draw, prey_dim_0) float64 ...
process_noise (chain, draw, process_noise_dim_0) float64 ...
prey_obs (chain, draw, prey_obs_dim_0) float64 ...
predator_obs (chain, draw, predator_obs_dim_0) float64 ...
idata for data2draws
<xarray.Dataset>
Dimensions: (chain: 4, draw: 25, initial_outcome_dim_0: 3,
integrated_result_dim_0: 20,
integrated_result_dim_1: 3, prey_dim_0: 20,
predator_dim_0: 20, process_noise_dim_0: 20,
prey_obs_posterior_dim_0: 20,
predator_obs_posterior_dim_0: 20)
Coordinates:
* chain (chain) int64 1 2 3 4
* draw (draw) int64 0 1 2 3 4 5 6 ... 18 19 20 21 22 23 24
Dimensions without coordinates: initial_outcome_dim_0, integrated_result_dim_0,
integrated_result_dim_1, prey_dim_0,
predator_dim_0, process_noise_dim_0,
prey_obs_posterior_dim_0,
predator_obs_posterior_dim_0
Data variables: (12/14)
m_noise_scale (chain, draw) float64 ...
pred_birth_frac (chain, draw) float64 ...
prey_birth_frac (chain, draw) float64 ...
prey__init (chain, draw) float64 ...
predator__init (chain, draw) float64 ...
process_noise__init (chain, draw) float64 ...
... ...
prey (chain, draw, prey_dim_0) float64 ...
predator (chain, draw, predator_dim_0) float64 ...
process_noise (chain, draw, process_noise_dim_0) float64 ...
prey_obs_posterior (chain, draw, prey_obs_posterior_dim_0) float64 ...
predator_obs_posterior (chain, draw, predator_obs_posterior_dim_0) float64 ...
loglik (chain, draw) float64 ...
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hyunjimoon
commented on August 26, 2024
Other option would be working with cmdstanpy's dataset:
data2draws_data <xarray.Dataset>
Dimensions: (draw: 25, chain: 4, initial_outcome_dim_0: 3,
integrated_result_dim_0: 20,
integrated_result_dim_1: 3, prey_dim_0: 20,
predator_dim_0: 20, process_noise_dim_0: 20,
prey_obs_posterior_dim_0: 20,
predator_obs_posterior_dim_0: 20)
Coordinates:
* chain (chain) int64 1 2 3 4
* draw (draw) int64 0 1 2 3 4 5 6 ... 18 19 20 21 22 23 24
Dimensions without coordinates: initial_outcome_dim_0, integrated_result_dim_0,
integrated_result_dim_1, prey_dim_0,
predator_dim_0, process_noise_dim_0,
prey_obs_posterior_dim_0,
predator_obs_posterior_dim_0
Data variables: (12/14)
m_noise_scale (chain, draw) float64 0.009761 0.01051 ... 0.0116
pred_birth_frac (chain, draw) float64 0.04619 0.04625 ... 0.04621
prey_birth_frac (chain, draw) float64 0.7822 0.7825 ... 0.7822
prey__init (chain, draw) float64 30.0 30.0 30.0 ... 30.0 30.0
predator__init (chain, draw) float64 4.0 4.0 4.0 ... 4.0 4.0 4.0
process_noise__init (chain, draw) float64 0.0 0.0 0.0 ... 0.0 0.0 0.0
... ...
prey (chain, draw, prey_dim_0) float64 30.18 ... 40.82
predator (chain, draw, predator_dim_0) float64 4.024 ... 6...
process_noise (chain, draw, process_noise_dim_0) float64 0.0 .....
prey_obs_posterior (chain, draw, prey_obs_posterior_dim_0) float64 3...
predator_obs_posterior (chain, draw, predator_obs_posterior_dim_0) float64 ...
loglik (chain, draw) float64 nan nan nan ... nan nan nan
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hyunjimoon
commented on August 26, 2024
For now this is dealt by calling data2draws S different number of times
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Related Issues (20)
- Functions declared twice with two draws2data2draws in one model HOT 2
- Sampling restart: failed to integrate to next output time (0.01) in less than max_num_steps steps
- Prior_draw multiIndex cannot be serialized while storing inferencedata as netcdf file HOT 1
- Different dimension for pre-defined kwargs and data HOT 3
- Decoupling input (S, M, N, P, Q) and output (stan_files, data, plot)
- System for maintaining sbc.nc file HOT 3
- Documenting context type classification HOT 1
- Recycling model creates dataFunc twice in function file HOT 1
- kwargs update to include observed data causes problem in to dataset HOT 1
- Multiindex after stacking chain, draw for sbc.prior inferencedata
- updating time step to savepars
- Time index wise plot HOT 1
- wrong parentheses order in builder
- set_prior is sensitive to the input order HOT 2
- sbc rank histogram bug
- multiple subscript HOT 3
- Testing new stanify - replicated? datastructure? HOT 7
- test new interface HOT 1
- speed up with shared metric information
- mkdir stanfile edge cases
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