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Merge pull request #64 from mrc-ide/mrc-5159
Rename from mcstate2 to monty
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,20 +1,20 @@ | ||
| Package: mcstate2 | ||
| Title: Next Generation mcstate | ||
| Version: 0.1.9 | ||
| Package: monty | ||
| Title: Monte Carlo Models | ||
| Version: 0.2.0 | ||
| Authors@R: c(person("Rich", "FitzJohn", role = c("aut", "cre"), | ||
| email = "[email protected]"), | ||
| person("Imperial College of Science, Technology and Medicine", | ||
| role = "cph")) | ||
| Description: Experimental sources for the next generation of mcstate, | ||
| which will support much of the old mcstate functionality but new | ||
| things like better parameter interfaces, Hamiltonian Monte Carlo, | ||
| and other features. | ||
| now called 'monty', which will support much of the old mcstate | ||
| functionality but new things like better parameter interfaces, | ||
| Hamiltonian Monte Carlo, and other features. | ||
| License: MIT + file LICENSE | ||
| Encoding: UTF-8 | ||
| Roxygen: list(markdown = TRUE) | ||
| RoxygenNote: 7.3.2 | ||
| URL: https://mrc-ide.github.io/mcstate2, https://github.com/mrc-ide/mcstate2 | ||
| BugReports: https://github.com/mrc-ide/mcstate2/issues | ||
| URL: https://mrc-ide.github.io/monty, https://github.com/mrc-ide/monty | ||
| BugReports: https://github.com/mrc-ide/monty/issues | ||
| Imports: | ||
| R6, | ||
| cli, | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,45 +1,45 @@ | ||
| # Generated by roxygen2: do not edit by hand | ||
|
|
||
| S3method("+",mcstate_model) | ||
| S3method(cnd_footer,mcstate2_parse_error) | ||
| S3method(coda::as.mcmc.list,mcstate_samples) | ||
| S3method(posterior::as_draws_array,mcstate_samples) | ||
| S3method(posterior::as_draws_df,mcstate_samples) | ||
| S3method(print,mcstate_model) | ||
| S3method(print,mcstate_observer) | ||
| S3method(print,mcstate_packer) | ||
| S3method(print,mcstate_runner) | ||
| S3method(print,mcstate_sampler) | ||
| S3method(print,mcstate_samples) | ||
| export(mcstate_differentiation) | ||
| export(mcstate_domain_expand) | ||
| export(mcstate_dsl) | ||
| export(mcstate_dsl_distributions) | ||
| export(mcstate_dsl_error_explain) | ||
| export(mcstate_dsl_parse_distribution) | ||
| export(mcstate_model) | ||
| export(mcstate_model_combine) | ||
| export(mcstate_model_density) | ||
| export(mcstate_model_direct_sample) | ||
| export(mcstate_model_gradient) | ||
| export(mcstate_model_properties) | ||
| export(mcstate_observer) | ||
| export(mcstate_packer) | ||
| export(mcstate_rng) | ||
| export(mcstate_rng_distributed_pointer) | ||
| export(mcstate_rng_distributed_state) | ||
| export(mcstate_rng_pointer) | ||
| export(mcstate_runner_parallel) | ||
| export(mcstate_runner_serial) | ||
| export(mcstate_runner_simultaneous) | ||
| export(mcstate_sample) | ||
| export(mcstate_sample_continue) | ||
| export(mcstate_sampler_adaptive) | ||
| export(mcstate_sampler_hmc) | ||
| export(mcstate_sampler_nested_adaptive) | ||
| export(mcstate_sampler_nested_random_walk) | ||
| export(mcstate_sampler_random_walk) | ||
| S3method("+",monty_model) | ||
| S3method(cnd_footer,monty_parse_error) | ||
| S3method(coda::as.mcmc.list,monty_samples) | ||
| S3method(posterior::as_draws_array,monty_samples) | ||
| S3method(posterior::as_draws_df,monty_samples) | ||
| S3method(print,monty_model) | ||
| S3method(print,monty_observer) | ||
| S3method(print,monty_packer) | ||
| S3method(print,monty_runner) | ||
| S3method(print,monty_sampler) | ||
| S3method(print,monty_samples) | ||
| export(monty_differentiation) | ||
| export(monty_domain_expand) | ||
| export(monty_dsl) | ||
| export(monty_dsl_distributions) | ||
| export(monty_dsl_error_explain) | ||
| export(monty_dsl_parse_distribution) | ||
| export(monty_model) | ||
| export(monty_model_combine) | ||
| export(monty_model_density) | ||
| export(monty_model_direct_sample) | ||
| export(monty_model_gradient) | ||
| export(monty_model_properties) | ||
| export(monty_observer) | ||
| export(monty_packer) | ||
| export(monty_rng) | ||
| export(monty_rng_distributed_pointer) | ||
| export(monty_rng_distributed_state) | ||
| export(monty_rng_pointer) | ||
| export(monty_runner_parallel) | ||
| export(monty_runner_serial) | ||
| export(monty_runner_simultaneous) | ||
| export(monty_sample) | ||
| export(monty_sample_continue) | ||
| export(monty_sampler_adaptive) | ||
| export(monty_sampler_hmc) | ||
| export(monty_sampler_nested_adaptive) | ||
| export(monty_sampler_nested_random_walk) | ||
| export(monty_sampler_random_walk) | ||
| export(with_trace_random) | ||
| importFrom(R6,R6Class) | ||
| importFrom(rlang,cnd_footer) | ||
| useDynLib(mcstate2, .registration = TRUE) | ||
| useDynLib(monty, .registration = TRUE) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,93 +1,93 @@ | ||
| # Generated by cpp11: do not edit by hand | ||
|
|
||
| mcstate_rng_alloc <- function(r_seed, n_streams, deterministic, is_float) { | ||
| .Call(`_mcstate2_mcstate_rng_alloc`, r_seed, n_streams, deterministic, is_float) | ||
| monty_rng_alloc <- function(r_seed, n_streams, deterministic, is_float) { | ||
| .Call(`_monty_monty_rng_alloc`, r_seed, n_streams, deterministic, is_float) | ||
| } | ||
|
|
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| mcstate_rng_jump <- function(ptr, is_float) { | ||
| invisible(.Call(`_mcstate2_mcstate_rng_jump`, ptr, is_float)) | ||
| monty_rng_jump <- function(ptr, is_float) { | ||
| invisible(.Call(`_monty_monty_rng_jump`, ptr, is_float)) | ||
| } | ||
|
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| mcstate_rng_long_jump <- function(ptr, is_float) { | ||
| invisible(.Call(`_mcstate2_mcstate_rng_long_jump`, ptr, is_float)) | ||
| monty_rng_long_jump <- function(ptr, is_float) { | ||
| invisible(.Call(`_monty_monty_rng_long_jump`, ptr, is_float)) | ||
| } | ||
|
|
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| mcstate_rng_random_real <- function(ptr, n, n_threads, is_float) { | ||
| .Call(`_mcstate2_mcstate_rng_random_real`, ptr, n, n_threads, is_float) | ||
| monty_rng_random_real <- function(ptr, n, n_threads, is_float) { | ||
| .Call(`_monty_monty_rng_random_real`, ptr, n, n_threads, is_float) | ||
| } | ||
|
|
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| mcstate_rng_random_normal <- function(ptr, n, n_threads, algorithm, is_float) { | ||
| .Call(`_mcstate2_mcstate_rng_random_normal`, ptr, n, n_threads, algorithm, is_float) | ||
| monty_rng_random_normal <- function(ptr, n, n_threads, algorithm, is_float) { | ||
| .Call(`_monty_monty_rng_random_normal`, ptr, n, n_threads, algorithm, is_float) | ||
| } | ||
|
|
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| mcstate_rng_uniform <- function(ptr, n, r_min, r_max, n_threads, is_float) { | ||
| .Call(`_mcstate2_mcstate_rng_uniform`, ptr, n, r_min, r_max, n_threads, is_float) | ||
| monty_rng_uniform <- function(ptr, n, r_min, r_max, n_threads, is_float) { | ||
| .Call(`_monty_monty_rng_uniform`, ptr, n, r_min, r_max, n_threads, is_float) | ||
| } | ||
|
|
||
| mcstate_rng_exponential_rate <- function(ptr, n, r_rate, n_threads, is_float) { | ||
| .Call(`_mcstate2_mcstate_rng_exponential_rate`, ptr, n, r_rate, n_threads, is_float) | ||
| monty_rng_exponential_rate <- function(ptr, n, r_rate, n_threads, is_float) { | ||
| .Call(`_monty_monty_rng_exponential_rate`, ptr, n, r_rate, n_threads, is_float) | ||
| } | ||
|
|
||
| mcstate_rng_exponential_mean <- function(ptr, n, r_mean, n_threads, is_float) { | ||
| .Call(`_mcstate2_mcstate_rng_exponential_mean`, ptr, n, r_mean, n_threads, is_float) | ||
| monty_rng_exponential_mean <- function(ptr, n, r_mean, n_threads, is_float) { | ||
| .Call(`_monty_monty_rng_exponential_mean`, ptr, n, r_mean, n_threads, is_float) | ||
| } | ||
|
|
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| mcstate_rng_normal <- function(ptr, n, r_mean, r_sd, n_threads, algorithm, is_float) { | ||
| .Call(`_mcstate2_mcstate_rng_normal`, ptr, n, r_mean, r_sd, n_threads, algorithm, is_float) | ||
| monty_rng_normal <- function(ptr, n, r_mean, r_sd, n_threads, algorithm, is_float) { | ||
| .Call(`_monty_monty_rng_normal`, ptr, n, r_mean, r_sd, n_threads, algorithm, is_float) | ||
| } | ||
|
|
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| mcstate_rng_binomial <- function(ptr, n, r_size, r_prob, n_threads, is_float) { | ||
| .Call(`_mcstate2_mcstate_rng_binomial`, ptr, n, r_size, r_prob, n_threads, is_float) | ||
| monty_rng_binomial <- function(ptr, n, r_size, r_prob, n_threads, is_float) { | ||
| .Call(`_monty_monty_rng_binomial`, ptr, n, r_size, r_prob, n_threads, is_float) | ||
| } | ||
|
|
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| mcstate_rng_nbinomial <- function(ptr, n, r_size, r_prob, n_threads, is_float) { | ||
| .Call(`_mcstate2_mcstate_rng_nbinomial`, ptr, n, r_size, r_prob, n_threads, is_float) | ||
| monty_rng_nbinomial <- function(ptr, n, r_size, r_prob, n_threads, is_float) { | ||
| .Call(`_monty_monty_rng_nbinomial`, ptr, n, r_size, r_prob, n_threads, is_float) | ||
| } | ||
|
|
||
| mcstate_rng_hypergeometric <- function(ptr, n, r_n1, r_n2, r_k, n_threads, is_float) { | ||
| .Call(`_mcstate2_mcstate_rng_hypergeometric`, ptr, n, r_n1, r_n2, r_k, n_threads, is_float) | ||
| monty_rng_hypergeometric <- function(ptr, n, r_n1, r_n2, r_k, n_threads, is_float) { | ||
| .Call(`_monty_monty_rng_hypergeometric`, ptr, n, r_n1, r_n2, r_k, n_threads, is_float) | ||
| } | ||
|
|
||
| mcstate_rng_gamma_scale <- function(ptr, n, r_shape, r_scale, n_threads, is_float) { | ||
| .Call(`_mcstate2_mcstate_rng_gamma_scale`, ptr, n, r_shape, r_scale, n_threads, is_float) | ||
| monty_rng_gamma_scale <- function(ptr, n, r_shape, r_scale, n_threads, is_float) { | ||
| .Call(`_monty_monty_rng_gamma_scale`, ptr, n, r_shape, r_scale, n_threads, is_float) | ||
| } | ||
|
|
||
| mcstate_rng_gamma_rate <- function(ptr, n, r_shape, r_rate, n_threads, is_float) { | ||
| .Call(`_mcstate2_mcstate_rng_gamma_rate`, ptr, n, r_shape, r_rate, n_threads, is_float) | ||
| monty_rng_gamma_rate <- function(ptr, n, r_shape, r_rate, n_threads, is_float) { | ||
| .Call(`_monty_monty_rng_gamma_rate`, ptr, n, r_shape, r_rate, n_threads, is_float) | ||
| } | ||
|
|
||
| mcstate_rng_poisson <- function(ptr, n, r_lambda, n_threads, is_float) { | ||
| .Call(`_mcstate2_mcstate_rng_poisson`, ptr, n, r_lambda, n_threads, is_float) | ||
| monty_rng_poisson <- function(ptr, n, r_lambda, n_threads, is_float) { | ||
| .Call(`_monty_monty_rng_poisson`, ptr, n, r_lambda, n_threads, is_float) | ||
| } | ||
|
|
||
| mcstate_rng_cauchy <- function(ptr, n, r_location, r_scale, n_threads, is_float) { | ||
| .Call(`_mcstate2_mcstate_rng_cauchy`, ptr, n, r_location, r_scale, n_threads, is_float) | ||
| monty_rng_cauchy <- function(ptr, n, r_location, r_scale, n_threads, is_float) { | ||
| .Call(`_monty_monty_rng_cauchy`, ptr, n, r_location, r_scale, n_threads, is_float) | ||
| } | ||
|
|
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| mcstate_rng_beta <- function(ptr, n, r_a, r_b, n_threads, is_float) { | ||
| .Call(`_mcstate2_mcstate_rng_beta`, ptr, n, r_a, r_b, n_threads, is_float) | ||
| monty_rng_beta <- function(ptr, n, r_a, r_b, n_threads, is_float) { | ||
| .Call(`_monty_monty_rng_beta`, ptr, n, r_a, r_b, n_threads, is_float) | ||
| } | ||
|
|
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| mcstate_rng_multinomial <- function(ptr, n, r_size, r_prob, n_threads, is_float) { | ||
| .Call(`_mcstate2_mcstate_rng_multinomial`, ptr, n, r_size, r_prob, n_threads, is_float) | ||
| monty_rng_multinomial <- function(ptr, n, r_size, r_prob, n_threads, is_float) { | ||
| .Call(`_monty_monty_rng_multinomial`, ptr, n, r_size, r_prob, n_threads, is_float) | ||
| } | ||
|
|
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| mcstate_rng_state <- function(ptr, is_float) { | ||
| .Call(`_mcstate2_mcstate_rng_state`, ptr, is_float) | ||
| monty_rng_state <- function(ptr, is_float) { | ||
| .Call(`_monty_monty_rng_state`, ptr, is_float) | ||
| } | ||
|
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| mcstate_rng_pointer_init <- function(n_streams, seed, long_jump, algorithm) { | ||
| .Call(`_mcstate2_mcstate_rng_pointer_init`, n_streams, seed, long_jump, algorithm) | ||
| monty_rng_pointer_init <- function(n_streams, seed, long_jump, algorithm) { | ||
| .Call(`_monty_monty_rng_pointer_init`, n_streams, seed, long_jump, algorithm) | ||
| } | ||
|
|
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| mcstate_rng_pointer_sync <- function(obj, algorithm) { | ||
| invisible(.Call(`_mcstate2_mcstate_rng_pointer_sync`, obj, algorithm)) | ||
| monty_rng_pointer_sync <- function(obj, algorithm) { | ||
| invisible(.Call(`_monty_monty_rng_pointer_sync`, obj, algorithm)) | ||
| } | ||
|
|
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| test_rng_pointer_get <- function(obj, n_streams) { | ||
| .Call(`_mcstate2_test_rng_pointer_get`, obj, n_streams) | ||
| .Call(`_monty_test_rng_pointer_get`, obj, n_streams) | ||
| } | ||
|
|
||
| test_xoshiro_run <- function(obj) { | ||
| .Call(`_mcstate2_test_xoshiro_run`, obj) | ||
| .Call(`_monty_test_xoshiro_run`, obj) | ||
| } |
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