version 0.3.1

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ruminate
 Title: A Pharmacometrics Data Transformation and Analysis Tool
-Version: 0.2.4
+Version: 0.3.1
 Authors@R: 
     person("John", "Harrold", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-2052-4373"))
@@ -10,19 +10,20 @@ BugReports: https://github.com/john-harrold/ruminate/issues
 URL: https://ruminate.ubiquity.tools/
 Encoding: UTF-8
 Depends: R (>= 4.2.0)
-Imports: digest, dplyr, DT, flextable, formods (>= 0.1.6), ggplot2,
+Imports: digest, dplyr, DT, flextable, formods (>= 0.2.0), ggplot2,
         onbrand (>= 1.0.3), PKNCA (>= 0.10.2), plotly, rhandsontable,
-        rlang, shiny, shinyAce, shinyWidgets, rxode2 (>= 2.1.2), stats,
-        stringr, tidyr, utils, yaml
-Suggests: cli, clipr, gridExtra, knitr, nlmixr2lib, nonmem2rx,
-        prompter, rmarkdown, readxl, rxode2et, shinydashboard, testthat
+        rlang, shiny, shinyAce, shinyWidgets, stats, stringr, tidyr,
+        utils, yaml, zip
+Suggests: babelmixr2, cli, clipr, gridExtra, knitr, nlmixr2lib(>=
+        0.3.0), nonmem2rx, nlmixr2(>= 3.0.0), prompter, rmarkdown,
+        readxl, rxode2 (>= 3.0.0), shinybusy, shinydashboard, testthat
         (>= 3.0.0), ubiquity
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Config/testthat/edition: 3
 VignetteBuilder: knitr
 NeedsCompilation: no
-Packaged: 2024-05-27 05:13:29 UTC; jmh
+Packaged: 2025-01-10 14:59:10 UTC; jmh
 Author: John Harrold [aut, cre] (<https://orcid.org/0000-0003-2052-4373>)
 Maintainer: John Harrold <[email protected]>
 Repository: CRAN
-Date/Publication: 2024-05-28 02:20:03 UTC
+Date/Publication: 2025-01-10 15:50:06 UTC

MD5

@@ -1,68 +1,137 @@
-821b90dd6c9a8b2dbb1915dd176477df *DESCRIPTION
+e57dfec6a74a756cdf36b413e21b44e4 *DESCRIPTION
 c75dff1ced8e1f4ae311ec986bdc4bc7 *LICENSE
-69dfc30f58bc84bc6f549b007a617ad7 *NAMESPACE
-b6035a93caccb9c688f0663eb5816c68 *NEWS.md
-705189a63f1fece8d33cedd262bd2e03 *R/NCA_Server.R
-4e44e78f2e945f8f1b29e295ca20b4b4 *R/ruminate.R
-d6d821e4262736c06c4e09cf370229be *R/simulate_rules.R
-0424038a16d2a5fd31f37a07bfb9490b *README.md
-baebd2fd579dde4eccad531a01730bfb *build/vignette.rds
-dfafb626d3d2e8be8f5538d16448e730 *inst/doc/deployment.R
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-c9c2d4e563454e6b1d0029341cc05819 *inst/doc/noncompartmental_analysis.R
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+59774574f48b772ca5fe741d99c96614 *NEWS.md
+7c9792066249d95d41cea973b79e3171 *R/CTS_Server.R
+6dcb25a37e0bb7304ef4f1e4e22cd9d1 *R/MB_Server.R
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 0e9ed425f6ddd590bb3ee344c35dab9b *inst/doc/noncompartmental_analysis.Rmd
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 55cc875211bdfb5a406b3d933ba71f0c *inst/docker/Dockerfile
-7eaf2d0e809cc2d18ed2d8ae684e3c69 *inst/docker/install_packages.R
-cd33e1af8c168ec1486ab755c0dea428 *inst/docker/local_container
-d66f894d395489b276f80acfafa5f15c *inst/templates/NCA.yaml
+eae6837cc5ee9425b161e404c972c6a9 *inst/docker/install_packages.R
+7061bc5a6fca670503fb3cac105a0f49 *inst/docker/local_container
+253ef298cf5021c2cc5b8117e7b6b8fe *inst/preload/CTS_preload.yaml
+f6beedd896a27690f3409005644edb4e *inst/preload/CTS_preload_minimal.yaml
+6a2cd5c4d990cd656802f1931642c299 *inst/preload/MB_preload.yaml
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+3feb4c96fd61591834767957ab6b87f7 *inst/templates/NCA.yaml
 032b7e7f26c652304efbe73f3c03cbb4 *inst/templates/NCA_module_components.R
-222f0d3e0418f3118fc42c1883f2cfbb *inst/templates/ruminate.R
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 136462ad7c4be0fe5b0323d84f4e93cf *inst/test_apps/simulate_rules_ext_funcs.R
-31898fefaa018adb20b672a23d83a522 *inst/test_apps/simulate_rules_funcs.R
+840bc7603970d7cca96fdccc265582d7 *inst/test_apps/simulate_rules_funcs.R
 c13cdc8c6af0f0bc5ff3f644d07b686b *inst/test_apps/test_rxode2_system.R
 7d8e97d1328e210272bb952bd5ddf524 *inst/test_data/dose_from_cols.csv
 b32c70ef35b8eb746db4566f323ca664 *inst/test_data/dose_from_rows.csv
 557838cbec9e76ee4c6e8f7c9903bb10 *inst/test_data/sparse_data.csv
-ec65d77e96b95f16b2bddb9ea32b16bf *man/NCA_Server.Rd
-7400df8189b28ea60f06ee6cd9c414dd *man/NCA_add_int.Rd
-d08c98ed20f5368c994b8dddf4f3c38f *man/NCA_append_report.Rd
+a3e3f31dc1225a99cde041ff86593daf *man/CTS_Server.Rd
+983004500e8dc570b794749feaae3366 *man/CTS_add_covariate.Rd
+ed2919ba2c4e60f8acf9b8e94309f79b *man/CTS_add_rule.Rd
+1aa6a13035f4bf1c37a18e6070521e91 *man/CTS_append_report.Rd
+d4ca07afae9d40ce38f4a71b0b3f2046 *man/CTS_change_source_model.Rd
+10952ed97946665226f19090a3144bb5 *man/CTS_del_current_element.Rd
+b4669050b08f03853b7410eced80fdbf *man/CTS_fetch_code.Rd
+b6a561294b298d5d1ab96fd4730a29ae *man/CTS_fetch_current_element.Rd
+2da6cb6794c14b244e97fa11b203f152 *man/CTS_fetch_ds.Rd
+a5854f6572a5438fda04bfe283eb1cb5 *man/CTS_fetch_sc_meta.Rd
+3f3fe146ed0eeee16ba401bce5582d5d *man/CTS_fetch_state.Rd
+7d2dafcc83d89532d601fc0d05b69ad9 *man/CTS_init_element_model.Rd
+c40769e0077a8172bd0674169f2ac03d *man/CTS_init_state.Rd
+6000a93c44b1537c135a2a656dde2ea1 *man/CTS_mk_preload.Rd
+7c8d1e3423022bc58def1e53bd3d4259 *man/CTS_new_element.Rd
+1467364c0828243eeb933527e93818e7 *man/CTS_plot_element.Rd
+4990c7db9dad6e17f99ed17df37d4e79 *man/CTS_preload.Rd
+6424dd98778f60eacbfafed11ca9b1f5 *man/CTS_set_current_element.Rd
+ecb4801d8c48a8104d7cc5f34915d03e *man/CTS_sim_isgood.Rd
+9a7c843d51a984de0e698899553465da *man/CTS_simulate_element.Rd
+26e6cc750bcb0f66e3dcda986837a3aa *man/CTS_test_mksession.Rd
+5e6d8c180d19db6be1ca92d3f093e772 *man/CTS_update_checksum.Rd
+76c5b8435bae36855dfe6582fed87171 *man/MB_Server.Rd
+7de4ea4b8f49bd55f62d4a98e399d036 *man/MB_append_report.Rd
+cebeb6db51ce2478547e7c0e5a5907f6 *man/MB_build_code.Rd
+f85e84f3e4b4167434f258a73a49e901 *man/MB_del_current_element.Rd
+7445d4a2d822671cfae018e5b00647ee *man/MB_fetch_appends.Rd
+e6f4b5cc633afe6e183cd279f651aeb2 *man/MB_fetch_catalog.Rd
+dbf7a61bac408a7c915ae00642435274 *man/MB_fetch_code.Rd
+cf1bb815a64a58b35591bcb63981d165 *man/MB_fetch_component.Rd
+d23d878064cd14dcc6e71a687e269e50 *man/MB_fetch_current_element.Rd
+4cee495cc77aeb54f7fcf8505d8516c4 *man/MB_fetch_mdl.Rd
+d3607486e0dcd16ffc01d23f8ef7e10b *man/MB_fetch_state.Rd
+c085dd0f13f5d2b419723ea915bc9649 *man/MB_init_state.Rd
+516f683dd8146e353a57c1a4ecb39160 *man/MB_mk_preload.Rd
+16f5986a2d63d9821f4afa8a071e6308 *man/MB_new_element.Rd
+9d86fc26c3f338eaacef2bbbf3d884db *man/MB_preload.Rd
+444fdc0dd4f75ab6d1b0a3f67b9252be *man/MB_set_current_element.Rd
+5a455284371eb6060ebf98fee0c970b4 *man/MB_test_catalog.Rd
+92e4f2d978160b352226f060c8bf01f3 *man/MB_test_mksession.Rd
+00d3eb8375dcd9b0ce7c28e7dee2697b *man/MB_update_checksum.Rd
+fb3069489ba2183e2ac57a5bdd4bdba7 *man/MB_update_model.Rd
+716dccae9aa585ce7994f527f8f4fd27 *man/NCA_Server.Rd
+e9c6be8ef964982355760b5c0dab69ed *man/NCA_add_int.Rd
+bd87deaad26c03351ed65e30dfae9b6c *man/NCA_append_report.Rd
 869079044ae13c2c8eb689cc93ae0cdf *man/NCA_fetch_PKNCA_meta.Rd
-5d9ecb108512b47e314200cf44d160d9 *man/NCA_fetch_ana_ds.Rd
-01b570683106b2319f6e6ea033cc8c7b *man/NCA_fetch_ana_pknca.Rd
-f4b43b650018840fac04da0d742ea390 *man/NCA_fetch_code.Rd
-7dd4377ba9628ed4726c27cf441e3151 *man/NCA_fetch_current_ana.Rd
-0a93f5aa1d444ec9fc318ccf062a8b43 *man/NCA_fetch_current_obj.Rd
+d3009ad9339635cb4c1ad18b301dd96f *man/NCA_fetch_ana_ds.Rd
+7675dc97223831534fdf6e70276e3ee1 *man/NCA_fetch_ana_pknca.Rd
+73f6c0cad8b568627c10c9bab3b73db6 *man/NCA_fetch_code.Rd
+cb99d9ac9067a4e7e78f78a54080468c *man/NCA_fetch_current_ana.Rd
+ef5d76ff30bf1bc8a01a30b3c740c6aa *man/NCA_fetch_current_obj.Rd
 a6d65b50ad37e2aa9eaf78f39d0bddd8 *man/NCA_fetch_data_format.Rd
-a0ccf02754fcf91f9ae6ce95e67bd7cc *man/NCA_fetch_ds.Rd
+8edef64b7bb680e18e801707550b825c *man/NCA_fetch_ds.Rd
 f6f0157d5288fb5dc50d4540427a3caf *man/NCA_fetch_np_meta.Rd
-ac8203d8760ef3a855bcf8db24ec53c7 *man/NCA_fetch_state.Rd
-1950a5f1e04b13f91823a8022d368ea9 *man/NCA_find_col.Rd
+0756fa62393b22568c22e7f0418a06c8 *man/NCA_fetch_state.Rd
+4c6722319fa5dda857670b58d2b43a11 *man/NCA_find_col.Rd
 0e93b5c68e1e6fe3f1b5007b1e4ac931 *man/NCA_init_state.Rd
 63eccdc1a359a01a695f146c8931670a *man/NCA_load_scenario.Rd
-100da85c86eb5abdf0c61a5d3dcb8bcb *man/NCA_mkactive_ana.Rd
-b9c898c3afce3e3633cf71b1dce70d2a *man/NCA_new_ana.Rd
-7eaf8309234f5c93247ca95aa4965fab *man/NCA_process_current_ana.Rd
-46e788646a63b0b8ce7464412093ed83 *man/NCA_set_current_ana.Rd
-543f25a7bdab2b999e1b1de0dd8921bd *man/NCA_test_mksession.Rd
+192f9740de30662d93260b738f40cdaf *man/NCA_mk_preload.Rd
+083b86dda761024ba0dcaa5be56f4513 *man/NCA_mkactive_ana.Rd
+406c94add1ca0c678eff0ec5e3955007 *man/NCA_new_ana.Rd
+4b1f027e7444be6f4fc405724d12a619 *man/NCA_preload.Rd
+ce625c596167ef5881c9177f5a7540d9 *man/NCA_process_current_ana.Rd
+d78dde23d1aff18a06e9631d6181bc02 *man/NCA_set_current_ana.Rd
+1b85cd6b2c5eea7942e1067586118aee *man/NCA_test_mksession.Rd
 611954f5bfe6ea615fb5049dd756946d *man/apply_route_map.Rd
 2761c9f5bd2cda91dc0c714d20e17d63 *man/dose_records_builder.Rd
+857813e08d87da2876a7f57c23841e5e *man/fetch_rxinfo.Rd
+2c1203064b252f838325588c82e7b4e2 *man/fetch_rxtc.Rd
 b9e5c76579fb1fb8e78a77d8126bd527 *man/figures/logo.png
-b8aad6ce651b8612f5bce653b2c3a6de *man/mk_figure_ind_obs.Rd
-bfc41fe5b0194c4681bf67863d309958 *man/mk_table_ind_obs.Rd
-08eb367677788de42c3912a8c46a565c *man/mk_table_nca_params.Rd
-b2ecaf17d6dcccb4d4a8d0108e693f2a *man/nca_builder.Rd
-3a0d62ad7a550e863bfdaab787cc8d7d *man/ruminate.Rd
+37140a9076b99224199b457aad81d8d7 *man/mk_figure_ind_obs.Rd
+5864c8b71d22b3a2d1e6d6fd75826063 *man/mk_rx_obj.Rd
+73df2fa51f28906f6d65c750fac2fa08 *man/mk_subjects.Rd
+eedf829e9e200620503e1cf18aae8196 *man/mk_table_ind_obs.Rd
+ac456b4a52a1f3833831ecd3e036dedb *man/mk_table_nca_params.Rd
+6d6a0ef694010bc266bf1e52aa8077fe *man/nca_builder.Rd
+aa77c104c0b08abae64db5f229c8571a *man/plot_sr_ev.Rd
+adebcd82c41276d45e77a747154c7172 *man/plot_sr_tc.Rd
+a7a14d98e41065f7c764d39bef526df4 *man/ruminate.Rd
 00903b9adbdb4b369512b2d440bb32da *man/ruminate_check.Rd
-46e0221fc3ae596094a6ed89b1abb44e *man/run_nca_components.Rd
+c8cef9357a72290409f9ae0c7df6ecac *man/run_nca_components.Rd
+a00681187ad9444c1f2abcb5f6407fc2 *man/rx2other.Rd
+e12d67dc53dc27755b46820a4f7d8f54 *man/simulate_rules.Rd
 c8f327d23d2d19f4d7f6fb2ff5de1485 *tests/testthat.R
-8370972831cc6c9080daf72a78f4efa7 *tests/testthat/test-NCA.R
+7c850344e8377dab55209fa4084a7085 *tests/testthat/test-CTS.R
+c57b210dee7f82c6ebf97b2c2601a4e7 *tests/testthat/test-NCA.R
+03f68057a26723439e2c6de9cfe33eef *tests/testthat/test-fetch_rxinfo.R
 4bca8ac82fa2bcb697f10b887bf7408c *tests/testthat/test-span_table.R
 405556c04d675b545ce9515939407741 *vignettes/NCA_presim.RData
-ef690d629d1346fa291ff325e111e812 *vignettes/deployment.Rmd
+1355b20aacf295f3145e6676c5278314 *vignettes/deployment.Rmd
 0e9ed425f6ddd590bb3ee344c35dab9b *vignettes/noncompartmental_analysis.Rmd
-a3b7c3b2026748a3db165b64a0f3394c *vignettes/rmdhunks/simulate_rules.Rmd
+2e90df2025a3934b0b90670f1ea6fce8 *vignettes/rmdhunks/simulate_rules.Rmd

NAMESPACE

@@ -1,5 +1,46 @@
 # Generated by roxygen2: do not edit by hand
 
+export(CTS_Server)
+export(CTS_add_covariate)
+export(CTS_add_rule)
+export(CTS_append_report)
+export(CTS_change_source_model)
+export(CTS_del_current_element)
+export(CTS_fetch_code)
+export(CTS_fetch_current_element)
+export(CTS_fetch_ds)
+export(CTS_fetch_sc_meta)
+export(CTS_fetch_state)
+export(CTS_init_state)
+export(CTS_mk_preload)
+export(CTS_new_element)
+export(CTS_plot_element)
+export(CTS_preload)
+export(CTS_set_current_element)
+export(CTS_sim_isgood)
+export(CTS_simulate_element)
+export(CTS_test_mksession)
+export(CTS_update_checksum)
+export(MB_Server)
+export(MB_append_report)
+export(MB_build_code)
+export(MB_del_current_element)
+export(MB_fetch_appends)
+export(MB_fetch_catalog)
+export(MB_fetch_code)
+export(MB_fetch_component)
+export(MB_fetch_current_element)
+export(MB_fetch_mdl)
+export(MB_fetch_state)
+export(MB_init_state)
+export(MB_mk_preload)
+export(MB_new_element)
+export(MB_preload)
+export(MB_set_current_element)
+export(MB_test_catalog)
+export(MB_test_mksession)
+export(MB_update_checksum)
+export(MB_update_model)
 export(NCA_Server)
 export(NCA_append_report)
 export(NCA_fetch_PKNCA_meta)
@@ -13,25 +54,33 @@ export(NCA_fetch_ds)
 export(NCA_fetch_np_meta)
 export(NCA_fetch_state)
 export(NCA_find_col)
+export(NCA_mk_preload)
 export(NCA_mkactive_ana)
 export(NCA_new_ana)
+export(NCA_preload)
 export(NCA_process_current_ana)
 export(NCA_set_current_ana)
 export(NCA_test_mksession)
 export(apply_route_map)
 export(dose_records_builder)
+export(fetch_rxinfo)
 export(mk_figure_ind_obs)
+export(mk_rx_obj)
+export(mk_subjects)
 export(mk_table_ind_obs)
 export(mk_table_nca_params)
 export(nca_builder)
+export(plot_sr_ev)
+export(plot_sr_tc)
 export(ruminate)
 export(ruminate_check)
 export(run_nca_components)
+export(rx2other)
+export(simulate_rules)
 import(dplyr)
 import(formods)
 import(ggplot2)
 import(rhandsontable)
-import(rxode2)
 import(shiny)
 import(tidyr)
 importFrom(digest,digest)

NEWS.md

@@ -1,4 +1,13 @@
-# ruminate 0.2.4 (development version)
+# ruminate 0.3.0 (development version)
+
+- Fix for rxode 3.0 release.
+- Using new yaml save methodology for formods, and will break previous saved states
+- Added preload() and mk_preload() files
+- Updated `templates/ruminate.R` and `templates/ruminate_development.R` apps
+  to use the preload file in the unzipped analysis state.
+
+
+# ruminate 0.2.4 
 
 - Fixed issue where changes in data views was leading to PH appearing in the 
   NCA data source selection