Package: ruminate 0.2.5

ruminate: A Pharmacometrics Data Transformation and Analysis Tool

Exploration of pharmacometrics data involves both general tools (transformation and plotting) and specific techniques (non-compartmental analysis). This kind of exploration is generally accomplished by utilizing different packages. The purpose of 'ruminate' is to create a 'shiny' interface to make these tools more broadly available while creating reproducible results.

Authors:John Harrold [aut, cre]

ruminate_0.2.5.tar.gz
ruminate_0.2.5.zip(r-4.5)ruminate_0.2.5.zip(r-4.4)ruminate_0.2.5.zip(r-4.3)
ruminate_0.2.5.tgz(r-4.4-any)ruminate_0.2.5.tgz(r-4.3-any)
ruminate_0.2.5.tar.gz(r-4.5-noble)ruminate_0.2.5.tar.gz(r-4.4-noble)
ruminate_0.2.5.tgz(r-4.4-emscripten)ruminate_0.2.5.tgz(r-4.3-emscripten)
ruminate.pdf |ruminate.html✨
ruminate/json (API)
NEWS

# Install 'ruminate' in R:
install.packages('ruminate', repos = c('https://john-harrold.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/john-harrold/ruminate/issues

On CRAN:

6.55 score 69 scripts 195 downloads 74 exports 114 dependencies

Last updated 5 days agofrom:c6f14831d6. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 17 2024
R-4.5-winERRORNov 17 2024
R-4.5-linuxERRORNov 17 2024
R-4.4-winERRORNov 17 2024
R-4.4-macERRORNov 17 2024
R-4.3-winERRORNov 17 2024
R-4.3-macERRORNov 17 2024

Exports:apply_route_mapCTS_add_covariateCTS_add_ruleCTS_append_reportCTS_change_source_modelCTS_del_current_elementCTS_fetch_codeCTS_fetch_current_elementCTS_fetch_dsCTS_fetch_sc_metaCTS_fetch_stateCTS_init_stateCTS_new_elementCTS_plot_elementCTS_preloadCTS_ServerCTS_set_current_elementCTS_sim_isgoodCTS_simulate_elementCTS_test_mksessionCTS_update_checksumdose_records_builderfetch_rxinfoMB_append_reportMB_build_codeMB_del_current_elementMB_fetch_appendsMB_fetch_catalogMB_fetch_codeMB_fetch_componentMB_fetch_current_elementMB_fetch_mdlMB_fetch_stateMB_init_stateMB_new_elementMB_preloadMB_ServerMB_set_current_elementMB_test_catalogMB_test_mksessionMB_update_checksumMB_update_modelmk_figure_ind_obsmk_rx_objmk_subjectsmk_table_ind_obsmk_table_nca_paramsNCA_append_reportnca_builderNCA_fetch_ana_dsNCA_fetch_ana_pkncaNCA_fetch_codeNCA_fetch_current_anaNCA_fetch_current_objNCA_fetch_data_formatNCA_fetch_dsNCA_fetch_np_metaNCA_fetch_PKNCA_metaNCA_fetch_stateNCA_find_colNCA_mkactive_anaNCA_new_anaNCA_preloadNCA_process_current_anaNCA_ServerNCA_set_current_anaNCA_test_mksessionplot_sr_evplot_sr_tcruminateruminate_checkrun_nca_componentsrx2othersimulate_rules

Dependencies:askpassbackportsbase64encbitbit64bslibcachemcellrangercheckmateclicliprcolorspacecommonmarkcpp11crayoncrosstalkcurldata.tabledigestdplyrDTevaluatefansifarverfastmapflextablefontawesomefontBitstreamVerafontLiberationfontquiverformodsfsgdtoolsgenericsggforceggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttpuvhttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeofficeronbrandopensslpillarpkgconfigPKNCAplotlypolyclipprettyunitsprogresspromisespurrrR6raggrappdirsRColorBrewerRcppRcppEigenreadrreadxlrematchrhandsontablerlangrmarkdownsassscalesshinyshinyAceshinyWidgetssourcetoolsstringistringrsyssystemfontstextshapingtibbletidyrtidyselecttinytextweenrtzdbutf8uuidvctrsviridisLitevroomwithrwritexlxfunxml2xtableyamlzip

Clinical Trial Simulation

Rendered fromclinical_trial_simulation.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2024-10-08
Started: 2023-12-27

Deployment and Customization

Rendered fromdeployment.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2024-10-05
Started: 2023-09-01

Model Building

Rendered frommodel_builder.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2024-05-16
Started: 2023-10-01

Noncompartmental Analysis

Rendered fromnoncompartmental_analysis.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2023-12-27
Started: 2023-04-17

Readme and manuals

Help Manual

Help pageTopics
Applies Route Mapping to Datasetapply_route_map
Add Covariate to ElemetntCTS_add_covariate
Add Rule to ElementCTS_add_rule
Append Report ElementsCTS_append_report
Change the Source ModelCTS_change_source_model
Deletes Current cohortCTS_del_current_element
Fetch Module CodeCTS_fetch_code
Fetches Current cohortCTS_fetch_current_element
Fetch Clinical Trial Simulator Module DatasetsCTS_fetch_ds
Fetches Simulation Parameter Meta InformationCTS_fetch_sc_meta
Fetch Clinical Trial Simulator StateCTS_fetch_state
Initializes Cohort When Model ChangesCTS_init_element_model
Initialize CTS Module StateCTS_init_state
New Clinical Trial Simulation CohortCTS_new_element
Plots the Specified ElementCTS_plot_element
Preload Data for CTS ModuleCTS_preload
Clinical Trial Simulator State ServerCTS_Server
Sets the Value for the Current cohortCTS_set_current_element
Checks Simulation in Element for GoodnessCTS_sim_isgood
Simulates the Specified ElementCTS_simulate_element
Populate Session Data for Module TestingCTS_test_mksession
Updates CTS Module ChecksumCTS_update_checksum
Builds Dose Records Dataframedose_records_builder
Fetches Information from an rxode2 Objectfetch_rxinfo
Extracts Timecourse and Merges Covariatesfetch_rxtc
Append Report ElementsMB_append_report
Build Code to Generate ModelMB_build_code
Deletes Current modelMB_del_current_element
Fetches List of Available ModelsMB_fetch_appends
Fetches List of Available ModelsMB_fetch_catalog
Fetch Module CodeMB_fetch_code
Fetch Selected Current Model ComponentMB_fetch_component
Fetches Current modelMB_fetch_current_element
Fetch Model Builder Module ModelsMB_fetch_mdl
Fetch Model Builder StateMB_fetch_state
Initialize MB Module StateMB_init_state
New Model Building ModelMB_new_element
Preload Data for MB ModuleMB_preload
Model Builder State ServerMB_Server
Sets the Value for the Current modelMB_set_current_element
Tests the Model CatalogMB_test_catalog
Populate Session Data for Module TestingMB_test_mksession
Update MB Module ChecksumMB_update_checksum
Updates Current Element with rxode2 ModelMB_update_model
Creates Figures of Individual Observations from PKNCA Resultmk_figure_ind_obs
Makes an rxode2 Objectmk_rx_obj
Fetches Information from an rxode2 Objectmk_subjects
Creates Tables of Individual Observations from PKNCA Resultmk_table_ind_obs
Create Tabular Output from PKNCA Resultsmk_table_nca_params
Adds Analysis Interval to Current AnalysisNCA_add_int
Append Report ElementsNCA_append_report
Builds NCA Code from ui Elementsnca_builder
Fetch Analysis DatasetNCA_fetch_ana_ds
Fetch PKNCA Results ObjectNCA_fetch_ana_pknca
Fetch Module CodeNCA_fetch_code
Fetches Current AnalysisNCA_fetch_current_ana
Fetches the Current Analysis ObjectNCA_fetch_current_obj
Fetches Details About Data RequirementsNCA_fetch_data_format
Fetch Module DatasetsNCA_fetch_ds
Fetches NCA Parameter Meta InformationNCA_fetch_np_meta
Fetches PKNCA MetadataNCA_fetch_PKNCA_meta
Fetch ruminate StateNCA_fetch_state
Determines Default Column NameNCA_find_col
Initialize NCA Module StateNCA_init_state
Loads Pre-Defined ScenarioNCA_load_scenario
Fetch PKNCA Results ObjectNCA_mkactive_ana
Initialize New AnalysisNCA_new_ana
Preload Data for NCA ModuleNCA_preload
Processes Current Analysis to be RunNCA_process_current_ana
Fetch Non-Compartmental Analysis StateNCA_Server
Sets Current AnalysisNCA_set_current_ana
Populate Session Data for Module TestingNCA_test_mksession
Plots Timecourse of Rules Simulationsplot_sr_ev
Plots Timecourse of Rules Simulationsplot_sr_tc
ruminate: Shiny app and module to facilitate pharamacometrics analysisruminate-package ruminate
Checks 'ruminate' Dependenciesruminate_check
Runs NCA for the Current Analysisrun_nca_components
Converts an rxode2 Object Into Specified Model Formatrx2other
Rule-Based simulatessimulate_rules