Package: ruminate 0.4.0

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. Currently there are modules for uploading one or more datasets, data wrangling, plot genreation, non-compartmental analysis, construction of ODE-based models, and constructing and running adaptive trial simualtions. Analyses can be saved and reloaded later. It's possible to create workflows to automate analyses. There is integrated reporting in Word, Powerpoint and Excel. You can also generate scripts to replicate what was done in the app to create a stand-alone script to run in validated environments.

Authors:John Harrold [aut, cre]

ruminate_0.4.0.tar.gz
ruminate_0.4.0.zip(r-4.7)ruminate_0.4.0.zip(r-4.6)ruminate_0.4.0.zip(r-4.5)
ruminate_0.4.0.tgz(r-4.6-any)ruminate_0.4.0.tgz(r-4.5-any)
ruminate_0.4.0.tar.gz(r-4.7-any)ruminate_0.4.0.tar.gz(r-4.6-any)
ruminate_0.4.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ruminate/json (API)

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

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

Pkgdown/docs site:https://ruminate.ubiquity.tools

On CRAN:

Conda:

5.57 score 5 stars 134 scripts 217 downloads 84 exports 117 dependencies

Last updated from:2b58cceec2. Checks:1 WARNING, 7 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING374
source / vignettesERROR335
linux-release-x86_64ERROR388
macos-release-arm64ERROR294
macos-oldrel-arm64ERROR278
windows-develERROR609
windows-releaseERROR561
windows-oldrelERROR539
wasm-releaseOK187

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_mk_preloadCTS_new_elementCTS_plot_elementCTS_preloadCTS_ServerCTS_set_current_elementCTS_sim_isgoodCTS_simulate_elementCTS_test_mksessionCTS_update_checksumdose_records_builderfetch_rxinfoflag_nca_dsMB_append_reportMB_build_codeMB_del_current_elementMB_fetch_appendsMB_fetch_catalogMB_fetch_codeMB_fetch_componentMB_fetch_current_elementMB_fetch_mdlMB_fetch_stateMB_init_stateMB_mk_preloadMB_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_ind_obs_flagsmk_table_nca_paramsNCA_append_reportnca_append_report_figsNCA_append_report_oldnca_append_report_tblsnca_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_mk_preloadNCA_mkactive_anaNCA_new_anaNCA_preloadNCA_process_current_anaNCA_reset_manual_flagsNCA_ServerNCA_set_current_anaNCA_test_mksessionNCA_update_checksumplot_sr_evplot_sr_tcruminateruminate_checkrun_nca_componentsrx2othersimulate_rules

Dependencies:askpassbackportsbase64encbitbit64bslibcachemcellrangercheckmateclicliprcommonmarkcpp11crayoncrosstalkcurldata.tabledigestdplyrDTevaluatefarverfastmapflextablefontawesomefontBitstreamVerafontLiberationfontquiverforcatsforeignformodsfsgdtoolsgenericsggforceggplot2gluegtablehavenhighrhmshtmltoolshtmlwidgetshttpuvhttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSmemoisemimenlmeofficeronbrandopensslotelpillarpkgconfigPKNCAplotlypolyclipprettyunitsprogresspromisespurrrR.methodsS3R.ooR.utilsR6raggrappdirsRColorBrewerRcppreadrreadxlrematchrhandsontableriorlangrmarkdownS7sassscalesshinyshinyAceshinyWidgetssourcetoolsstringistringrsyssystemfontstextshapingtibbletidyrtidyselecttinytextweenrtzdbutf8uuidvctrsviridisLitevroomwithrwritexlxfunxml2xtableyamlzip

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
Make List of Current CTS StateCTS_mk_preload
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
Creates Dataset Flagsflag_nca_ds
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
Make List of Current MB StateMB_mk_preload
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
Creates Tables of Manual Flags for Individual Observations from PKNCA Resultmk_table_ind_obs_flags
Create Tabular Output from PKNCA Resultsmk_table_nca_params
Adds Analysis Interval to Current AnalysisNCA_add_int
Append Report ElementsNCA_append_report
Append NCA Figures to Reportnca_append_report_figs
Append Report ElementsNCA_append_report_old
Append NCA Tables to Reportnca_append_report_tbls
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
Make List of Current NCA StateNCA_mk_preload
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
Reset Manual FlagsNCA_reset_manual_flags
Fetch Non-Compartmental Analysis StateNCA_Server
Sets Current AnalysisNCA_set_current_ana
Populate Session Data for Module TestingNCA_test_mksession
Updates NCA Module ChecksumNCA_update_checksum
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