Package: campsisnca 1.7.2
Nicolas Luyckx
campsisnca: Non-Compartmental Analysis for Campsis Simulation Platform
A flexible and user-friendly non-compartmental analysis (NCA) toolkit designed to work seamlessly with simulated pharmacokinetic data generated using the 'campsis' ecosystem. The package provides a comprehensive framework to compute standard and custom NCA metrics, including exposure (AUC), peak/trough concentrations, half-life and time-above/below thresholds, with support for configurable time windows and summary statistics. 'campsisnca' integrates tightly with 'campsis' and 'campsismod', enabling streamlined workflows from simulation to analysis. In addition, the package provides a JSON-based interface to define NCA analyses, metrics and options using formal schemas, allowing analyses to be created, validated and executed outside of R and facilitating reproducibility, automation and system integration. The package also includes utilities for generating formatted summary tables and exporting results in multiple formats suitable for reporting. Trapezoidal rule implementation for AUC calculation is based on the 'qpNCA' package by Huisman, Jolling, Mehta and Bergsma (2021) <doi:10.32614/CRAN.package.qpNCA>, following methodology from Rowland and Tozer (2011, ISBN:978-0-683-07404-8). The package itself is licensed under the GPL (>= 3); the JSON schema files shipped in inst/extdata are licensed separately under the Creative Commons Attribution 4.0 International (CC BY 4.0).
Authors:
campsisnca_1.7.2.tar.gz
campsisnca_1.7.2.zip(r-4.7-any)campsisnca_1.7.2.zip(r-4.6-any)campsisnca_1.7.2.zip(r-4.5-any)
campsisnca_1.7.2.tgz(r-4.6-any)campsisnca_1.7.2.tgz(r-4.5-any)
campsisnca_1.7.2.tar.gz(r-4.7-any)campsisnca_1.7.2.tar.gz(r-4.6-any)
campsisnca_1.7.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
campsisnca/json (API)
| # Install 'campsisnca' in R: |
| install.packages('campsisnca', repos = c('https://calvagone.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/calvagone/campsisnca/issues
- pk_bolus_md - Simulated Pharmacokinetic Dataset
Last updated from:84c9b0c38b. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 303 | ||
| source / vignettes | OK | 266 | ||
| linux-release | OK | 298 | ||
| macos-release | OK | 173 | ||
| macos-oldrel | OK | 199 | ||
| windows-devel | OK | 212 | ||
| windows-release | OK | 232 | ||
| windows-oldrel | OK | 306 | ||
| wasm-release | OK | 192 |
Exports:%>%apply_time_windowapplyTimeWindowAUCAvgcalculateCAtCavgCFBChangeFromBaselineCmaxCmincompute_nca_metric_summarycomputeTimeAboveBelowCtroughCustomMetricCustomMetricTblcvdiscard_category_columndiscardCategoryColumnextract_brace_valuesgenerate_table_codegeocvgeomeanget_character_cols_onlyget_default_nameget_latex_nameget_strataget_unitgetCampsisncaOptiongetCampsisncaOptionsglue_stat_displayi_valuei_value_tbli_valuesiValueLastMaxmetrics.1cptmetrics.2cptmetrics.commonMinNCAAnalysisNCAMetricsNCAMetricsTableNCAOptionsNCATablepreserve_column_levelsremove_column_levelsReplicatedNCATablerestore_column_levelssave_column_levelssestat_display_stringThalfThalf.1cptthalf.1cpt.requiredThalf.2cpt.distThalf.2cpt.effthalf.2cpt.requiredThalf.2cpt.zTimeAboveLimitTimeBelowLimittimerangeTimeWindowTmaxTmintoGtUndefinedNCAOptionsUndefinedTimeWindowValueAt
Dependencies:assertthatbase64encbigDbitbit64bitopsbslibcachemcampsiscampsismodcardscardxclicliprcodetoolscommonmarkcpp11crayoncurldigestdplyrevaluatefarverfastmapfontawesomefsfurrrfuturegenericsggplot2globalsgluegtgtablegtsummaryhighrhmshtmltoolshtmlwidgetsisobandjquerylibjsonlitejsonvalidatejuicyjuiceknitrlabelingLaplacesDemonlifecyclelistenvlitedownmagrittrmarkdownMASSmemoisemimeparallellypillarpkgconfigprettyunitsprogressprogressrpurrrR6rappdirsRColorBrewerRcppreactablereactRreadrrlangrmarkdownS7sassscalesstringistringrtibbletidyrtidyselecttinytextzdbutf8V8vctrsviridisLitevroomwithrxfunxml2yaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Abstract avg metric class. | abstract_avg_metric-class |
| Abstract last metric class. | abstract_last_metric-class |
| Abstract max metric class. | abstract_max_metric-class |
| Abstract min metric class. | abstract_min_metric-class |
| Abstract time above/below limit class. | abstract_time_above_or_below_limit_metric-class |
| Abstract value at metric class. | abstract_value_at_metric-class |
| Apply time window. | apply_time_window apply_time_window,ANY,nca_time_window,character-method |
| Apply time window. | applyTimeWindow |
| AUC. | AUC |
| AUC metric class. | auc_metric-class |
| Avg. | Avg |
| Avg metric class. | avg_metric-class |
| Calculate. | calculate calculate,nca_analyses,ANY-method calculate,nca_analysis,ANY-method calculate,nca_metric,ANY-method calculate,nca_table,ANY-method calculate,replicated_nca_table,campsis_output-method calculate,theoretical_thalf_metric,ANY-method |
| The Campsis Output Class Union | campsis_output campsis_output-class |
| The Campsisnca Output Class Union | campsisnca_output campsisnca_output-class |
| Campsisnca table class (see this class as an interface) | campsisnca_tbl campsisnca_tbl-class |
| CAt (concentration at specific time). | CAt |
| Cavg. | Cavg |
| Cavg metric class. | cavg_metric-class |
| Alias for Change from Baseline (CFB). | CFB |
| Change from Baseline metric class. | cfb_metric-class |
| Change from Baseline (CFB). | ChangeFromBaseline |
| Cmax. | Cmax |
| Cmax metric class. | cmax_metric-class |
| Cmin | Cmin |
| Cmin metric class. | cmin_metric-class |
| Compute NCA metric summary. | compute_nca_metric_summary |
| Compute the duration of a line segment above or below a certain limit. | computeTimeAboveBelow |
| Concentration at metric class. | conc_at_metric-class |
| Ctrough. Last time in x shall be considered as the trough time. Similar to Last, but for concentrations. | Ctrough |
| Ctrough metric class. | ctrough_metric-class |
| Custom metric class. | custom_metric-class |
| Custom metric (input data as time and value vectors). | CustomMetric |
| Custom metric (input data as tibble). | CustomMetricTbl |
| Compute the coefficient of variation. | cv |
| Dataframe export type class. | dataframe_type-class |
| Custom deparse function. Works similarly to deparse1. However, lines are trimmed before being concatenated. | deparse_digits |
| Deparse 1 line. | deparse_one_line |
| Discard category column. | discard_category_column |
| Discard category column. | discardCategoryColumn |
| Export replicated NCA table. | export,replicated_nca_table,character-method |
| Extract values from within braces. | extract_brace_values |
| Generate table code. | generate_table_code generate_table_code,nca_table,logical-method |
| Compute the geometric CV. | geocv |
| Compute the geometric mean. | geomean |
| Filter Column Names to Character (and Optionally Factor) Columns | get_character_cols_only |
| Get default name. | get_default_name get_default_name,auc_metric-method get_default_name,avg_metric-method get_default_name,cavg_metric-method get_default_name,cfb_metric-method get_default_name,cmax_metric-method get_default_name,cmin_metric-method get_default_name,conc_at_metric-method get_default_name,ctrough_metric-method get_default_name,last_metric-method get_default_name,max_metric-method get_default_name,min_metric-method get_default_name,nca_metric-method get_default_name,thalf_metric-method get_default_name,theoretical_thalf_metric-method get_default_name,time_above_limit_metric-method get_default_name,time_below_limit_metric-method get_default_name,tmax_metric-method get_default_name,tmin_metric-method get_default_name,value_at_metric-method |
| Get digits code for gtsummary. | get_digits_code |
| Get labels code for gtsummary. | get_labels_code |
| Get the name of the metric in LaTeX notation (with subscript coded with an underscore and brackets). | get_latex_name get_latex_name,abstract_avg_metric-method get_latex_name,abstract_max_metric-method get_latex_name,abstract_min_metric-method get_latex_name,abstract_value_at_metric-method get_latex_name,cfb_metric-method get_latex_name,ctrough_metric-method get_latex_name,last_metric-method get_latex_name,nca_metric-method get_latex_name,thalf_metric-method get_latex_name,theoretical_thalf_metric-method get_latex_name,tmax_metric-method get_latex_name,tmin_metric-method |
| Get statistics code for gtsummary. | get_statistics_code |
| Get all stratas. | get_strata get_strata,nca_table,logical-method |
| Get table summary code. | get_table_summary_code |
| Get the unit corresponding to the given metric. | get_unit get_unit,nca_analysis,character-method get_unit,nca_metrics,character-method get_unit,nca_table,character-method |
| Get the variable type code for gtsummary. | get_variable_type_code |
| Get Campsisnca option logic. | getCampsisncaOption |
| Glue stat display string. | glue_stat_display |
| Gt export type class. | gt_type-class |
| Gt summary export type class. | gtsummary_type-class |
| Compute the individual value of an individual. | i_value i_value,abstract_avg_metric,numeric,numeric-method i_value,abstract_last_metric,numeric,numeric-method i_value,abstract_max_metric,numeric,numeric-method i_value,abstract_min_metric,numeric,numeric-method i_value,abstract_time_above_or_below_limit_metric,numeric,numeric-method i_value,abstract_value_at_metric,numeric,numeric-method i_value,auc_metric,numeric,numeric-method i_value,cfb_metric,numeric,numeric-method i_value,custom_metric,numeric,numeric-method i_value,thalf_metric,numeric,numeric-method i_value,tmax_metric,numeric,numeric-method i_value,tmin_metric,numeric,numeric-method |
| Compute the individual value of an individual. | i_value_tbl i_value_tbl,custom_metric,tbl_df-method |
| Compute the individual values on a simulation output. | i_values i_values,nca_metric-method |
| Individual Campsisnca table class | individual_campsisnca_tbl individual_campsisnca_tbl-class |
| Individual (wide format) Campsisnca table class | individual_wide_campsisnca_tbl individual_wide_campsisnca_tbl-class |
| Compute the individual value of an individual. | iValue |
| Last value. | Last |
| Last metric class. | last_metric-class |
| Max. | Max |
| Max metric class. | max_metric-class |
| Theoretical metrics for 1-cpt model results. | metrics.1cpt |
| Theoretical metrics for 2-cpt model results. | metrics.2cpt |
| Pre-processing for metrics.1cpt and metrics.2cpt. | metrics.common |
| Min. | Min |
| Min metric class. | min_metric-class |
| NCA analyses class. | nca_analyses-class |
| NCA analysis class. | nca_analysis-class |
| NCA metric class. See this class as abstract class. | nca_metric-class |
| NCA metrics class. See this class as a list of NCA metrics. | nca_metrics-class |
| NCA options class. | nca_options-class |
| NCA table class. | nca_table-class |
| NCA time window class. | nca_time_window-class |
| Create an NCA analysis. | NCAAnalysis |
| NCA metrics | NCAMetrics |
| NCA table (deprecated). | NCAMetricsTable |
| NCA options used for calculation of metrics. | NCAOptions |
| NCA table. | NCATable |
| Simulated Pharmacokinetic Dataset (Multiple-Dose Bolus) | pk_bolus_md |
| Preserve Existing Column Value Order as Factor Levels | preserve_column_levels |
| Strip Factor Class from Columns | remove_column_levels |
| Replicated NCA table class. | replicated_nca_table-class |
| Replicated NCA table. | ReplicatedNCATable |
| Restore Factor Levels and Optionally Reorder Rows | restore_column_levels |
| Extract and Save Column Factor Levels | save_column_levels |
| Compute the standard error. | se |
| Return the evaluated statistics display string. This method was kept for backward compatibility in the tests. It is recommended to call `export(dest="dataframe", type="summary_pretty")` on the NCA table instead. | stat_display_string stat_display_string,nca_metric-method |
| Summary Campsisnca table class | summary_campsisnca_tbl summary_campsisnca_tbl-class |
| Summary (pretty format) Campsisnca table class | summary_pretty_campsisnca_tbl summary_pretty_campsisnca_tbl-class |
| Summary (wide format) Campsisnca table class | summary_wide_campsisnca_tbl summary_wide_campsisnca_tbl-class |
| Terminal half life computed by making a linear regression in the log domain on the given data x. | Thalf |
| Thalf metric class. | thalf_metric-class |
| Theoretical half life for a 1-compartment model. | Thalf.1cpt |
| Thalf metric required columns for a 1-compartment model. | thalf.1cpt.required |
| Theoretical distribution half life for a 2-compartment model. | Thalf.2cpt.dist |
| Theoretical effective half life for a 2-compartment model. | Thalf.2cpt.eff |
| Thalf metric required columns for a 2-compartment model. | thalf.2cpt.required |
| Theoretical elimination half life for a 2-compartment model. | Thalf.2cpt.z |
| Theoretical thalf metric class. | theoretical_thalf_metric-class |
| Time above limit metric class. | time_above_limit_metric-class |
| Time below limit metric class. | time_below_limit_metric-class |
| Time above a certain limit. | TimeAboveLimit |
| Time below a certain limit. | TimeBelowLimit |
| Filter CAMPSIS dataset based on min and max time. | timerange |
| Create a time window object. | TimeWindow |
| Tmax. | Tmax |
| Tmax metric class. | tmax_metric-class |
| Tmin. | Tmin |
| Tmin metric class. | tmin_metric-class |
| Gtsummary to Gt. | toGt |
| NOTE: This method has been adapted from the 'qpNCA' package by Huisman, Jolling, Mehta and Bergsma (2021) <doi:10.32614/CRAN.package.qpNCA>, following methodology from Rowland and Tozer (2011, ISBN:978-0-683-07404-8). | trap |
| Undefined NCA options class. | undefined_nca_options-class |
| Undefined NCA time window class. | undefined_nca_time_window-class |
| Undefined NCA options. | UndefinedNCAOptions |
| Create an undefined time window. | UndefinedTimeWindow |
| Value at metric class. | value_at_metric-class |
| Value at (value at specific time). | ValueAt |