Introduction | Response Surface Methods | The URSA Model | The MuSyC Model | The Deviation Methods | Bliss Deviation | Highest Single Agent | Loewe Additive | Zero-Interaction Potency | Deviation Functions in braidrm | The Combination Index
Package: braidrm 1.0.3
braidrm: Fitting Combined Action with the BRAID Response Surface Model
Contains functions for evaluating, analyzing, and fitting combined action dose response surfaces with the Bivariate Response to Additive Interacting Doses (BRAID) model of combined action, along with tools for implementing other combination analysis methods, including Bliss independence, combination index, and additional response surface methods.
Authors:
braidrm_1.0.3.tar.gz
braidrm_1.0.3.zip(r-4.7)braidrm_1.0.3.zip(r-4.6)braidrm_1.0.3.zip(r-4.5)
braidrm_1.0.3.tgz(r-4.6-any)braidrm_1.0.3.tgz(r-4.5-any)
braidrm_1.0.3.tar.gz(r-4.7-any)braidrm_1.0.3.tar.gz(r-4.6-any)
braidrm_1.0.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
braidrm/json (API)
| # Install 'braidrm' in R: |
| install.packages('braidrm', repos = c('https://nathanieltwarog.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/nathanieltwarog/braidrm/issues
Datasets:
- additiveExample - Example Additive Surface
- antagonisticExample - Example Antagonistic Surface
- coactiveExample - Example Coactive Surface
- incompleteExample - Example Partial or Incomplete Surface
- oppositionalExample - Example Oppositional Surface
- protectiveExample - Example Protective Surface
- synergisticExample - Example Synergistic Surface
Last updated from:57bddc615a. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 151 | ||
| source / vignettes | OK | 179 | ||
| linux-release-x86_64 | OK | 127 | ||
| macos-release-arm64 | OK | 94 | ||
| macos-oldrel-arm64 | OK | 84 | ||
| windows-devel | OK | 107 | ||
| windows-release | OK | 104 | ||
| windows-oldrel | OK | 85 | ||
| wasm-release | OK | 102 |
Exports:blissDeviationblissReferencebraidrmcalcBraidBootstrapcalcBraidConfIntdeviationSurfaceestimateChouIndexestimateChouIndicesestimateCombinationIndexestimateCombinationIndicesestimateFlippedIAEestimateIAEevalBraidModelevalFlippedBraidModelevalMusycModelevalUrsaModelfindBestBraidfitBraidFlippedfitCoactiveBraid_partialfitCoactiveBraid_purefitMusycModelfitOppositionalBraid_AfitOppositionalBraid_BfitProtectiveBraid_AfitProtectiveBraid_BfitUrsaModelhsaDeviationhsaReferenceinvertBraidModelinvertBraidModel_AinvertBraidModel_BinvertFlippedBraidModelinvertFlippedBraidModel_AinvertFlippedBraidModel_BkappaPriorloeweDeviationloeweReferencereferenceSurfacezipDeviationzipReferencezipSmoothed
Dependencies:basicdrm
Additional Approaches
Last update: 2024-09-18
Started: 2024-09-18
Basic BRAID Usage
The BRAID Model | Evaluate BRAID Surfaces | Fitting BRAID Surfaces
Last update: 2024-09-18
Started: 2024-09-18
Bayesian Stabilization of kappa
The Problem | The Solution: Bayesian Stabilization | Using Bayesian Stabilization in the braidrm Package
Last update: 2024-09-18
Started: 2024-09-18
BRAID Confidence Intervals
The Reason for Confidence Intervals | Confidence Intervals on Derived Quantities | A Caveat
Last update: 2024-09-18
Started: 2024-09-18
Derivation of the BRAID Model
Background: The Hill Equation | First Steps: The Assumptions | Generalizing | The Final Model
Last update: 2024-09-18
Started: 2024-09-18
Setting BRAID Models and Constraints
Basic Selections | Precise Model Selection | Maximal Effect Links | Parameter Bounds | Direction Constraint
Last update: 2024-09-18
Started: 2024-09-18
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Example Additive Surface | additiveExample |
| Example Antagonistic Surface | antagonisticExample |
| BRAID Response Surface Fitting | braidrm braidrm.default braidrm.formula print.braidrm print.summary.braidrm summary.braidrm |
| BRAID Parameter Confidence Intervals | calcBraidBootstrap |
| Generic BRAID confidence intervals | calcBraidConfInt |
| Example Coactive Surface | coactiveExample |
| Non-interacting Reference Surfaces | blissDeviation blissReference deviationSurface hsaDeviation hsaReference loeweDeviation loeweReference referenceSurface zipDeviation zipReference zipSmoothed |
| Combination Index | estimateChouIndex estimateChouIndices estimateCombinationIndex estimateCombinationIndices |
| BRAID Response Surface Combined Potency | estimateFlippedIAE estimateIAE estimateIAE.braidrm estimateIAE.braidrmflip estimateIAE.default |
| Evaluate the BRAID response surface model | evalBraidModel |
| Evaluate Flipped BRAID Surfaces | evalFlippedBraidModel |
| Evaluate MuSyC Response Surfaces | evalMusycModel |
| Evaluate URSA response surface model | evalUrsaModel |
| Select Best BRAID Response Fit | findBestBraid findBestBraid.default findBestBraid.formula |
| Fit Flipped BRAID Surfaces | fitBraidFlipped fitCoactiveBraid_partial fitCoactiveBraid_pure fitOppositionalBraid_A fitOppositionalBraid_B fitProtectiveBraid_A fitProtectiveBraid_B |
| MuSyC Response Surface Fitting | fitMusycModel fitMusycModel.default fitMusycModel.formula |
| URSA Response Surface Fitting | fitUrsaModel fitUrsaModel.default fitUrsaModel.formula |
| Example Partial or Incomplete Surface | incompleteExample |
| Invert a BRAID Response Surface Model | invertBraidModel invertBraidModel_A invertBraidModel_B |
| Invert Flipped BRAID Surfaces | invertFlippedBraidModel invertFlippedBraidModel_A invertFlippedBraidModel_B |
| Braid kappa Bayesian Prior | kappaPrior |
| Example Oppositional Surface | oppositionalExample |
| Example Protective Surface | protectiveExample |
| Example Synergistic Surface | synergisticExample |
