Package: personalized 0.2.8

personalized: Estimation and Validation Methods for Subgroup Identification and Personalized Medicine

Provides functions for fitting and validation of models for subgroup identification and personalized medicine / precision medicine under the general subgroup identification framework of Chen et al. (2017) <doi:10.1111/biom.12676>. This package is intended for use for both randomized controlled trials and observational studies and is described in detail in Huling and Yu (2021) <doi:10.18637/jss.v098.i05>.

Authors:Jared Huling [aut, cre], Aaron Potvien [ctb], Alexandros Karatzoglou [cph], Alex Smola [cph]

personalized_0.2.8.tar.gz
personalized_0.2.8.zip(r-4.7)personalized_0.2.8.zip(r-4.6)personalized_0.2.8.zip(r-4.5)
personalized_0.2.8.tgz(r-4.6-any)personalized_0.2.8.tgz(r-4.5-any)
personalized_0.2.8.tar.gz(r-4.7-any)personalized_0.2.8.tar.gz(r-4.6-any)
personalized_0.2.8.tgz(r-4.6-emscripten)
manual.pdf |manual.html
DESCRIPTION |NEWS
card.svg |card.png
personalized/json (API)

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

Bug tracker:https://github.com/jaredhuling/personalized/issues

Pkgdown/docs site:https://jaredhuling.org

Datasets:
  • LaLonde - National Supported Work Study Data

On CRAN:

Conda:

causal-inferenceheterogeneity-of-treatment-effectindividualized-treatment-rulespersonalized-medicineprecision-medicinesubgroup-identificationtreatment-effectstreatment-scoring

7.87 score 33 stars 1 packages 125 scripts 630 downloads 11 exports 77 dependencies

Last updated from:da31260c36. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK242
source / vignettesOK244
linux-release-x86_64OK257
macos-release-arm64OK256
macos-oldrel-arm64OK196
windows-develOK225
windows-releaseOK237
windows-oldrelOK241
wasm-releaseOK151

Exports:check.overlapcreate.augmentation.functioncreate.propensity.functionfit.subgroupplotComparesubgroup.effectssummarize.subgroupstreat.effectstreatment.effectsvalidate.subgroupweighted.ksvm

Dependencies:askpassbase64encbslibcachemclicodetoolscpp11crosstalkcurldata.tabledigestdplyrevaluatefarverfastmapfontawesomeforeachfsgenericsggplot2glmnetgluegtablehighrhtmltoolshtmlwidgetshttrisobanditeratorsjquerylibjsonlitekernlabknitrlabelinglaterlatticelazyevallifecyclemagrittrMatrixmemoisemgcvmimenlmeopensslotelpillarpkgconfigplotlypromisespurrrR6rappdirsRColorBrewerRcppRcppEigenrlangrmarkdownS7sassscalesshapestringistringrsurvivalsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunxgboostyaml

Estimation of Flexible ITRs with xgboost
First simulate data with complicated conditional average treatment effect/benefit score | Setup | Using xgboost for estimation of ITRs | Comparing performance with linear ITRs

Last update: 2022-09-02
Started: 2022-06-14

Usage of the Personalized Package
Introduction to personalized | Choice of $M$ function | Choice of $f$ | Variable Selection | Extension to multi-category treatments | Quick Usage Reference | Creating and Checking Propensity Score Model | Fitting Subgroup Identification Models | Evaluating Treatment Effects within Estimated Subgroups | User Guide | Overview | Creating and Checking a propensity Score Model | Observational Studies | Randomized Controlled Trials | Explanation of Major Function Arguments | x | y | trt | propensity.func | loss | method | larger.outcome.better | cutpoint | retcall | ... | Continuous Outcomes | Binary Outcomes | Count Outcomes | Time-to-event Outcomes | Efficiency Augmentation | Plotting Fitted Models | Comparing Subgroups from a Fitted Model | Validating Subgroup Identification Models | Repeated Training/Test Splitting | Bootstrap Bias Correction | Plotting Validated Models

Last update: 2022-06-27
Started: 2017-05-25

Utilities for Improving Estimation Efficiency via Augmentation and for Propensity Score Estimation
Efficiency augmentation | Propensity score utilities | Augmentation utilities | Comparing performance with augmentation

Last update: 2022-06-27
Started: 2019-11-06

Multi-category Treatments with personalized
Example with multi-category treatments | More details on propensity scores for multi-category treatments

Last update: 2022-06-22
Started: 2019-09-28

Readme and manuals

Help Manual

Help pageTopics
Check propensity score overlapcheck.overlap
Creation of augmentation functionscreate.augmentation.function
Creation of propensity fitting functioncreate.propensity.function
Fitting subgroup identification modelsfit.subgroup
National Supported Work Study DataLaLonde
Plotting results for fitted subgroup identification modelsplot.subgroup_fitted plot.subgroup_validated
Plot a comparison results for fitted or validated subgroup identification modelsplotCompare
Function to predict either benefit scores or treatment recommendationspredict.subgroup_fitted predict.wksvm
Printing individualized treatment effectsprint.individual_treatment_effects
Printing results for fitted subgroup identification modelsprint.subgroup_fitted print.subgroup_summary print.subgroup_validated
Computes treatment effects within various subgroupssubgroup.effects
Summarizing covariates within estimated subgroupssummarize.subgroups summarize.subgroups.default summarize.subgroups.subgroup_fitted
Summary of results for fitted subgroup identification modelssummary.subgroup_fitted summary.wksvm
Calculation of covariate-conditional treatment effectstreat.effects treatment.effects treatment.effects.default treatment.effects.subgroup_fitted
Validating fitted subgroup identification modelsvalidate.subgroup
Fit weighted kernel svm model.weighted.ksvm