Package: pscore 0.4.0

pscore: Standardizing Physiological Composite Risk Endpoints

Provides a number of functions to simplify and automate the scoring, comparison, and evaluation of different ways of creating composites of data. It is particularly aimed at facilitating the creation of physiological composites of metabolic syndrome symptom score (MetSSS) and allostatic load (AL). Provides a wrapper to calculate the MetSSS on new data using the Healthy Hearts formula.

Authors:Joshua F. Wiley [aut, cre]

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pscore.pdf |pscore.html✨
pscore/json (API)
NEWS

# Install 'pscore' in R:

install.packages('pscore', repos = c('https://jwiley.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jwiley/score-project/issues

Datasets:

BioDB - Biomarker Thresholds Database
MetSSS_model - MetSSS Model

On CRAN:

10 exports 2 stars 1.71 score 147 dependencies 4 mentions 13 scripts 220 downloads

Last updated 2 years agofrom:f4882a7cb6. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Aug 27 2024
R-4.5-win	OK	Aug 27 2024
R-4.5-linux	OK	Aug 27 2024
R-4.4-win	OK	Aug 27 2024
R-4.4-mac	OK	Aug 27 2024
R-4.3-win	OK	Jul 28 2024
R-4.3-mac	OK	Jul 28 2024

Exports:CompositeData CompositeReady dropData factorComposite mahalanobisComposite MetSSS MetSSS_model predictCS prepareComposite sumComposite

Dependencies:abind backports base64enc bit bit64 boot broom bslib cachem car carData checkmate cli clipr cluster codetools colorspace corrplot cowplot cpp11 crayon data.table DEoptimR Deriv digest doBy dplyr emmeans estimability evaluate extraoperators fansi farver fastmap fontawesome forcats foreach foreign Formula fs fst fstcore generics ggplot2 ggpubr ggrepel ggsci ggsignif glmnet glue GPArotation gridExtra gtable haven highr Hmisc hms htmlTable htmltools htmlwidgets isoband iterators jomo jquerylib jsonlite JWileymisc knitr labeling lattice lavaan lifecycle lme4 magrittr MASS Matrix MatrixModels memoise mgcv mice microbenchmark mime minqa mitml mnormt modelr multcomp multcompView munsell mvtnorm nlme nloptr nnet numDeriv ordinal pan pbivnorm pbkrtest pillar pkgconfig plyr polspline polynom prettyunits progress psych purrr quadprog quantreg R6 rappdirs RColorBrewer Rcpp RcppEigen readr reshape2 rlang rmarkdown rms robustbase rpart rstatix rstudioapi sandwich sass scales shape SparseM stringi stringr survival TH.data tibble tidyr tidyselect tinytex tzdb ucminf utf8 vctrs VGAM viridis viridisLite vroom withr xfun yaml zoo

Metabolic Syndrom Severity Score (MetSSS)

Rendered frommetsss.Rmdusingknitr::rmarkdownon Aug 27 2024.

Last update: 2022-05-13
Started: 2022-05-11

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Internal function to prepare data for prediction	.preparePredict
Biomarker Thresholds Database	BioDB
An constructor function for the S4 CompositeData class	CompositeData
A S4 class to represent data for creating a composite	CompositeData-class
An constructor function for the S4 CompositeReady class	CompositeReady
An S4 class to represent composite ready data	CompositeReady-class
Drop unnecessary data from a MahalanobisComposite object.	dropData
Score Data Using a Factor Model	factorComposite
Density Plot for a Long Dataset	ldensity
Score Data Using the Mahalanobis Distance	mahalanobisComposite
An S4 class to represent composite scores based on Mahalanobis distance	FactorScores-class MahalanobisScores-class SumScores-class
Score the MetSSS	MetSSS
MetSSS Model	MetSSS_model
Internal function to prepare data for prediction	predictCS
Prepare distance scores on data in preparation for composite scoring	prepareComposite
Score Data Using a simple sum	sumComposite