Package: LDLcalc 2.1

LDLcalc: Calculate and Predict the Low Density Lipoprotein Values

A wide variety of ways to calculate (through equations) or predict (using 9 Machine learning methods as well as a stack algorithm combination of them all) the Low Density Lipoprotein values of patients based on the values of three other metrics, namely Total Cholesterol , Triglycerides and High Density Lipoprotein. It can also calculate the variance of LDL and the Atherogenic Index of Plasma (AIP) using error propagation and bootstrapping.

Authors:Petros Paplomatas [aut, cre], Kostas Anagnostopoulos [aut]

LDLcalc_2.1.tar.gz
LDLcalc_2.1.zip(r-4.5)LDLcalc_2.1.zip(r-4.4)LDLcalc_2.1.zip(r-4.3)
LDLcalc_2.1.tgz(r-4.4-any)LDLcalc_2.1.tgz(r-4.3-any)
LDLcalc_2.1.tar.gz(r-4.5-noble)LDLcalc_2.1.tar.gz(r-4.4-noble)
LDLcalc_2.1.tgz(r-4.4-emscripten)LDLcalc_2.1.tgz(r-4.3-emscripten)
LDLcalc.pdf |LDLcalc.html✨
LDLcalc/json (API)

# Install 'LDLcalc' in R:

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

Bug tracker:https://github.com/paplomatasp/ldlcalc/issues

Datasets:

SampleData - Anonymous real data
model - A trained model
sampleA - Anonymous real data
sampleB - Anonymous real data

On CRAN:

34 exports 0.74 score 101 dependencies 6 scripts 264 downloads

Last updated 7 months agofrom:6ec8b61b09. Checks:ERROR: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	FAIL	Sep 14 2024
R-4.5-win	ERROR	Sep 14 2024
R-4.5-linux	ERROR	Sep 14 2024
R-4.4-win	ERROR	Sep 14 2024
R-4.4-mac	ERROR	Sep 14 2024
R-4.3-win	ERROR	Sep 14 2024
R-4.3-mac	ERROR	Sep 14 2024

Exports:AIP_DensityPlotOfbootst AIP_HDLVrnc AIP_TGVrnc AIPbootVrnc AIPcalc AIPErrPrp AIPErrPrp2Ord chebyshev Corr_Plot CV CV_Range DensityPlotOfVar ErrorCorCov JSD JSDNormal LDL_CHOLVrnc LDL_DensityPlotOfbootst LDL_eq LDL_HDLVrnc LDL_ML_Main LDL_ML_Main_All_Models LDL_ML_Main_StackingAlgorithm LDL_ML_predict LDL_TGVrnc LDLallEq LDLbootVrnc LDLErrPrp plotAIP_HDLVrnc plotAIP_TGVrnc plotCholVrncToLDL PlotCorrWithRegrLine PlotDiscrHist plotHDLVrncToLDL plotTGVrncToLDL

Dependencies:askpass caret caretEnsemble class cli clock codetools colorspace corrplot cpp11 curl data.table diagram digest dplyr e1071 fansi farver foreach future future.apply generics ggplot2 globals glue gower gtable hardhat hms httr ipred isoband iterators janitor jsonlite KernSmooth labeling lares lattice lava lifecycle listenv lubridate magrittr MASS Matrix mgcv mime ModelMetrics moments munsell nlme nnet numDeriv openssl openxlsx parallelly patchwork pbapply philentropy pillar pkgconfig plyr poorman pROC prodlim progressr proxy purrr R6 RColorBrewer Rcpp recipes resample reshape2 rlang rpart rpart.plot rvest scales selectr shape snakecase SQUAREM stringi stringr survival sys tibble tidyr tidyselect timechange timeDate tzdb utf8 vctrs viridisLite withr xml2 yaml zip

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Help page	Topics
Plot density of bootstrap and empirical variance for AIP	AIP_DensityPlotOfbootst
Calculate the variance of AIP when HDL changes.	AIP_HDLVrnc
Calculate the variance of AIP when TG changes.	AIP_TGVrnc
Calculate variance of AIP using Bootstrapping.	AIPbootVrnc
Calculation of Atherogenic Index of Plasma (AIP)	AIPcalc
Variance of Atherogenic Index of Plasma (AIP) using Error Propagation.	AIPErrPrp
Second Order Taylor expansion AIP Error propagation variance	AIPErrPrp2Ord
Chebysev's inequality	chebyshev
Correlation plot	Corr_Plot
Calculate the CV of a set of values.	CV
Change variance of distribution while keeping the mean constant	CV_Range
Plot variance density	DensityPlotOfVar
Calculate correlation and covariance of residuals	ErrorCorCov
Calculate the Jensen-Shannon divergence (JSD)	JSD
Calculate the Jensen-Shannon divergence (JSD) between a discrete empirical distribution and the normal distribution.	JSDNormal
Calculate LDL variance when cholesterol variance changes	LDL_CHOLVrnc
Plot density of bootstrap and empirical variance for LDL	LDL_DensityPlotOfbootst
Calculates and returns the LDL Value for any of the 12 different equations	LDL_eq
Calculate LDL variance when HDL variance changes	LDL_HDLVrnc
Create, train, assess and return an ML prediction model.	LDL_ML_Main
Create, train, assess and return all ML prediction models	LDL_ML_Main_All_Models
Create, train, assess and return a Stacking Algorithm Machine Learning prediction model	LDL_ML_Main_StackingAlgorithm
Predict LDL value(s)	LDL_ML_predict
Calculate LDL variance when triglyceride variance changes	LDL_TGVrnc
Calculates and returns the LDL values using all available equations	LDLallEq
Calculate variance of LDL using bootstrapping.	LDLbootVrnc
Calculate LDL variance using error propagation	LDLErrPrp
A trained model	model
Plots AIP variance versus increasing HDL variance	plotAIP_HDLVrnc
Plots AIP variance versus increasing triglyceride variance	plotAIP_TGVrnc
Plots LDL variance versus increasing cholesterol variance	plotCholVrncToLDL
Scatterplot of pairs of parameters	PlotCorrWithRegrLine
Plot discrete histogram	PlotDiscrHist
Plots LDL variance versus increasing HDL variance	plotHDLVrncToLDL
Plots LDL variance versus increasing triglyceride variance	plotTGVrncToLDL
Anonymous real data	sampleA
Anonymous real data	sampleB
Anonymous real data	SampleData

Package: LDLcalc 2.1

LDLcalc: Calculate and Predict the Low Density Lipoprotein Values

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)