Package: mcradds 1.1.1.9000

mcradds: Processing and Analyzing of Diagnostics Trials

Provides methods and functions to analyze the quantitative or qualitative performance for diagnostic assays, and outliers detection, reader precision and reference range are discussed. Most of the methods and algorithms refer to CLSI (Clinical & Laboratory Standards Institute) recommendations and NMPA (National Medical Products Administration) guidelines. In additional, relevant plots are constructed by 'ggplot2'.

Authors:Kai Gu [aut, cre, cph]

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

# Install 'mcradds' in R:

install.packages('mcradds', repos = c('https://kaigu1990.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/kaigu1990/mcradds/issues

Datasets:

PDL1RP - PD-L1 Reader Precision Data
adsl_sub - CDISC ADSL Subsetting Data
calcium - Reference Interval Data
glucose - Inermediate Precision Data
ldlroc - Two-sampled Paired Test Data
nonparRanks - Nonparametric Rank Number of Reference Interval
platelet - Quantitative Measurement Data
qualData - Simulated Qualitative Data

On CRAN:

in-vitro-diagnostic ivd mcr

4.30 score 1 stars 7 scripts 194 downloads 36 exports 82 dependencies

Last updated 2 months agofrom:097752819c. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 04 2024
R-4.5-win	OK	Nov 04 2024
R-4.5-linux	OK	Nov 04 2024
R-4.4-win	OK	Nov 04 2024
R-4.4-mac	OK	Nov 04 2024
R-4.3-win	OK	Nov 04 2024
R-4.3-mac	OK	Nov 04 2024

Exports:%>%anovaVCA aucTest autoplot blandAltman calcBias cat_with_newline descfreq descvar diagTab dixon_outlier ESD_test esd.critical getAccuracy getCoefficients getOutlier h_difference h_factor h_fmt_count_perc h_fmt_est h_fmt_num h_fmt_range h_summarize mcreg nonparRI pearsonTest printSummary refInterval robustRI size_ci_corr size_ci_one_prop size_corr size_one_prop spearmanTest tukey_outlier VCAinference

Dependencies:askpass backports base64enc boot cellranger checkmate class cli colorspace cpp11 crayon curl data.table DescTools digest dplyr e1071 Exact expm fansi farver fastmap formatters generics ggplot2 gld glue gtable hms htmltools httr isoband jsonlite labeling lattice lifecycle lme4 lmom magrittr MASS Matrix mcr mgcv mime minqa munsell mvtnorm nlme nloptr numDeriv openssl pillar pkgconfig plyr prettyunits pROC progress proxy purrr R6 RColorBrewer Rcpp RcppArmadillo RcppEigen readxl rematch rlang robslopes rootSolve rstudioapi scales stringi stringr sys tibble tidyr tidyselect utf8 VCA vctrs viridisLite withr

Introduction to mcradds

Rendered frommcradds.Rmdusingknitr::rmarkdownon Nov 04 2024.

Last update: 2023-12-04
Started: 2023-09-22

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
'mcradds' Package	mcradds-package mcradds
CDISC ADSL Subsetting Data	adsl_sub
ANOVA-Type Estimation of Variance Components for Random Models	anovaVCA
AUC Test for Paired Two-sample Measurements	aucTest
Generate a 'ggplot' for Bland-Altman Plot and Regression Plot	autoplot autoplot,BAsummary-method autoplot,MCResult-method
BAsummary Class	BAsummary BAsummary-class
Calculate Statistics for Bland-Altman	blandAltman
Systematical Bias Between Reference Method and Test Method	calcBias
Reference Interval Data	calcium
Concatenate and Print with Newline	cat_with_newline
Descriptive Statistics Class	Desc Desc-class
Summarize Frequency Counts and Percentages	descfreq
Summarize Descriptive Statistics	descvar
Creates Contingency Table	diagTab
Detect Dixon Outlier	dixon_outlier
EDS Test for Outliers	ESD_test
Compute Critical Value for ESD Test	esd.critical
Summary Method for 'MCTab' Objects	getAccuracy getAccuracy,MCTab-method
Get Regression Coefficients	getCoefficients
Detect Outliers From 'BAsummary' Object	getOutlier getOutlier,BAsummary-method
Inermediate Precision Data	glucose
Compute Difference for Bland-Altman	h_difference
Factor Variable Per Levels	h_factor
Format count and percent	h_fmt_count_perc
Format and Concatenate to String	h_fmt_est
Format Numeric Data	h_fmt_num
Format and Concatenate to Range	h_fmt_range
Summarize Basic Statistics	h_summarize
Two-sampled Paired Test Data	ldlroc
Comparison of Two Measurement Methods Using Regression Analysis	mcreg
MCTab Class	MCTab MCTab-class
Nonparametric Rank Number of Reference Interval	nonparRanks
Nonparametric Method in Calculation of Reference Interval	nonparRI
PD-L1 Reader Precision Data	PDL1RP
Hypothesis Test for Pearson Correlation Coefficient	pearsonTest
Quantitative Measurement Data	platelet
Print Summary of a Regression Analysis	printSummary
Simulated Qualitative Data	qualData
Reference Interval Class	RefInt RefInt-class
Calculate Reference Interval and Corresponding Confidence Interval	refInterval
Robust Method in Calculation of Reference Interval	robustRI
SampleSize Class	SampleSize SampleSize-class
Show Method for Objects	show show,BAsummary-method show,Desc-method show,MCTab-method show,RefInt-method show,SampleSize-method show,tpROC-method
Sample Size for Testing Confidence Interval of Pearson's correlation	size_ci_corr
Sample Size for Testing Confidence Interval of One Proportion	size_ci_one_prop
Sample Size for Testing Pearson's correlation	size_corr
Sample Size for Testing One Proportion	size_one_prop
Hypothesis Test for Spearman Correlation Coefficient	spearmanTest
Test for Paired ROC Class	tpROC tpROC-class
Detect Tukey Outlier	tukey_outlier
Inferential Statistics for VCA-Results	VCAinference