Package: emery 0.7.2

Corie Drake

emery: Accuracy Statistic Estimation for Imperfect Gold Standards

Produce maximum likelihood estimates of common accuracy statistics for multiple measurement methods when a gold standard is not available. An R implementation of the expectation maximization algorithms described in Zhou et al. (2011) <doi:10.1002/9780470906514> with additional functions for creating simulated data and visualizing results. Supports binary, ordinal, and continuous measurement methods.

Authors:Corie Drake [aut, cre, cph]

emery_0.7.2.tar.gz
emery_0.7.2.zip(r-4.7)emery_0.7.2.zip(r-4.6)emery_0.7.2.zip(r-4.5)
emery_0.7.2.tgz(r-4.6-any)emery_0.7.2.tgz(r-4.5-any)
emery_0.7.2.tar.gz(r-4.7-any)emery_0.7.2.tar.gz(r-4.6-any)
emery_0.7.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
emery/json (API)

# Install 'emery' in R:

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

Bug tracker:https://github.com/therealcfdrake/emery/issues

On CRAN:

4.40 score 1 stars 2 scripts 233 downloads 26 exports 32 dependencies

Last updated from:ca3130ae74. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	138
source / vignettes	OK	213
linux-release-x86_64	OK	154
macos-release-arm64	OK	92
macos-oldrel-arm64	OK	89
windows-devel	OK	92
windows-release	OK	87
windows-oldrel	OK	96
wasm-release	OK	123

Exports:aggregate_boot_ML bin_auc boot_ML estimate_ML estimate_ML_binary estimate_ML_continuous estimate_ML_ordinal generate_multimethod_binary generate_multimethod_continuous generate_multimethod_data generate_multimethod_ordinal getNames getResults name_thing plot plot_ML plot_ML_binary plot_ML_continuous plot_ML_ordinal pollinate_ML pollinate_ML_binary pollinate_ML_continuous pollinate_ML_ordinal setFreqs show unique_obs_summary

Dependencies:cli cpp11 dplyr farver generics ggplot2 glue gtable isoband labeling lifecycle magrittr mvtnorm pillar pkgconfig purrr R6 rbibutils RColorBrewer Rdpack rlang S7 scales stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr

emery

Rendered fromemery.Rmdusingknitr::rmarkdown

Last update: 2024-02-13
Started: 2024-02-11

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Aggregate bootstrapped ML estimates	aggregate_boot_ML
Calculate AUC for single Se/Sp pair	bin_auc
Bootstrap ML accuracy statistic estimation for multi-method data	boot_ML
Censor data randomly rowwise	censor_data
Define the True disease state of a simulated sample	define_disease_state
Multivariate Normal Densities	dmvnorm
Estimate maximum likelihood accuracy statistics by expectation maximization	estimate_ML estimate_ML_binary estimate_ML_continuous estimate_ML_ordinal
Create data sets which simulate paired measurements of multiple methods	generate_multimethod_binary generate_multimethod_continuous generate_multimethod_data generate_multimethod_ordinal
Return names from MultiMethodMLEstimate object	getNames
Return names from MultiMethodMLEstimate object	getNames,MultiMethodMLEstimate-method
Return result from MultiMethodMLEstimate object	getResults
Return result from MultiMethodMLEstimate object	getResults,MultiMethodMLEstimate-method
S4 object containing the results of multi-method ML accuracy estimates	MultiMethodMLEstimate-class
Create unique names for a set of things	name_thing
Create new boot_ML class object	new_boot_ML
Create plots visualizing the ML estimation process and results.	plot_ML plot_ML_binary plot_ML_continuous plot_ML_ordinal
Create plots from a MultiMethodMLEstimate object	plot,MultiMethodMLEstimate-method
Plot univariate distributions of bootstrapped ML estimates	plot.boot_ML
Generate seed values for EM algorithm	pollinate_ML pollinate_ML_binary pollinate_ML_continuous pollinate_ML_ordinal
Generate a random initial starting point for EM algorithm	random_start random_start_binary random_start_ordinal
Set frequencies of MultiMethodMLEstimate objects	setFreqs
Set frequencies of MultiMethodMLEstimate objects	setFreqs,MultiMethodMLEstimate-method
Show a MultiMethodMLEstimate S4 object	show,MultiMethodMLEstimate-method
Reduce Data by Summarizing Observations	unique_obs_summary