Package: pwrFDR 2.8.9

pwrFDR: FDR Power

This is a package for calculating two differing notions of power, or deriving sample sizes for specified requisite power in multiple testing experiments under a variety of methods for control of the distribution of the False Discovery Proportion (FDP). More specifically, one can choose to control the FDP distribution according to control of its (i) mean, e.g. the usual BH-FDR procedure, or via the probability that it exceeds a given value, delta, via (ii) the Romano procedure, or via (iii) my procedure based upon asymptotic approximation. Likewise, we can think of the power in multiple testing experiments in terms of a summary of the distribution of the True Positive Proportion (TPP). The package will compute power, sample size or any other missing parameter required for power based upon (i) the mean of the TPP which is the average power (ii) the probability that the TPP exceeds a given value, lambda, via my asymptotic approximation procedure. The theoretical results are described in Izmirlian, G. (2020) Stat. and Prob. letters, <doi:10.1016/j.spl.2020.108713>, and an applied paper describing the methodology with a simulation study is in preparation.

Authors:Grant Izmirlian Jr <[email protected]>

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pwrFDR.pdf |pwrFDR.html✨
pwrFDR/json (API)

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

Peer review:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

29 exports 0.00 score 0 dependencies 17 scripts 243 downloads

Last updated 3 years agofrom:33ca882367. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 08 2024
R-4.5-win-x86_64NOTESep 08 2024
R-4.5-linux-x86_64NOTESep 08 2024
R-4.4-win-x86_64NOTESep 08 2024
R-4.4-mac-x86_64NOTESep 08 2024
R-4.4-mac-aarch64NOTESep 08 2024
R-4.3-win-x86_64NOTESep 08 2024
R-4.3-mac-x86_64NOTESep 08 2024
R-4.3-mac-aarch64NOTESep 08 2024

Exports:%,%%over%arg.valscc.ROCcCDF.RomcCDF.ToMcCDF.VoRCDF.PvalCDF.Pval.ar.eq.uCDF.Pval.HACDF.Pval.ua.eq.ucontrolFDPcriteriondetaildistses.ROCgentempfilenmif.0.rmif.na.xif.y.zlogitlogitInvnnapwrFDRpwrFDR.gridsd.rtm.Romsd.rtm.ToMsd.rtm.VoRview.presentation

Dependencies:

Readme and manuals

Help Manual

Help pageTopics
Division operator with divide by zero clobbering%over%
Extracts the full argument list and call attribute.arg.vals
Computes the optimal number of controls per case in hypothesis tests involving the ROC. Included here with the intent that it can be used in conjunction with 'pwrFDR' to allow power/sample size calculation for multiple tests of ROC curve based hypothesis. See details.cc.ROC
Computes the complimentary CDF for the significant call proportion, R_m/m.cCDF.Rom
Computes the complimentary CDF for the true positive proportion, T_m/M_m.cCDF.ToM
Computes the complimentary CDF for the false discovery proportion, V_m/R_m.cCDF.VoR
CDF of pooled (H0 and HA) population p-valuesCDF.Pval
Calculates the fixed point for the Romano procedure.CDF.Pval.ar.eq.u
CDF of p-values for test statistics distribted under HA.CDF.Pval.HA
Function which solves the implicit equation u = G( u alpha)CDF.Pval.ua.eq.u
Helper function for the BHCLT FDP control methodcontrolFDP
BH-FDR and Romano Criterioncriterion
The detail extraction function for simulated power objectsdetail
The Distribution family objectdists
Computes the equivalent Z-test effect size in hypothesis tests involving the ROC. Included here with the intent that it can be used in conjunction with 'pwrFDR' to allow power/sample size calculation for multiple tests of ROC curve based hypothesis. See details.es.ROC
Generate a tempfile namegentempfilenm
A helper function- remove if zero.if.0.rm
A helper function - substitute 'NA's with a specified 'x'.if.na.x
A helper function - substitute 'y''s with a specified 'z'.if.y.z
Computes the logit transformlogit
Computes the inverse logit transformlogitInv
A helper function- turns a missing column into 'NA's inside of a with statementnna
The paste operator%,% paste
Ensemble power or sample size under selected control of the FDPpwrFDR
Evaluate 'pwrFDR' on a grid.pwrFDR.grid
Extractor function for asymptotic sd[R_m/m] under selected FDP control methodsd.rtm.Rom
Extractor function for asymptotic sd[T_m/M_m] under selected FDP control methodsd.rtm.ToM
Extractor function for asymptotic sd[V_m/R_m] under selected FDP control methodsd.rtm.VoR
Call this function (without arguments) to open a presentation which describes the theory behind the package and presents a simulation study.view.presentation