Package: PDXpower 1.0.2

Shanpeng Li

PDXpower:Time to Event Outcome in Experimental Designs of Pre-Clinical Studies

Conduct simulation-based customized power calculation for clustered time to event data in a mixed crossed/nested design, where a number of cell lines and a number of mice within each cell line are considered to achieve a desired statistical power, motivated by Eckel-Passow and colleagues (2021) <doi:10.1093/neuonc/noab137> and Li and colleagues (2024) <doi:10.48550/arXiv.2404.08927>. This package provides two commonly used models for powering a design, linear mixed effects and Cox frailty model. Both models account for within-subject (cell line) correlation while holding different distributional assumptions about the outcome. Alternatively, the counterparts of fixed effects model are also available, which produces similar estimates of statistical power.

Authors:Shanpeng Li [aut, cre], Gang Li [ctb]

PDXpower_1.0.2.tar.gz
PDXpower_1.0.2.tar.gz(r-4.5-noble)PDXpower_1.0.2.tar.gz(r-4.4-noble)
PDXpower_1.0.2.tgz(r-4.4-emscripten)PDXpower_1.0.2.tgz(r-4.3-emscripten)
PDXpower.pdf |PDXpower.html✨
PDXpower/json (API)

# InstallPDXpower in R:

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

Datasets:

animals1 - Simulated preliminary animals uncensored data
animals2 - Simulated preliminary animals censored data

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

7 exports 0.36 score 93 dependencies 18 downloads

Last updated 6 days agofrom:4cdbb75858

Exports:plotpower PowANOVA PowANOVADat PowerTable PowFrailty PowFrailtyDat SimPDXdata

Dependencies:abind backports base64enc boot broom bslib cachem car carData cli colorspace commonmark corrplot cowplot cpp11 crayon Deriv digest doBy dplyr fansi farver fastmap fontawesome frailtypack fs generics ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra gtable htmltools httpuv isoband jquerylib jsonlite labeling later lattice lifecycle lme4 magrittr MASS Matrix MatrixModels memoise mgcv microbenchmark mime minqa modelr munsell nlme nloptr nnet numDeriv pbkrtest pillar pkgconfig polynom promises purrr quantreg R6 rappdirs RColorBrewer Rcpp RcppEigen rlang rootSolve rstatix sass scales shiny sourcetools SparseM statmod stringi stringr survC1 survival tibble tidyr tidyselect utf8 vctrs viridisLite withr xtable

Help page	Topics
Simulated preliminary animals uncensored data	animals1
Simulated preliminary animals censored data	animals2
A function to generate a four-panel power curve under specified number of PDX lines and number of individuals per PDX lines per treatment	plotpower
A function to obtain a power table with the combination of various number of PDX lines and number of individuals per PDX lines per treatment based on a prior knowledge of median survival	PowANOVA
A function to obtain a power table with the combination of various number of PDX lines and number of individuals per PDX lines per treatment based on a preliminary dataset	PowANOVADat
A function to obtain a power table with the combination of various number of PDX lines and number of individuals per PDX lines per treatment.	PowerTable
A function to obtain a power table with the combination of various number of PDX lines and number of individuals per PDX lines per treatment based on a prior knowledge of median survival	PowFrailty
A function to obtain a power table with the combination of various number of PDX lines and number of individuals per PDX lines per treatment based on a preliminary dataset	PowFrailtyDat
Print PowerTable	print.PowerTable
A function to calculate the power under pre-specified effect size, variance, and correlation using Monte Carlo sampling scheme by fitting ANOVA fixed effects model, ANOVA random effects model, Cox model, and frailty model.	SimPDXdata

Package: PDXpower 1.0.2

PDXpower:Time to Event Outcome in Experimental Designs of Pre-Clinical Studies

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)