Package: NMTox 0.1.0

NMTox: Dose-Response Relationship Analysis of Nanomaterial Toxicity

Perform an exploration and a preliminary analysis on the dose- response relationship of nanomaterial toxicity. Several functions are provided for data exploration, including functions for creating a subset of dataset, frequency tables and plots. Inference for order restricted dose- response data is performed by testing the significance of monotonic dose-response relationship, using Williams, Marcus, M, Modified M and Likelihood ratio tests. Several methods of multiplicity adjustment are also provided. Description of the methods can be found in <https://github.com/rahmasarina/dose-response-analysis/blob/main/Methodology.pdf>.

Authors:Rahmasari Nur Azizah [aut, cre], Geert Verheyen [aut, ths], Sabine Van Miert [aut, ths], Ziv Shkedy [aut, ths]

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

# Install 'NMTox' in R:

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

Datasets:

geninvitro - Genetic toxicity in vitro dataset
nm400 - NM-400 in vitro dataset

On CRAN:

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

1.00 score 153 downloads 15 exports 39 dependencies

Last updated 2 years agofrom:53eb4029a0. Checks:OK: 3 NOTE: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 13 2024
R-4.5-win	NOTE	Nov 13 2024
R-4.5-linux	NOTE	Nov 13 2024
R-4.4-win	NOTE	Nov 13 2024
R-4.4-mac	NOTE	Nov 13 2024
R-4.3-win	OK	Nov 13 2024
R-4.3-mac	OK	Nov 13 2024

Exports:adjPlot FrCtrl Frtab Frtab.sub Isoplot IsoPlot.nm IsoPval.nm Isotest IsoTest.nm nmplot nmplot.cat nmplot.n nmplot.ncat SplitData SubsetData

Dependencies:cli colorspace cpp11 dplyr fansi farver forcats generics ggplot2 glue gridExtra gtable Iso isoband labeling lattice lifecycle magrittr MASS Matrix mgcv munsell nlme pillar pkgconfig purrr R6 RColorBrewer rlang scales stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr

Help page	Topics
Plot the adjusted p-values, raw p-values and FDR level	adjPlot
Create a frequency table of the control values	FrCtrl
Generate the number of unique values, the list of unique values, or the number of observations of specified variable(s)	Frtab
Count the number of observations for each unique value of a variable on a subset of data	Frtab.sub
Genetic toxicity in vitro dataset	geninvitro
Create plot(s) of the observations, the sample means and the fitted isotonic regression curve	Isoplot
Create a plot of the observations, sample means and fitted isotonic regression curve for one nanomaterial	IsoPlot.nm
Calculate p-values based on permutation for both increasing and decreasing ordered alternatives	IsoPval.nm
Calculate the test statistics and p-values for testing monotonic trend	Isotest
Calculate the value of the test statistics for testing monotonic trend	IsoTest.nm
NM-400 in vitro dataset	nm400
Create plots of the dose and the response for each nanomaterial in the dataset	nmplot
Create plots of the dose and the response grouped by a variable	nmplot.cat
Create plots of the dose and the response for every unique value of a certain variable	nmplot.n
Create plots of the dose and the response differentiated by specified variables	nmplot.ncat
Split the data of each nanomaterial into different subsets of data	SplitData
Create a subset of data	SubsetData

Package: NMTox 0.1.0

NMTox: Dose-Response Relationship Analysis of Nanomaterial Toxicity

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