Learn R Programming

⚠️There's a newer version (1.1.8) of this package.Take me there.

NADA2

Table of Contents

Introduction

For many environmental professionals, the way to deal with “nondetects” is less than obvious. Values below detection or reporting limits result from measuring trace amounts of a variety of organic and inorganic chemicals. This package includes methods for plotting, computing summary statistics, hypothesis tests, and regression models for data with one or more detection limits. Most are adaptations of or direct use of existing methods found in survival analysis (such as in the survival package) and in cancer research (such as in the interval package).

This package is a series of new procedures or improvements on current ones in the NADA package developed through a series of webinars, online courses, and updates to Helsel (2004) and Helsel (2011).

  • Helsel, D.R., 2004. Nondetects and Data Analysis: Statistics for Censored Environmental Data, 1st edition. ed. Wiley-Interscience, Hoboken, N.J.
  • Helsel, D.R., 2011. Statistics for Censored Environmental Data Using Minitab© and R, 2nd edition. ed. Wiley-Interscience, Hoboken, N.J.

Citing package

citation('NADA2')
## 
## To cite package 'NADA2' in publications use:
## 
##   Paul Julian and Dennis Helsel (2021). NADA2: Data Analysis for
##   Censored Environmental Data. R package version 1.0.2.
##   https://github.com/SwampThingPaul/NADA2
## 
## A BibTeX entry for LaTeX users is
## 
##   @Manual{,
##     title = {NADA2: Data Analysis for Censored Environmental Data},
##     author = {Paul Julian and Dennis Helsel},
##     year = {2021},
##     note = {R package version 1.0.2},
##     url = {https://github.com/SwampThingPaul/NADA2},
##   }

Installation

Development version can be installed from this repo using:

install.packages("devtools");# if you do not have it installed on your PC
devtools::install_github("SwampThingPaul/NADA2")

To install the deployed version from CRAN use:

install.packages("NADA2")

Copy Link

Version

Install

install.packages('NADA2')

Monthly Downloads

367

Version

1.1.4

License

MIT + file LICENSE

Issues

Pull Requests

Stars

Forks

Maintainer

Paul Julian

Last Published

August 27th, 2023

Functions in NADA2 (1.1.4)

bestaic

Find the lowest AIC multiple regression model
cen2means

Censored data two-group test for difference in means
binaryMDS

Plot Nonmetric Multidimensional Scaling of binary censored data
binarySim

Binary similarity coefficient matrix
cboxplot

Draws censored boxplots
cen1way

Peto-Peto one-factor test
cenCompareCdfs

Comparison of empirical cdf of censored data
cenPredInt

Prediction interval for censored data
cenCompareQQ

Censored Q-Q Plot comparison
cen_signedranktest

Wilcoxcon Signed-Rank test for censored data
cen_signtest

Sign test for censored data
cenregQQ

Q-Q plot of censored regression residuals
censeaken

Seasonal Kendall permutation test on censored data
cenTolInt

Upper Tolerance interval for censored data
cenQQ

Q-Q Plot censored data
cenpermanova

Censored data one-factor permutation test
cenperm2

Censored two-group permutation test
cencorreg

Correlation and Regression with censored data
cenanova

ANOVA for censored data
equivalent_n

Censored data sample size
cen_paired

Censored data paired t-test
kenplot

Plot robust median ATS line for censored data
partplots

Partial plots for censored MLE regression
markers

Markers
ordranks

Computes ranks of data with one or multiple detection limits
ppw.test

Test for difference in left-censored samples
centrend

Trend analysis of censored data with a covariate
cen_ecdf

Censored Empirical Cumulative Distribution Function
centrendsea

Trend analysis of censored data with a covariate and seasonal blocks
uMDS

Plot U-score Nonmetric Multidimensional Scaling of censored data
computeS

Kendall's S-statistic for permutations of censored data
cfit

Compute an ECDF and Distribution Parameters for Censored Data
quantile_CI

quantile confidence interval
uscore

U-score (individual value)
uscores

Uscores for multiple columns of censored data
uscoresi

U-scores for interval-censored data (multiple columns)
Example1

Example1
ATSmini

Kendall's tau and ATS line for censored data
ROSci

Computes confidence intervals on regression on order statistics (ROS) mean
binaryClust

Cluster Matrix of Binary Censored Data
Usci

Interval-censored U-Score
Usc

U-scores for (non-interval, sinle-column) Censored Data
anosimPlot

Permutation Analysis of Similarity (anosim) for Censored Data
Example2

Example2
ReconLogistic

ReconLogistic
Example3

Example3
PbHeron

PbHeron
Gales_Creek

Gales_Creek
TCE2

TCE2
atrazine

Atrazine concentrations in Nebraska ground water
ATS

Akritas-Theil-Sen line for censored data
Brumbaugh

Brumbaugh
NADA2_survmean

Summary statistics of survival curve (from survival:::survmean)
Pollen_Thia

Thiamethoxam concentrations in pollen
binaryDiss

Binary dissimilarity coefficient matrix