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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")

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Version

Install

install.packages('NADA2')

Monthly Downloads

316

Version

2.0.1

License

MIT + file LICENSE

Issues

Pull Requests

Stars

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Maintainer

Paul Julian

Last Published

September 30th, 2025

Functions in NADA2 (2.0.1)

Maclist

Create maximal antichains from interval data
MLEintvl

Map maximal antichains to real-valued intervals
PbHeron

PbHeron
NADAprobs

Default Probability Values for Quantile Estimation
binaryDiss

Binary dissimilarity coefficient matrix
TCE2

TCE2
ROSci

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

Find the lowest AIC multiple regression model
binaryMDS

Plot Nonmetric Multidimensional Scaling of binary censored data
binaryClust

Cluster Matrix of Binary Censored Data
cencorreg

Correlation and Regression with censored data
cenken

Compute Kendall's Tau Correlation and ATS Line for Censored Data
cenpermanova

Censored data one-factor permutation test
cenregQQ

Q-Q plot of censored regression residuals
Usc

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

Q-Q Plot censored data
cen_signedranktest

Wilcoxcon Signed-Rank test for censored data
cenTolInt

Upper Tolerance interval for censored data
Usci

Interval-censored U-Score
hc_ppoints_uncen

Plotting Positions for Uncensored Observations (Cohn Method)
rescaleP

Rescale probability vector
cen1way

Peto-Peto one-factor test
cen2means

Censored data two-group test for difference in means
kenplot

Plot robust median ATS line for censored data
quantile_CI

quantile confidence interval
cenCompareQQ

Censored Q-Q Plot comparison
cenPredInt

Prediction interval for censored data
anosimPlot

Permutation Analysis of Similarity (anosim) for Censored Data
TCEReg

TCE Ground Waters of Long Island — with Explanatory Variables
cen2way

Parametric Two Factor Fixed Effects ANOVA for censored data
cen_signtest

Sign test for censored data
cen_paired

Censored data paired t-test
cen_ecdf

Censored Empirical Cumulative Distribution Function
atrazine

Atrazine concentrations in Nebraska ground water
cfit

Compute an ECDF and Distribution Parameters for Censored Data
cenCompareCdfs

Comparison of empirical cdf of censored data
cenanova

ANOVA for censored data
cenboxplot

Produces a censored boxplot
cboxplot

Draws censored boxplots
binarySim

Binary similarity coefficient matrix
ppw.test

Test for difference in left-censored samples
print.NADAList

Show Method for NADAList Objects
cohn

Calculate Cohn Numbers
censummary

Summary Statistics for Censored Data
cenperm2

Censored two-group permutation test
cenxyplot

Produces a censored x-y scatter plot
markers

Markers
cenpar.usr

Internal: Get Plotting Limits in Log or Linear Scale
centrendsea

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

Computes ranks of data with one or multiple detection limits
censeaken

Seasonal Kendall permutation test on censored data
censtats

Summary Statistics for Censored Data using ROS, MLE, and K-M
computeS

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

Uscores for multiple columns of censored data
uscore

U-score (individual value)
partplots

Partial plots for censored MLE regression
pctCen

Internal: Calculate Percent Censored Observations
centrend

Trend analysis of censored data with a covariate
equivalent_n

Censored data sample size
uMDS

Plot U-score Nonmetric Multidimensional Scaling of censored data
ros

Regression on Order Statistics (ROS)
splitQual

Internal: Split Qualified Numeric Vector Into Observations and Censoring
hc_ppoints

Compute plotting positions for censored and uncensored data
hc_ppoints_cen

Plotting Positions for Censored Observations (Cohn Method)
cenros

Class "ros"
uscoresi

U-scores for interval-censored data (multiple columns)
Example2

Example2
ATSmini

Kendall's tau and ATS line for censored data
EM

EM Algorithm for Interval-Censored Data
CuZn

CuZn
Example3

Example3
Cadmium

Cadmium
Gales_Creek

Gales_Creek
ATS

Akritas-Theil-Sen line for censored data
ShePyrene

ShePyrene
ReconLogistic

ReconLogistic
Brumbaugh

Brumbaugh
Pollen_Thia

Thiamethoxam concentrations in pollen
Example1

Example1
NADAList

NADA List Class
Macmat

Create clique matrix and Petrie pairs from maximal antichains