ecotoxicology: Methods for Ecotoxicology

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Implementation of the EPA's Ecological Exposure Research Division (EERD) tools (discontinued in 1999) for Probit and Trimmed Spearman-Karber Analysis. Probit and Spearman-Karber methods from Finney's book "Probit analysis a statistical treatment of the sigmoid response curve" with options for most accurate results or identical results to the book. Probit and all the tables from Finney's book (code-generated, not copied) with the generating functions included. Control correction: Abbott, Schneider-Orelli, Henderson-Tilton, Sun-Shepard. Toxicity scales: Horsfall-Barratt, Archer, Gauhl-Stover, Fullerton-Olsen, etc.

Author
Jose Gama [aut, cre, trl]
Date of publication
2015-10-14 12:25:39
Maintainer
Jose Gama <rxprtgama@gmail.com>
License
GPL (>= 3)
Version
1.0.1

View on CRAN

Man pages

AdjustAbbott
Calculate corrected efficacy % with Abbott's formula
AdjustHendersonTilton
Calculate corrected efficacy % with Henderson-Tilton's...
AdjustSchneiderOrelli
Calculate corrected efficacy % with Schneider-Orelli's...
AdjustSunShepard
Calculate corrected efficacy % with Sun-Shepard's formula
AphisRumicisDerrisMalaccensis
data on the toxicity to Aphis rumicis of an ether extract of...
ArcsinToPercentage
Convert Arcsin values to percentages
CalculateLC50
Calculate LC50 from a matrix with 3 columns: concentration,...
CalculateLCn
Calculate LC for N between 0 (LC0) and 100 (LC100)
Dunnett.t.Statistic
Critical Values of Dunnett's t Statistic
ecotoxicology-internal
Internal ecotoxicology functions
erfinv
Inverse error function
GenTableIFinney1964
Generate table I from Finney1964 "Transformation of...
GenTableIIFinney1964
Generate table II from Finney1964 "The weighting coefficient...
GenTableIIIFinney1964
Generate table III from Finney1964 "Maximum and minimum...
GenTableIVFinney1964
Generate table IV from Finney1964 "Working probits"
GenTableIXFinney1964
Generate table IX from Finney1964 "Minimum Working Probit,...
GenTableVFinney1964
Generate table V from Finney1964 "The Probability, P, the...
GenTableVIFinney1964
Generate table VI from Finney1964 "Distribution of chi^2"
GenTableVIIFinney1964
Generate table VII from Finney1964 "Distribution of t"
GenTableVIIIFinney1964
Generate table VIII from Finney1964 "The Weighting...
IsMonotonicallyDecreasing
Determine if a series is monotonically decreasing
IsMonotonicallyIncreasing
Determine if a series is monotonically increasing
MakeMonotonicallyDecreasing
Make monotonically decreasing sequence
MakeMonotonicallyIncreasing
Smoothed Mortality Proportion (monotonically increasing...
PercentageToArcsin
Convert percentages to Arcsin values
PercentageToProbit
Convert percentages to Probit values
ProbitApproxStandardErrorOfDosage
Approximate Standard Error of dosage
ProbitChi
Estimate the column for Chi calculation
ProbitEPA
Probit estimation similar to the EPA's Ecological Exposure...
ProbitFiducialLimits
Probit Fiducial Limits
ProbitFinney
Probit estimation regression with Finney's method
ProbitRegression
Probit regression line
ProbitStandardErrorOfDosage
Standard Error of dosage
ProbitStandardErrorRate
Standard Error of rate of increase of probit value per unit...
ProbitToPercentage
Convert Probit values to percentages
ProbitVALUEg
Probit value "g"
ProbitVarianceDosage
Variance of dosage
ProbitVarianceRate
Variance of rate of increase of probit value per unit...
Probitw
Calculate weighting coefficient from expected probit
ProbitWeightingCoef
Calculate the weighting coefficient
ProbitWorkingP
Calculate working probit
ProbitZ
Calculate the ordinate to the normal distribution...
ProbitZ4dec
Calculate the ordinate to the normal distribution...
ScaleArcher
Archer Scale for assessment of leaf damage
ScaleGauhlStover
Gauhl’s modification of Stover’s severity scoring system
ScaleHorsfallBarratt
Horsfall-Barratt Scale for Measuring Plant Disease
SheepsheadMinnow40SK
Mortality data from a fathead minnow larval survival and...
SpearmanKarber
Spearman Karber estimation
Table1Finney1964
Transformation of Percentages to Probits, table I of Finney,...
Table2Finney1964
The Weighting Coefficient and Q/Z, table II of Finney, 1964
Table3Finney1964
Maximum and Minimum working probits and Range, table III of...
Table4Finney1964
Working probits, table IV of Finney, 1964
Table5Finney1964
The Probability, P, the Ordinate, Z, and Z^2, table V of...
Table8Finney1964
The Weighting Coefficient in Wadley's Problem, table VIII of...
Table9Finney1964
Minimum Working Probit, Range, and Weighting Coefficient for...
TestMix2poisons
Generate table 26 from Finney1964 "The Function for Planning...
TSK
Trimmed Spearman-Karber method, as per Hamilton and EPA
WAAPPpestCount
WAAPP Pest Count scoring system

Files in this package

ecotoxicology
ecotoxicology/NAMESPACE
ecotoxicology/demo
ecotoxicology/demo/Finney.R
ecotoxicology/demo/TSKtest.R
ecotoxicology/demo/00Index
ecotoxicology/data
ecotoxicology/data/Dunnett.t.Statistic.rda
ecotoxicology/data/SheepsheadMinnow40SK.rda
ecotoxicology/data/Table2Finney1964.rda
ecotoxicology/data/Table9Finney1964.rda
ecotoxicology/data/Table4Finney1964.rda
ecotoxicology/data/Table8Finney1964.rda
ecotoxicology/data/Table3Finney1964.rda
ecotoxicology/data/Table1Finney1964.rda
ecotoxicology/data/AphisRumicisDerrisMalaccensis.rda
ecotoxicology/data/Table5Finney1964.rda
ecotoxicology/R
ecotoxicology/R/ecotoxicology.R
ecotoxicology/R/TSK.R
ecotoxicology/MD5
ecotoxicology/DESCRIPTION
ecotoxicology/man
ecotoxicology/man/GenTableIXFinney1964.Rd
ecotoxicology/man/PercentageToProbit.Rd
ecotoxicology/man/ScaleGauhlStover.Rd
ecotoxicology/man/ProbitEPA.Rd
ecotoxicology/man/ProbitApproxStandardErrorOfDosage.Rd
ecotoxicology/man/ProbitZ4dec.Rd
ecotoxicology/man/ScaleHorsfallBarratt.Rd
ecotoxicology/man/Table9Finney1964.Rd
ecotoxicology/man/Probitw.Rd
ecotoxicology/man/ScaleArcher.Rd
ecotoxicology/man/MakeMonotonicallyDecreasing.Rd
ecotoxicology/man/TSK.Rd
ecotoxicology/man/AphisRumicisDerrisMalaccensis.Rd
ecotoxicology/man/GenTableIVFinney1964.Rd
ecotoxicology/man/MakeMonotonicallyIncreasing.Rd
ecotoxicology/man/ProbitWeightingCoef.Rd
ecotoxicology/man/ProbitStandardErrorRate.Rd
ecotoxicology/man/ProbitStandardErrorOfDosage.Rd
ecotoxicology/man/ProbitVarianceRate.Rd
ecotoxicology/man/ProbitFinney.Rd
ecotoxicology/man/ecotoxicology-internal.Rd
ecotoxicology/man/Dunnett.t.Statistic.Rd
ecotoxicology/man/SheepsheadMinnow40SK.Rd
ecotoxicology/man/Table1Finney1964.Rd
ecotoxicology/man/GenTableIFinney1964.Rd
ecotoxicology/man/ProbitRegression.Rd
ecotoxicology/man/GenTableVIIIFinney1964.Rd
ecotoxicology/man/GenTableIIFinney1964.Rd
ecotoxicology/man/ProbitVarianceDosage.Rd
ecotoxicology/man/AdjustSchneiderOrelli.Rd
ecotoxicology/man/ProbitZ.Rd
ecotoxicology/man/ProbitToPercentage.Rd
ecotoxicology/man/Table8Finney1964.Rd
ecotoxicology/man/ProbitFiducialLimits.Rd
ecotoxicology/man/WAAPPpestCount.Rd
ecotoxicology/man/GenTableVIFinney1964.Rd
ecotoxicology/man/GenTableIIIFinney1964.Rd
ecotoxicology/man/ProbitWorkingP.Rd
ecotoxicology/man/Table5Finney1964.Rd
ecotoxicology/man/CalculateLC50.Rd
ecotoxicology/man/ProbitChi.Rd
ecotoxicology/man/GenTableVFinney1964.Rd
ecotoxicology/man/AdjustSunShepard.Rd
ecotoxicology/man/CalculateLCn.Rd
ecotoxicology/man/GenTableVIIFinney1964.Rd
ecotoxicology/man/erfinv.Rd
ecotoxicology/man/IsMonotonicallyIncreasing.Rd
ecotoxicology/man/PercentageToArcsin.Rd
ecotoxicology/man/Table2Finney1964.Rd
ecotoxicology/man/AdjustHendersonTilton.Rd
ecotoxicology/man/AdjustAbbott.Rd
ecotoxicology/man/Table4Finney1964.Rd
ecotoxicology/man/TestMix2poisons.Rd
ecotoxicology/man/ProbitVALUEg.Rd
ecotoxicology/man/ArcsinToPercentage.Rd
ecotoxicology/man/Table3Finney1964.Rd
ecotoxicology/man/IsMonotonicallyDecreasing.Rd
ecotoxicology/man/SpearmanKarber.Rd