ecotoxicology: Methods for Ecotoxicology

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.

AuthorJose Gama [aut, cre, trl]
Date of publication2015-10-14 09:20:55
MaintainerJose Gama <rxprtgama@gmail.com>
LicenseGPL (>= 3)
Version1.0.1

View on R-Forge

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

Functions

AdjustAbbott Man page
AdjustHendersonTilton Man page
AdjustSchneiderOrelli Man page
AdjustSunShepard Man page
AphisRumicisDerrisMalaccensis Man page
ArcsinToPercentage Man page
CalculateLC50 Man page
CalculateLCn Man page
Dunnett.t.Statistic Man page
erfinv Man page
GenTableIFinney1964 Man page
GenTableIIFinney1964 Man page
GenTableIIIFinney1964 Man page
GenTableIVFinney1964 Man page
GenTableIXFinney1964 Man page
GenTableVFinney1964 Man page
GenTableVIFinney1964 Man page
GenTableVIIFinney1964 Man page
GenTableVIIIFinney1964 Man page
IsMonotonicallyDecreasing Man page
IsMonotonicallyIncreasing Man page
MakeMonotonicallyDecreasing Man page
MakeMonotonicallyIncreasing Man page
PercentageToArcsin Man page
PercentageToProbit Man page
ProbitApproxStandardErrorOfDosage Man page
ProbitChi Man page
ProbitEPA Man page
ProbitFiducialLimits Man page
ProbitFinney Man page
ProbitRegression Man page
ProbitStandardErrorOfDosage Man page
ProbitStandardErrorRate Man page
ProbitToPercentage Man page
ProbitVALUEg Man page
ProbitVarianceDosage Man page
ProbitVarianceRate Man page
Probitw Man page
ProbitWeightingCoef Man page
ProbitWorkingP Man page
ProbitZ Man page
ProbitZ4dec Man page
ScaleArcher Man page
ScaleGauhlStover Man page
ScaleHorsfallBarratt Man page
SheepsheadMinnow40SK Man page
SpearmanKarber Man page
Table1Finney1964 Man page
Table2Finney1964 Man page
Table3Finney1964 Man page
Table4Finney1964 Man page
Table5Finney1964 Man page
Table8Finney1964 Man page
Table9Finney1964 Man page
TestMix2poisons Man page
TSK Man page
V1 Man page
V2 Man page
V3 Man page
V4 Man page
V5 Man page
V6 Man page
WAAPPpestCount Man page

Files

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

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