Package: ecotoxicology 1.0.1

Jose Gama

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.

Authors:Jose Gama [aut, cre, trl]

ecotoxicology_1.0.1.tar.gz
ecotoxicology_1.0.1.tar.gz(r-4.5-noble)ecotoxicology_1.0.1.tar.gz(r-4.4-noble)
ecotoxicology_1.0.1.tgz(r-4.4-emscripten)ecotoxicology_1.0.1.tgz(r-4.3-emscripten)
ecotoxicology.pdf |ecotoxicology.html✨
ecotoxicology/json (API)

# Install 'ecotoxicology' in R:

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

Datasets:

AphisRumicisDerrisMalaccensis - Data on the toxicity to Aphis rumicis of an ether extract of Derris malaccensis
Dunnett.t.Statistic - Critical Values of Dunnett's t Statistic
SheepsheadMinnow40SK - Mortality data from a fathead minnow larval survival and growth test
Table1Finney1964 - Transformation of Percentages to Probits, table I of Finney, 1964
Table2Finney1964 - The Weighting Coefficient and Q/Z, table II of Finney, 1964
Table3Finney1964 - Maximum and Minimum working probits and Range, table III of Finney, 1964
Table4Finney1964 - Working probits, table IV of Finney, 1964
Table5Finney1964 - The Probability, P, the Ordinate, Z, and Z^2, table V of Finney, 1964
Table8Finney1964 - The Weighting Coefficient in Wadley's Problem, table VIII of Finney, 1964
Table9Finney1964 - Minimum Working Probit, Range, and Weighting Coefficient for Inverse Sampling, table IX of Finney, 1964

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

53 exports 3 stars 0.23 score 0 dependencies 26 scripts 181 downloads

Last updated 9 years agofrom:3099df5a54. Checks:OK: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 04 2024
R-4.5-linux	OK	Sep 04 2024

Exports:AdjustAbbott AdjustHendersonTilton AdjustSchneiderOrelli AdjustSunShepard ArcsinToPercentage CalculateLC50 CalculateLCn erfinv GenTableIFinney1964 GenTableIIFinney1964 GenTableIIIFinney1964 GenTableIVFinney1964 GenTableIXFinney1964 GenTableVFinney1964 GenTableVIFinney1964 GenTableVIIFinney1964 GenTableVIIIFinney1964 IsMonotonicallyDecreasing IsMonotonicallyIncreasing MakeMonotonicallyDecreasing MakeMonotonicallyIncreasing PercentageToArcsin PercentageToProbit ProbitApproxStandardErrorOfDosage ProbitChi ProbitEPA ProbitFiducialLimits ProbitFinney ProbitRegression ProbitStandardErrorOfDosage ProbitStandardErrorRate ProbitToPercentage ProbitVALUEg ProbitVarianceDosage ProbitVarianceRate Probitw ProbitWeightingCoef ProbitWorkingP ProbitZ ProbitZ4dec ScaleArcher ScaleGauhlStover ScaleHorsfallBarratt SpearmanKarber TestMix2poisons TSK V1 V2 V3 V4 V5 V6 WAAPPpestCount

Dependencies:

Help page	Topics
Calculate corrected efficacy % with Abbott's formula	AdjustAbbott
Calculate corrected efficacy % with Henderson-Tilton's formula	AdjustHendersonTilton
Calculate corrected efficacy % with Schneider-Orelli's formula	AdjustSchneiderOrelli
Calculate corrected efficacy % with Sun-Shepard's formula	AdjustSunShepard
data on the toxicity to Aphis rumicis of an ether extract of Derris malaccensis	AphisRumicisDerrisMalaccensis
Convert Arcsin values to percentages	ArcsinToPercentage
Calculate LC50 from a matrix with 3 columns: concentration, number of exposed subjects and number of deaths	CalculateLC50
Calculate LC for N between 0 (LC0) and 100 (LC100)	CalculateLCn
Critical Values of Dunnett's t Statistic	Dunnett.t.Statistic
Inverse error function	erfinv
Generate table I from Finney1964 "Transformation of percentages to probits"	GenTableIFinney1964
Generate table II from Finney1964 "The weighting coefficient and Q/Z"	GenTableIIFinney1964
Generate table III from Finney1964 "Maximum and minimum working probits and range"	GenTableIIIFinney1964
Generate table IV from Finney1964 "Working probits"	GenTableIVFinney1964
Generate table IX from Finney1964 "Minimum Working Probit, Range, and Weighting Coefficient for Inverse Sampling"	GenTableIXFinney1964
Generate table V from Finney1964 "The Probability, P, the Ordinate, Z, and Z^2"	GenTableVFinney1964
Generate table VI from Finney1964 "Distribution of chi^2"	GenTableVIFinney1964
Generate table VII from Finney1964 "Distribution of t"	GenTableVIIFinney1964
Generate table VIII from Finney1964 "The Weighting Coefficient in Wadley's Problem"	GenTableVIIIFinney1964
Determine if a series is monotonically decreasing	IsMonotonicallyDecreasing
Determine if a series is monotonically increasing	IsMonotonicallyIncreasing
Make monotonically decreasing sequence	MakeMonotonicallyDecreasing
Smoothed Mortality Proportion (monotonically increasing sequence)	MakeMonotonicallyIncreasing
Convert percentages to Arcsin values	PercentageToArcsin
Convert percentages to Probit values	PercentageToProbit
Approximate Standard Error of dosage	ProbitApproxStandardErrorOfDosage
Estimate the column for Chi calculation	ProbitChi
Probit estimation similar to the EPA's Ecological Exposure Research Division (EERD) tool	ProbitEPA
Probit Fiducial Limits	ProbitFiducialLimits
Probit estimation regression with Finney's method	ProbitFinney
Probit regression line	ProbitRegression
Standard Error of dosage	ProbitStandardErrorOfDosage
Standard Error of rate of increase of probit value per unit increase in x	ProbitStandardErrorRate
Convert Probit values to percentages	ProbitToPercentage
Probit value "g"	ProbitVALUEg
Variance of dosage	ProbitVarianceDosage
Variance of rate of increase of probit value per unit increase in x	ProbitVarianceRate
Calculate weighting coefficient from expected probit	Probitw
Calculate the weighting coefficient	ProbitWeightingCoef
Calculate working probit	ProbitWorkingP
Calculate the ordinate to the normal distribution corresponding to the probability P	ProbitZ
Calculate the ordinate to the normal distribution corresponding to the probability P, exactly like Finney's	ProbitZ4dec
Archer Scale for assessment of leaf damage	ScaleArcher
Gauhl’s modification of Stover’s severity scoring system	ScaleGauhlStover
Horsfall-Barratt Scale for Measuring Plant Disease	ScaleHorsfallBarratt
Mortality data from a fathead minnow larval survival and growth test (40 organisms per concentration)	SheepsheadMinnow40SK
Spearman Karber estimation	SpearmanKarber
Transformation of Percentages to Probits, table I of Finney, 1964	Table1Finney1964
The Weighting Coefficient and Q/Z, table II of Finney, 1964	Table2Finney1964
Maximum and Minimum working probits and Range, table III of Finney, 1964	Table3Finney1964
Working probits, table IV of Finney, 1964	Table4Finney1964
The Probability, P, the Ordinate, Z, and Z^2, table V of Finney, 1964	Table5Finney1964
The Weighting Coefficient in Wadley's Problem, table VIII of Finney, 1964	Table8Finney1964
Minimum Working Probit, Range, and Weighting Coefficient for Inverse Sampling, table IX of Finney, 1964	Table9Finney1964
Generate table 26 from Finney1964 "The Function for Planning Tests of Mixtures of Two Poisons"	TestMix2poisons
Trimmed Spearman-Karber method, as per Hamilton and EPA	TSK
WAAPP Pest Count scoring system	WAAPPpestCount

Package: ecotoxicology 1.0.1

ecotoxicology: Methods for Ecotoxicology

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)