Package: HelpersMG 6.2

HelpersMG: Tools for Environmental Analyses, Ecotoxicology and Various R Functions

Contains miscellaneous functions useful for managing 'NetCDF' files (see <https://en.wikipedia.org/wiki/NetCDF>), get moon phase and time for sun rise and fall, tide level, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.

Authors:Marc Girondot [aut, cre]

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HelpersMG.pdf |HelpersMG.html✨
HelpersMG/json (API)
NEWS

# Install 'HelpersMG' in R:
install.packages('HelpersMG', repos = c('https://marc-girondot.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On CRAN:

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

89 exports 4 stars 1.85 score 29 dependencies 4 dependents 1 mentions 166 scripts 951 downloads

Last updated 25 days agofrom:4c13ba5e3a. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 24 2024
R-4.5-winNOTEAug 24 2024
R-4.5-linuxNOTEAug 24 2024
R-4.4-winNOTEAug 24 2024
R-4.4-macNOTEAug 24 2024
R-4.3-winNOTEAug 24 2024
R-4.3-macNOTEAug 24 2024

Exports:addS3Classas.parametersas.quantilesascbarplot_errbarcArrowsChangeCoordinatecharcomparecompare_AICcompare_AICccompare_BICcontingencyTable.compareconvert.tzcutterddbeta_newdcutterdggammaDIxdnbinom_newdSnbinomduplicated_packagesellipseExtractAIC.glmfitdistrquantilesflexitformat_ncdfFormatCompareAICIC_clean_dataIC_correlation_simplifyIC_threshold_matrixiCutterind_long_latindex.periodicinsideinvlogitLD50LD50_MHmcmcLD50_MHmcmc_plist.packageslocal.searchlogitMHalgoGenminmax.periodicmodeled.histmodifyVectormoon.infoMovingWindowNagelkerkeScaledR2newcompassRosenewmap.scaleopenwdpggammaplot_addplot_errbarpSnbinomqggammaqSnbinomqvlmerr2normRandomFromHessianOrMCMCrcutterread_folderRectangleRegressionrggammaRM_addRM_deleteRM_duplicateRM_getRM_listrmnormrnbinom_newrSnbinomScalePreviousPlotSEfromHessianseries.comparesetPriorsshow_namesimilarspecify_decimalsun.infosymbol.Femalesymbol.Malesymmetricizetide.infotnirpuniversalmclapplywget

Dependencies:clicodacolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Tools for Environmental Analyses, Ecotoxicology and Various R FunctionsHelpersMG-package
Add a S3 class to an object.addS3Class
Extract mcmc object from a mcmcComposite objectas.mcmc.mcmcComposite
Extract parameters from mcmcComposite objectas.parameters
Extract quantile distribution from mcmcComposite objectas.quantiles
Return the codes (in UTF-8) of a stringasc
Plot a barplot graph with error bar on ybarplot_errbar
Draw curved lines with arrowheadcArrows
Return a value in a changed coordinateChangeCoordinate
Return the characters defined by the codeschar
Run a shiny application for basic functions of comparisoncompare
Compares the AIC of several outputscompare_AIC
Compares the AICc of several outputscompare_AICc
Compares the BIC of several outputscompare_BIC
Contingency table comparison using Akaike weightcontingencyTable.compare
Convert one Date-Time from one timezone to anotherconvert.tz
Distribution of the fitted distribution without cut.cutter
Write an ASCII Representation of a vector objectd
Density for the Beta distributions.dbeta_new
Distribution of the fitted distribution without cut.dcutter
Generalized gamma distribution.dggamma pggamma qggamma rggamma
Return an index of quantitative asymmetry and complexity named Developmental Instability Index (DIx)DIx
Random numbers for the negative binomial distribution.dnbinom_new
Distribution of the sum independent negative binomial random variables.dSnbinom pSnbinom qSnbinom rSnbinom
List the duplicated packages with their locationsduplicated_packages
Plot an ellipseellipse
Return AIC, AICc or BIC from a glm objectExtractAIC.glm
Parameters of beta, normal or gamma distribution based on quantiles.fitdistrquantiles
Return the flexitflexit
Return an array with ncdf dataformat_ncdf
Format data to be used with compare_AIC()FormatCompareAIC
Clean the dataframe before to be used with IC_threshold_matrixIC_clean_data
Simplify the correlation matrixIC_correlation_simplify
Calculate correlation matrixIC_threshold_matrix
Run a shiny application to fit bone sectioniCutter
Return or the index in ncdf object from lat/longitude or inverseind_long_lat
Estimate indices in periodic timeseries based on anchored minimum and maximumindex.periodic
Search a string within files of a folderinside
Return the inverse logitinvlogit
Estimate the parameters that best describe LD50LD50
Metropolis-Hastings algorithm for LD50LD50_MHmcmc
Generates set of parameters to be used with LD50_MHmcmc()LD50_MHmcmc_p
List the installed packages with their locationslist.packages
Return path of file searched for in local disk based on its file namelocal.search
Return the logitlogit
Return Log Likelihood generated by FormatCompareAIClogLik.compareAIC
Return log likelihood of a cutter fitted modellogLik.cutter
Return Log Likelihood of a fit generated by LD50logLik.LD50
Merge two mcmcComposite resultsmerge.mcmcComposite
Monte-Carlo Markov-chain with Metropolis-Hastings algorithmMHalgoGen
Search for minimum and maximum indices in periodic timeseriesminmax.periodic
Return the theoretical value for the histogram barmodeled.hist
Modifies Elements of a VectormodifyVector
Moon phase based on a datemoon.info
Return a moving average of a vector.MovingWindow
Return the scaled R2 defined by Nagelkerke (1991)NagelkerkeScaledR2
Display a compass rosenewcompassRose
Add Scale to Existing Unprojected Mapnewmap.scale
Open a finder window with current working directory in MacOS X and windowsopenwd
Add a plot to a previous oneplot_add
Plot a xy graph with error bar on x and/or yplot_errbar
Plot results of cutter that best describe distributionplot.cutter
Clean the dataframe before to be used with IC_threshold_matrixplot.IconoCorel
Plot results of LD50() that best describe LD50plot.LD50
Plot the result of a mcmcComposite objectplot.mcmcComposite
Plot a prior defined with setPriors functionplot.PriorsmcmcComposite
Estimate survival according to dosespredict.LD50
Print results of cutter that best describe distributionprint.cutter
Quasi Variances for lmer Model Coefficientsqvlmer
Random generation for Gaussian distributions different at left and rightr2norm
Random numbers based on Hessian matrix or MCMCRandomFromHessianOrMCMC
Random values of unobserved values of cut distribution.rcutter
Read files present in a folder and creates a list with the content of these filesread_folder
Return parameters of rectangle regressionRectangleRegression
Create a results managment or add a value in a results managment to an objectRM_add
Delete a results managment or a result within a results managment from an objectRM_delete
Duplicate a results managment within an object.RM_duplicate
Get a value in a results managment to an objectRM_get
Return the list of results managment of an object.RM_list
Generate random numbers from the multivariate normal distributionrmnorm
Random numbers for the negative binomial distribution.rnbinom_new
Return the scale of the previous plotScalePreviousPlot
Standard error of parameters based on Hessian matrixSEfromHessian
Data series comparison using Akaike weightseries.compare
Set priors for MHalgoGen()setPriors
Show the name of a pointshow_name
Test if two vectors contains the same elements independently of their ordersimilar
Return a number as character with specified number of decimalsspecify_decimal
Summarize the result of a mcmcComposite objectsummary.mcmcComposite
Estimate the time of sunrise and sunset according to longitude, latitude and datesun.info
Plot a female symbol in the plotting regionsymbol.Female
Plot a male symbol in the plotting regionsymbol.Male
Make a matrix symmetricsymmetricize
Annual tide calendar for one particular locationtide.info
Read an ASCII text representation of a named or not vector objecttnirp
Run the function FUN on X using parallel computinguniversalmclapply
Download a file from internet and save it locallywget