Tools for Environmental Analyses, Ecotoxicology and Various R Functions

Documentation for package ‘HelpersMG’ version 5.9

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Tools for Environmental Analyses, Ecotoxicology and Various R Functions

-- A --

addS3Class	Add a S3 class to an object.
as.mcmc.mcmcComposite	Extract mcmc object from a mcmcComposite object
as.parameters	Extract parameters from mcmcComposite object
as.quantiles	Extract quantile distribution from mcmcComposite object
asc	Return the codes (in UTF-8) of a string

-- B --

Plot a barplot graph with error bar on y

-- C --

cArrows	Draw curved lines with arrowhead
ChangeCoordinate	Return a value in a changed coordinate
char	Return the characters defined by the codes
compare	Run a shiny application for basic functions of comparison
compare_AIC	Compares the AIC of several outputs
compare_AICc	Compares the AICc of several outputs
compare_BIC	Compares the BIC of several outputs
contingencyTable.compare	Contingency table comparison using Akaike weight
convert.tz	Convert one Date-Time from one timezone to another
cutter	Distribution of the fitted distribution without cut.

-- D --

d	Write an ASCII Representation of a vector object
dbeta_new	Density for the Beta distributions.
dcutter	Distribution of the fitted distribution without cut.
dggamma	Generalized gamma distribution.
DIx	Return an index of quantitative asymmetry and complexity named Developmental Instability Index (DIx)
dnbinom_new	Random numbers for the negative binomial distribution.
dSnbinom	Distribution of the sum of random variable with negative binomial distributions.
duplicated_packages	List the duplicated packages with their locations

-- E --

ellipse	Plot an ellipse
ExtractAIC.glm	Return AIC, AICc or BIC from a glm object

-- F --

fitdistrquantiles	Parameters of beta, normal or gamma distribution based on quantiles.
flexit	Return the flexit
FormatCompareAIC	Format data to be used with compare_AIC()
format_ncdf	Return an array with ncdf data

-- I --

iCutter	Run a shiny application to fit bone section
IC_clean_data	Clean the dataframe before to be used with IC_threshold_matrix
IC_correlation_simplify	Simplify the correlation matrix
IC_threshold_matrix	Calculate correlation matrix
index.periodic	Estimate indices in periodic timeseries based on anchored minimum and maximum
ind_long_lat	Return or the index in ncdf object from lat/longitude or inverse
inside	Search a string within files of a folder
invlogit	Return the inverse logit

-- L --

LD50	Estimate the parameters that best describe LD50
LD50_MHmcmc	Metropolis-Hastings algorithm for LD50
LD50_MHmcmc_p	Generates set of parameters to be used with LD50_MHmcmc()
list.packages	List the installed packages with their locations
local.search	Return path of file searched for in local disk based on its file name
logit	Return the logit
logLik.compareAIC	Return Log Likelihood generated by FormatCompareAIC
logLik.cutter	Return log likelihood of a cutter fitted model
logLik.LD50	Return Log Likelihood of a fit generated by LD50

-- M --

merge.mcmcComposite	Merge two mcmcComposite results
MHalgoGen	Monte-Carlo Markov-chain with Metropolis-Hastings algorithm
minmax.periodic	Search for minimum and maximum indices in periodic timeseries
modeled.hist	Return the theoretical value for the histogram bar
modifyVector	Modifies Elements of a Vector
moon.info	Moon phase based on a date
MovingWindow	Return a moving average of a vector.

-- N --

NagelkerkeScaledR2	Return the scaled R2 defined by Nagelkerke (1991)
newcompassRose	Display a compass rose
newmap.scale	Add Scale to Existing Unprojected Map

-- O --

Open a finder window with current working directory in MacOS X and windows

-- P --

pggamma	Generalized gamma distribution.
plot.cutter	Plot results of cutter that best describe distribution
plot.IconoCorel	Clean the dataframe before to be used with IC_threshold_matrix
plot.LD50	Plot results of LD50() that best describe LD50
plot.mcmcComposite	Plot the result of a mcmcComposite object
plot.PriorsmcmcComposite	Plot a prior defined with setPriors function
plot_add	Add a plot to a previous one
plot_errbar	Plot a xy graph with error bar on x and/or y
predict.LD50	Estimate survival according to doses
print.cutter	Print results of cutter that best describe distribution
pSnbinom	Distribution of the sum of random variable with negative binomial distributions.

-- Q --

qggamma	Generalized gamma distribution.
qSnbinom	Distribution of the sum of random variable with negative binomial distributions.
qvlmer	Quasi Variances for lmer Model Coefficients

-- R --

r2norm	Random generation for Gaussian distributions different at left and right
RandomFromHessianOrMCMC	Random numbers based on Hessian matrix or MCMC
rcutter	Random values of unobserved values of cut distribution.
read_folder	Read files present in a folder and creates a list with the content of these files
RectangleRegression	Return parameters of rectangle regression
rggamma	Generalized gamma distribution.
rmnorm	Generate random numbers from the multivariate normal distribution
RM_add	Create a results managment or add a value in a results managment to an object
RM_delete	Delete a results managment or a result within a results managment from an object
RM_duplicate	Duplicate a results managment within an object.
RM_get	Get a value in a results managment to an object
RM_list	Return the list of results managment of an object.
rnbinom_new	Random numbers for the negative binomial distribution.
rSnbinom	Distribution of the sum of random variable with negative binomial distributions.

-- S --

ScalePreviousPlot	Return the scale of the previous plot
SEfromHessian	Standard error of parameters based on Hessian matrix
series.compare	Data series comparison using Akaike weight
setPriors	Set priors for MHalgoGen()
show_name	Show the name of a point
similar	Test if two vectors contains the same elements independently of their order
specify_decimal	Return a number as character with specified number of decimals
summary.mcmcComposite	Summarize the result of a mcmcComposite object
sun.info	Estimate the time of sunrise and sunset according to longitude, latitude and date
symbol.Female	Plot a female symbol in the plotting region
symbol.Male	Plot a male symbol in the plotting region
symmetricize	Make a matrix symmetric

-- T --

tide.info	Annual tide calendar for one particular location
tnirp	Read an ASCII text representation of a named or not vector object

-- U --

Run the function FUN on X using parallel computing

-- W --

wget	Download a file from internet and save it locally