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HelpersMG (version 4.2)

Tools for Environmental Analyses, Ecotoxicology and Various R Functions

Description

Contains many functions useful for managing 'NetCDF' files (see ), get tide levels on any point of the globe, get moon phase and time for sun rise and fall, 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.

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Version

Install

install.packages('HelpersMG')

Monthly Downloads

1,162

Version

4.2

License

GPL-2

Maintainer

Marc Girondot

Last Published

June 15th, 2020

Functions in HelpersMG (4.2)

FormatCompareAIC

Format data to be used with compare_AIC()
ExtractAIC.glm

Return AIC, AICc or BIC from a glm object
IC_threshold_matrix

Calculate correlation matrix
IC_correlation_simplify

Simplify the correlation matrix
RectangleRegression

Return parameters of rectangle regression
ChangeCoordinate

Return a value in a changed coordinate
RandomFromHessianOrMCMC

Random numbers based on Hessian matrix or MCMC
DIx

Return an index of quantitative asymmetry and complexity named Developmental Instability Index (DIx)
LD50

Estimate the parameters that best describe LD50
as.quantiles

Extract quantile distribution from mcmcComposite object
LD50_MHmcmc

Metropolis-Hastings algorithm for LD50
HelpersMG-package

Tools for Environmental Analyses, Ecotoxicology and Various R Functions
compare_AICc

Compares the AICc of several outputs
compare_BIC

Compares the BIC of several outputs
as.parameters

Extract parameters from mcmcComposite object
logLik.compareAIC

Return Log Likelihood generated by FormatCompareAIC
convert.tz

Convert one Date-Time from one timezone to another
RM_list

Return the list of results managment of an object.
contingencyTable.compare

Contingency table comparison using Akaike weight
RM_get

Get a value in a results managment to an object
logLik.LD50

Return Log Likelihood of a fit generated by LD50
as.mcmc.mcmcComposite

Extract mcmc object from a mcmcComposite object
inside.search

Search a string within files of a folder
MovingWindow

Return a moving average of a vector.
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.
ScalePreviousPlot

Return the scale of the previous plot
SEfromHessian

Standard error of parameters based on Hessian matrix
duplicate.packages

List the duplicated packages with their locations
minmax.periodic

Search for minimum and maximum indices in periodic timeseries
plot.IconoCorel

Clean the dataframe before to be used with IC_threshold_matrix
modeled.hist

Return the theoretical value for the histogram bar
plot.LD50

Plot results of LD50() that best describe LD50
ellipse

Plot an ellipse
IC_clean_data

Clean the dataframe before to be used with IC_threshold_matrix
tide.info

Annual tide calendar for one particular location
ind_long_lat

Return or the index in ncdf object from lat/longitude or inverse
asc

Return the codes (in UTF-8) of a string
index.periodic

Estimate indices in periodic timeseries based on anchored minimum and maximum
invlogit

Return the inverse logit
RM_add

Create a results managment or add a value in a results managment to an object
barplot_errbar

Plot a barplot graph with error bar on y
logit

Return the logit
qSnbinom

Quantile function for the sum of random variable with negative binomial distributions.
merge.mcmcComposite

Merge two mcmcComposite results
LD50_MHmcmc_p

Generates set of parameters to be used with LD50_MHmcmc()
cArrows

Draw curved lines with arrowhead
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
tnirp

Read an ASCII text representation of a named or not vector object
d

Write an ASCII Representation of a vector object
dSnbinom

Density for the sum of random variable with negative binomial distributions.
MHalgoGen

Monte-Carlo Markov-chain with Metropolis-Hastings algorithm
qvlmer

Quasi Variances for lmer Model Coefficients
growlnotify

Send growl notification for MacOs X system.
flexit

Return the flexit
modifyVector

Modifies Elements of a Vector
moon.info

Moon phase based on a date
newmap.scale

Add Scale to Existing Unprojected Map
sun.info

Estimate the time of sunrise and sunset according to longitude, latitude and date
chr

Return the characters defined by the codes
plot_errbar

Plot a xy graph with error bar on x and/or y
symbol.Female

Plot a female symbol in the plotting region
clean.knitr

Delete temporary files created during knitr compile
compare

Run a shiny application for basic functions of comparison
compare_AIC

Compares the AIC of several outputs
plot_add

Add a plot to a previous one
pSnbinom

Distribution function for the sum of random variable with negative binomial distributions.
similar

Test if two vectors contains the same elements independently of their order
plot.mcmcComposite

Plot the result of a mcmcComposite object
summary.mcmcComposite

Summarize the result of a mcmcComposite object
predict.LD50

Estimate survival according to doses
read_folder

Read files present in a folder and creates a list with the content of these files
series.compare

Data series comparison using Akaike weight
r2norm

Random generation for Gaussian distributions different at left and right
symbol.Male

Plot a male symbol in the plotting region
universalmclapply

Run the function FUN on X using parallel computing
symmetricize

Make a matrix symmetric
newcompassRose

Display a compass rose
rSnbinom

Random generation for the sum of random variable with negative binomial distributions.
newdbeta

Density for the Beta distributions.
wget

Download a file from internet and save it locally