Package: Irescale 2.3.0

Irescale: Calculate and Rectify Moran's I

Provides a scaling method to obtain a standardized Moran's I measure. Moran's I is a measure for the spatial autocorrelation of a data set, it gives a measure of similarity between data and its surrounding. The range of this value must be [-1,1], but this does not happen in practice. This package scale the Moran's I value and map it into the theoretical range of [-1,1]. Once the Moran's I value is rescaled, it facilitates the comparison between projects, for instance, a researcher can calculate Moran's I in a city in China, with a sample size of n1 and area of interest a1. Another researcher runs a similar experiment in a city in Mexico with different sample size, n2, and an area of interest a2. Due to the differences between the conditions, it is not possible to compare Moran's I in a straightforward way. In this version of the package, the spatial autocorrelation Moran's I is calculated as proposed in Chen(2013) <arxiv:1606.03658>.

Authors:Ivan Fuentes, Thomas DeWitt, Thomas Ioerger, Michael Bishop

Irescale_2.3.0.tar.gz
Irescale_2.3.0.zip(r-4.5)Irescale_2.3.0.zip(r-4.4)Irescale_2.3.0.zip(r-4.3)
Irescale_2.3.0.tgz(r-4.4-any)Irescale_2.3.0.tgz(r-4.3-any)
Irescale_2.3.0.tar.gz(r-4.5-noble)Irescale_2.3.0.tar.gz(r-4.4-noble)
Irescale_2.3.0.tgz(r-4.4-emscripten)Irescale_2.3.0.tgz(r-4.3-emscripten)
Irescale.pdf |Irescale.html✨
Irescale/json (API)

# Install 'Irescale' in R:
install.packages('Irescale', repos = c('https://jivfur.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.

2.70 score 3 scripts 137 downloads 34 exports 56 dependencies

Last updated 5 years agofrom:796d127996. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 30 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 30 2024
R-4.4-macNOTEOct 30 2024
R-4.3-winOKOct 30 2024
R-4.3-macOKOct 30 2024

Exports:buildStabilityTablebuildStabilityTableForCorrelationcalculateDistMatrixFromBoardcalculateEuclideanDistancecalculateLocalIcalculateManhattanDistancecalculateMoranIcalculatePvaluecalculateWeightedDistMatrixconvexHullcoorexpectedValueIiCorrectionItoPearsonCorrelationloadChessBoardloadDistanceMatrixloadFileloadSatelliteImagelocalICorrectionnullDristributionplotHistogramOverlayCorrelationplotHistogramOverlayNormalprocrustesrectifyIrhoresamplingIresamplingLocalIrescaleIsaveFilestandardizestandardizedByColumnsummaryLocalIVectorsummaryVectortransformImageToListtransformImageToMatrix

Dependencies:bmpclassclicolorspacecpp11digestdownloadere1071fansifarverfBasicsggplot2gluegssgtableigraphimagerisobandjpeglabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigplyrpngproxypurrrR6rbibutilsRColorBrewerRcppRdpackreadbitmapreshape2rlangscalesspspatialstablediststringistringrtibbletifftimeDatetimeSeriesutf8vctrsviridisLitewithr

Moran's I rescaling

Ivan Fuentes, Thomas Dewiit, Thomas Ioerger, Michael Bishop

Rendered fromrectifiedI.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2019-11-21
Started: 2019-11-21

Readme and manuals

Help Manual

Help pageTopics
Finds how many iterations are necessary to achieve stability in resampling method.buildStabilityTable
Finds how many iterations are necessary to achieve stability in resampling method for rectifying I through pearson corrrelation.buildStabilityTableForCorrelation
Calculates the distance in a chessboard-alike structure.calculateDistMatrixFromBoard
Given a 2D data structure, it calculates the euclidean distance among all the points.calculateEuclideanDistance
Computing the Local Moran's IcalculateLocalI
Calculates the manhattan distance.calculateManhattanDistance
Calculates the Moran's I using the algorithm proposed by Chen (Chen 2013).calculateMoranI
p-value calculation.calculatePvalue
Calculates a weighted representation of the distance matrix.calculateWeightedDistMatrix
Plots the convexhull polygon from the data (latitude, longitude), and calculates the center of the convexhull and its area.convexHull
Transforms a x,y position in a cartesian plane into a position in a 1D array.coor
Calculates the expected value for local IexpectedValueI
Scaling process for Moran's I.iCorrection
Calculate the equivalence r from the I percentile in the I-Null Distribution.ItoPearsonCorrelation
Loads a chessboard or matrix alike input file.loadChessBoard
Loads a distance matrix. Instead of computing the distance from latitute and longitude 'LoadDistanceMatrix' Loads the distance matrix, avoiding computing it from latitude and longitude.loadDistanceMatrix
Loads a file with latitude, longitude and variable of interestloadFile
Loads a Satellite image in PNG formatloadSatelliteImage
Scaling process for Local Moran's I.localICorrection
Calculate a distribution of how the var of interest is correlated to anullDristribution
Creates an overlay of the histogram of the data and the theorical normal distribution.plotHistogramOverlayCorrelation
Creates an overlay of the histogram of the data and the theorical normal distribution.plotHistogramOverlayNormal
Procrustes distance between two surfacesprocrustes
Rectify I using a correlation method for all the variables in an input file.rectifyIrho
Calculates n permutations of the variable of interest to calculate n different I in order to create the Null distribution.resamplingI
Calculates n permutations of the variable of interest to calculate n different I in order to create the Null distribution.resamplingLocalI
Performs the rescale for all the variables in an input file.rescaleI
Saves a report with important statistics to describe the sample.saveFile
Standardize the input vectorstandardize
Scales a matrix by column.standardizedByColumn
Calculates statistic for the received Matrix.summaryLocalIVector
Calculates statistic for the received vector.summaryVector
Transforms the image in the object need it to run the analysis.transformImageToList
Transforms the image to a matrix.transformImageToMatrix