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Changelog

Source: NEWS.md

HiClimR 2.2.1

CRAN release: 2022-01-20

  • Updated package website
  • Updated package DESCRIPTION and README
  • Updated package dependencies and WORDLIST
  • Style and format Fortran code

HiClimR 2.2.0

CRAN release: 2021-05-31

  • Fixed NOTE: Found (possibly) invalid URLs

HiClimR 2.1.9

CRAN release: 2021-04-02

  • Updated citation in package DESCRIPTION
  • Updated NAMESPACE and documentation
  • Fixed spelling errors
  • Updated lifecycle URL in the README

HiClimR 2.1.8

CRAN release: 2021-01-05

  • Code cleanup and formatting
  • Removed HISTORY comments from source code
  • Replaced 1:n expressions with seq_len(n)
  • Updated citation, manual, and user information
  • Updated documents after code formatting
  • Updated package DESCRIPTION and added reference DOI
  • Updated package URL: https://hsbadr.github.io/HiClimR/
  • README: Updated README.md and added NEWS.md

HiClimR 2.1.7

CRAN release: 2020-11-05

  • Updated package DESCRIPTION and author information
  • Updated copyright year to 2021
  • README: Added Markdown badges
  • README: Added Digital Object Identifier (DOI) badge
  • README: Linked version and download badges to CRAN
  • README: Updated URLs

HiClimR 2.1.6

CRAN release: 2020-02-22

  • README: Added CRAN downloads badge
  • R: Fix non-informative failure for unsupported input of a vector

HiClimR 2.1.5

CRAN release: 2019-12-10

HiClimR 2.1.4

CRAN release: 2019-01-20

  • Added vignette for HiClimR Bug Reporting
  • HiClimR2nc: Updated documentation and examples
  • man: Use \code{} instead of \bold{} for classes

HiClimR 2.1.3

CRAN release: 2019-01-11

  • Fixed spelling errors and allowed custom words
  • HiClimR2nc: Fixed timeseries variable definition
  • README: Link HiClimR to CRAN package page

HiClimR 2.1.2

  • Fixed example ERROR in CRAN checks
  • Added example to export NetCDF-4 file
  • Updated dependencies and suggested packages

HiClimR 2.1.1

CRAN release: 2019-01-03

  • fastCor: Fixed row/col names of the correlation matrix
  • fastCor: Cleaned up zero-variance data check
  • Examples: Minor comment update

HiClimR 2.1.0

  • Supported contiguity constraint based on geographic distance
  • Exporting region map and mean timeseries into NetCDF-4 file
  • Replaced multi-variate with multivariate
  • Renamed weightedVar to weightMVC
  • Updated citation information
  • Updated and cleaned up package DESCRIPTION
  • Updated and cleaned up README

HiClimR 2.0.0

  • Fixed NOTE: Registering native routines
  • fastCor: Removed zero-variance data
  • fastCor: Introduced optBLAS
  • fastCor: Code cleanup
  • Reformatted R source code
  • Updated and fixed the examples
  • Updated CRU TS dataset citation
  • Updated README and all URLs

HiClimR 1.2.3

CRAN release: 2015-08-06

  • Fixed geogMask confusing country codes/names
  • Fixed geogMask filtering InDispute areas
  • Corrected data construction in the user manual
    • x should be created using as.vector(t(x0))
    • x0 is the n by m original data matrix
    • n = length(unique(lon)) and m = length(unique(lat))
  • coarseR now returns the original row numbers
  • Minor README corrections and updates

HiClimR 1.2.2

CRAN release: 2015-07-22

  • Changes for Undefined global functions
  • Checking geographic masking output
  • Minor README corrections and updates

HiClimR 1.2.1

CRAN release: 2015-05-24

  • Updating variance for multivariate clustering
  • More plotting options (pch and cex)
  • geogMask supports ungridded data
  • Updated user manual with the following notes:
    • longitudes takes values from -180 to 180 (not 0 to 360)
    • for gridded data, the rows of input data matrix for each variable is ordered by longitudes
      • check rownames(TestCase$x) for example!
        • each row represents a station (grid point)
        • row name is in the form of longitude,latitude
  • Minor verbose fixes and updates
  • Minor README corrections and updates
  • Citation updated: technical paper has been published

HiClimR 1.2.0

CRAN release: 2015-03-27

  • Multivariate clustering (MVC)
    • the input matrix x can now be a list of matrices (one matrix for each variable)
      • length(x) = nvars where nvars is the number of variables
      • number of rows N = number of objects (e.g., stations) to be clustered
      • number of columns M may vary for each variables
        • e.g., different temporal periods or record lengths
    • Each variable is separately preprocessed to allow for all possible options
      • preprocessing is specified by lists with length of nvars (number of variables)
        • length(meanThresh) = length(x) = nvars
        • length(varThresh) = length(x) = nvars
        • length(detrend) = length(x) = nvars
        • length(standardize) = length(x) = nvars
        • length(weightMVC) = length(x) = nvars
      • filtering with meanThresh and varThresh thresholds
      • detrending with detrend option, if requested
      • standardization with standardize option, if requested
        • strongly recommended since variables may have different magnitudes
      • weighting by the new weightMVC option (default is 1)
      • combining variables by column (for each object: spatial points or stations)
      • applying PCA (if requested) and computing the correlation/dissimilarity matrix
  • Preliminary big data support
    • function fastCor can now split the data matrix into nSplit splits
    • adds a logical parameter upperTri to fastCor function
      • computes only the upper-triangular half of the correlation/dissimilarity matrix
      • it includes all required information since the correlation/dissimilarity matrix is symmetric
      • this almost halves memory use, which can be very important for big data.
    • fixes “integer overflow” for very large number of objects to be clustered
  • Adds a logical parameter verbose for printing processing information
  • Adds a logical parameter dendrogram for plotting dendrogram
  • Uses \dontrun{} to skip time-consuming examples
  • Backward compatibility with previous versions
  • The user manual is updated and revised

HiClimR 1.1.6

CRAN release: 2015-03-02

  • Setting minimum k = 2, for objective tree cutting
    • this addresses an issue caused by undefined k = NULL in validClimR function
    • when all inter-cluster correlations are significant at the user-specified significance level
  • Code reformatting using formatR
  • Package description and URLs have been revised
  • Source code is now maintained on GitHub by authors

HiClimR 1.1.5

CRAN release: 2014-11-13

  • Updating description, URL, and citation info

HiClimR 1.1.4

CRAN release: 2014-09-02

  • Addresses an issue for zero-length mask vector: Error in -mask : invalid argument to unary operator
    • this error was introduced in v1.1.2+ after fixing the data-mean bug

HiClimR 1.1.3

CRAN release: 2014-08-28

  • The user manual is revised
  • lonSkip and latSkip renamed to lonStep and latStep, respectively
  • Minor bug fixes

HiClimR 1.1.2

CRAN release: 2014-07-27

  • A bug has been fixed where data mean is added to centered data if standardize = FALSE
    • objective tree cut and data component are now corrected
      • to match input parameters especially when clustering of raw data
      • centered data was used in previous versions

HiClimR 1.1.1

CRAN release: 2014-07-14

  • Minor bug fixes and memory optimizations especially for the geographic masking function geogMask
  • The limit for data size has been removed (use with caution)
  • A logical parameter InDispute is added to geogMask function to optionally consider areas in dispute for geographic masking by country

HiClimR 1.1.0

CRAN release: 2014-05-16

  • Code cleanup and bug fixes
  • An issue with fastCor function that degrades its performance on 32-bit machines has been fixed
    • A significant performance improvement can only be achieved when building R on 64-bit machines with an optimized BLAS library, such as ATLAS, OpenBLAS, or the commercial Intel MKL
  • The citation info has been updated to reflect the current status of the technical paper

HiClimR 1.0.9

CRAN release: 2014-05-07

  • Minor changes and fixes for CRAN
  • For memory considerations,
    • smaller test case with 1 degree resolution instead of 0.5 degree
    • the resolution option (res parameter) in geographic masking is removed
    • Mask data is only available in 0.1 degree (~10 km) resolution
  • LazyLoad and LazyData are enabled in the description file
  • The worldMask and TestCase data are converted to lists to avoid conflicts of variable names (lon, lat, info, and mask) with lazy loading

HiClimR 1.0.8

  • Code cleanup and bug fixes
  • Region maps are unified for both gridded and ungridded data

HiClimR 1.0.7

  • Hybrid hierarchical clustering feature that utilizes the pros of the available methods
    • especially the better overall homogeneity in Ward’s method and the separation and objective tree cut of the regional linkage method.
    • The logical parameter hybrid is added to enable a second clustering step
      • using regional linkage for reconstructing the upper part of the tree at a cut
      • defined by kH (number of clusters to restart with using the regional linkage method)
      • If kH = NULL, the tree will be reconstructed for the upper part with the first merging cost larger than the mean merging cost for the entire tree
        • merging cost is the loss of overall homogeneity at each merging step
  • If hybrid clustering is requested, the updated upper-part of the tree will be used for cluster validation.

HiClimR 1.0.6

  • Code cleanup and bug fixes

HiClimR 1.0.5

  • Code cleanup and bug fixes
  • Adds support to generate region maps for ungridded data

HiClimR 1.0.4

  • Code cleanup and bug fixes
  • The coarseR function is called inside the core HiClimR function
  • Adds coords component to the output tree for the longitude and latitude coordinates
    • they may be changed by coarsening
  • validClimR function does not require lon and lat arguments
    • they are now available in the output tree (coords component)

HiClimR 1.0.3

  • Code cleanup and bug fixes
  • One main/wrapper function HiClimR internally calls all other functions
  • Unified component names for all functions
  • Objective tree cut is supported only for the regional linkage method
    • Otherwise, the number of clusters k should be specified
  • The new clustering method has been renamed from HiClimR to regional linkage method

HiClimR 1.0.2

  • Code cleanup and bug fixes.
  • adds a new feature that to return the preprocessed data used for clustering, by a logical argument retData.
    • the data will be returned in a componentdata of the output tree
    • this can be used to utilize HiCLimR preprocessing options for further analysis
  • Ordered regions vector for the selected number of clusters are now returned in the region component
    • length equals the number of spatial elements N

HiClimR 1.0.1

  • Code cleanup and bug fixes
  • Adds a new feature in validCLimR that enables users to exclude very small clusters from validation indices interCor, intraCor, diffCor, and statSum, by setting a value for the minimum cluster size (minSize > 1)
    • the excluded clusters can be identified from the output of validClimR in clustFlag component, which takes a value of 1 for valid clusters or 0 for excluded clusters
    • in HiClimR (currently, regional linkage) method, noisy spatial elements (or stations) are isolated in very small-size clusters or individuals since they do not correlate well with any other elements
    • this should be followed by a quality control step
  • Adds coarseR function for coarsening spatial resolution of the input matrix x

HiClimR 1.0.0

  • Initial version of HiClimR package that modifies hclust function in stats library
  • Adds a new clustering method to the set of available methods
  • The new method is explained in the context of a spatiotemporal problem, in which N spatial elements (e.g., stations) are divided into k regions, given that each element has observations (or timeseries) of length M
    • minimizes the inter-regional correlation between region means
    • modifies average update formulae by incorporating the standard deviation of the mean of the merged region
    • a function of the correlation between the individual regions, and their standard deviations before merging
    • equals the average of their standard deviations if and only if the correlation between the two merged regions is 100%.
    • in this special case, the new method is reduced to the classic average linkage clustering method
  • Several features are included to facilitate spatiotemporal analysis applications:
    • options for preprocessing and postprocessing
    • efficient code execution for large datasets.
    • cluster validation function validClimR
    • implements an objective tree cut to find an optimal number of clusters
  • Applicable to any correlation-based clustering