NEWS

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sparrpowR 0.2.8 (2024-01-23)

sparrpowR v0.2.8

• Fixed bug in calculation of False Discovery Rate in internal pval_correct() function
• Fixed 'Moved Permanently' content by replacing the old URL with the new URL

sparrpowR v0.2.7

• Migrated R-spatial dependency
• Replaced raster and sp in Imports with terra because of imminent package retirement
• geojsonsf, ggmap, ggplot2, sf, tidyterra are now Suggests because they are used in the vignette
• Updated vignette and documentation throughout
• Added GitHub R-CMD-check
• Updated citation style for CITATION file

sparrpowR v0.2.6

• Replaced if() conditions comparing class() to string with inherits()
• Added future::plan(future::multisession) in tests to remove the files in temp directory
• Updated maintainer contact information

sparrpowR v0.2.5

• Updated dependencies spatstat.core and spatstat.linnet packages based on feedback from the Spatstat Team (Adrian Baddeley and Ege Rubak). All random generators in spatstat.core were moved to a new package spatstat.random
  • spatstat.geom, spatstat.core, spatstat.linnet, and spatstat (>=2.0-0) are no longer Depends.
  • spatstat.geom and spatstat.random are now Imports
  • spatstat.data is now Suggests
  • See the GitHub merge pull request.
• Fixed annotation typos in the pval_correct() function

sparrpowR v0.2.4

• Addressed ERROR on R-devel CRAN environments by setting parallelly.makeNodePSOCK.setup_strategy = sequential for all CRAN tests as suggested by the maintainer for the future and parallelly packages who is actively working on a solution. See the GitHub issue.

sparrpowR v0.2.3

• Following advice from future package maintainer, now spatial_power() and jitter_power() functions reset future strategy when exiting
• Addressed ERROR in MacOS CRAN environments by setting the parallelly.makeNodePSOCK.setup_strategy = sequential for MacOS environments running tcltk until parallelly (>=1.26.1-9002) is on CRAN. This workaround was suggested by the parallelly maintainer. See the GitHub issue.

sparrpowR v0.2.2

• Removed LazyData: true from 'DESCRIPTION' file because the package has no data accessed via a data() command and has no data/ directory (in response to CRAN NOTE: 'LazyData' is specified without a 'data' directory)
• Changed hyperlink for Stamen basemap in 'vignette' file with a Hypertext Transfer Protocol Secure destination
• Added 'CITATION' file
• Deprecation badges in 'jitter_power.Rd' and 'spatial_power.Rd' files now hyperlink to lifecycle r-lib.org site

sparrpowR v0.2.1

• Updated vignette with appropriate hyperlinks

sparrpowR v0.2.0

• Updates to dependencies
  • Updated spatstat package to new subsetted packages based on feedback from the Spatstat Team (Adrian Baddeley and Ege Rubak). spatstat.geom and spatstat.core packages replace spatstat package in Depends
  • Imports lifecycle package to document deprecated argument cascon in spatial_power() and jitter_power() functions
  • Replaced parallel and doParallel packages in Imports with doFuture, doRNG, and future packages to allow for parallel processing in spatial_power() and jitter_power() functions to work across all CRAN environments
  • Removed utils package from Imports because the progress bar in spatial_power() and jitter_power() functions is now produced with a helper function in utils.R that imports the iterators package
  • Removed tidyverse package from Suggests
• Changes to DESCRIPTION
  • Added ORCID for all authors and contributors
  • Fixed typos in Description
• Changes to spatial_data()
  • Used as.solist() to specify appropriate class to lists
• Changes to spatial_power()
  • Added p_correct argument to apply a multiple testing correction
  • Fixed typos in documentation
  • Deprecated cascon argument (moved to spatial_plots() function)
  • Estimates case-only power (lower tail) and case/control (lower and upper tail) and captures both outputs. Case-only is now a one-tailed hypothesis test by default. The arguments lower_tail and upper_tail have been replaced with argument alpha
  • Used as.solist() to specify appropriate class to lists
• Changes to spatial_plots():
  • Added cascon argument to toggle the display of case-only power (lower tail) or case/control (lower and upper tail) output
  • Added plot_title argument to toggle the display of titles in plots. Changed the default title names.
  • Removed main panel title in plots
  • Fixed default colors and removed mislabled midpoint color
  • Removed annotation from plot.ppp() in plot #3 and plot #2 (if points are not plotted)
  • Added scale argument to scale text for higher resolution plots
  • Added horizontal argument to toggle the display of the color key to be on the right (vertical) or bottom (horizontal) of plots
  • Added plot_axes argument to toggle the display of axes in plots
  • Added plot_square argument to toggle the margins of plots
  • Changed the value of cex.axis and cex in plots
  • Updated documentation with correct order of cols
• Changes to jitter_power()
  • Added p_correct argument to apply a multiple testing correction
  • Specified all packages for functions
  • Deprecated cascon argument (moved to spatial_plots() function)
  • Estimates case-only power (lower tail) and case/control (lower and upper tail) and captures both outputs. Case-only is now a one-tailed hypothesis test by default. The arguments lower_tail and upper_tail have been replaced with argument alpha
  • Used as.solist() to specify appropriate class to lists
  • Updated example to reflect new updates
• Changes to vignette
  • Set global chunk options
  • Named code chunks
  • Increased the sim_total value for a more realistic example
  • Specify all packages for functions
  • Updated code to reflect updates to functions in sparrpowR
  • Updated code to use sf package
  • Updated explanation of the cascon argument to plot various hypothesis tests
  • Changed cols values to be more visible
  • Used cut instead of reclassify in raster package for categorical plot
  • Created a new section called "Advanced Features" that has a new example run in parallel with a False Discovery Rate procedure.
  • Added detail about fewer-than-expected simulated point locations in the first example
  • Updated plots that spatially project data with CRS strings for PROJ6
• Added utils.R file
  • Removed the helper comb() function functions from jitter_power(), spatial_power(), and spatial_plots() and added to the utils.R file
  • Removed utils package from Imports because the progress bar in spatial_power() and jitter_power() functions is now produced with a helper progBar() function
• Added zzz.R file
• Added package.R file
• Updated testthat checks for parallelization and multiple testing correction in spatial_power() and jitter_power() functions