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ecotrends 1.0

• replaced ‘year’ with ‘period’ in messages and outputs

• following CRAN requests:

  • replaced cat() with message() conditional on ‘verbosity’ argument

  • replaced getwd() with tempfile() in Examples

  • replaced dontrun{} with donttest{} in examples that take long to run but are feasible without extra software; then replaced instead with if(interactive()), because check still runs the donttest{} section

ecotrends 0.23

• getImportance()

  • added ‘palette’ argument

• getModels()

  • periods (years) not automatically sorted, but rather taken as in input ‘rasts’
  • help file: improved description of ‘rasts’ layer names

ecotrends 0.22

• getImportance()

  • added ‘plot’ and associated arguments

ecotrends 0.21

• getImportance()

  • new function

ecotrends 0.20

• getTrend(), DESCRIPTION

  • replaced Kendall::MannKendall() with trend::mk.test() to reduce package dependencies; and eventually removed also mk.test, as slope and significance are sufficient and both are provided by trend::sens.slope()
  • full ouput includes just slope, upper and lower confidence limits, and p-value

ecotrends 0.19

• getTrend()

  • added Sen’s slope and associated statistics from trend::sens.slope()

ecotrends 0.18

• getModels()

  • new default 10 (not 0) for ‘nreps’
  • added collinear() new argument ‘quiet=TRUE’ after ‘collinear’ update
  • output has the same structure (list of lists) with or without replicates, for code consistency

• getPredictions()

  • output is now SpatRasterDataset (not single SpatRaster if no replicates, or list of SpatRasters if replicates), for code consistency
  • fixed error when producing output file if replicates
  • argument ‘mods’ can be directly the output of getModels (not mods$models)

• getPerformance()

  • output now includes both train and test performance, number of train and test presences, and TSS train and test thresholds
  • fixed code for plot=TRUE when replicates
  • argument ‘data’ replaced with ‘mods’ for safer use
  • aded ‘sep.plots’ and ‘reset.par’ arguments to modEvA::optiThresh()

• getTrend()

  • implemented for replicates, converting SpatRasterDataset to SpatRaster and using mean prediction

• DESCRIPTION

  • included additional authors
  • increased version dependence for collinear, to use non-default value for new argument ‘quiet’
  • increased version dependence for modEvA, to use ‘sep.plots’ and ‘reset.par’ (new) argument values

ecotrends 0.17

• getPerformance()

  • implemented output for replicates (still test performance only)

ecotrends 0.16

• getPerformance()

  • added pbg = TRUE to modEvA functions (requires modEvA >= 3.20)
  • ‘plot’ default changed to FALSE, as it can be slow for large datasets
  • started implementing for models with replicates
  • name of first column of output changed to ‘model’ rather than ‘year’, to accomodate replicates

ecotrends 0.15

• getPredictions()

  • implemented for models with replicates

ecotrends 0.14

• getModels()

  • added ‘bias’ argument (requires fuzzySim >= 4.25)

ecotrends 0.13

• getModels()

  • integrated test + nreps arguments in output ‘data’
  • named list of replicate models

ecotrends 0.12

• getModels()

  • implemented ‘test’ and ‘nreps’ arguments in output ‘models’
  • help file mentions that constant variables and different collinearity structures may produce models with different sets of variables among periods

• getPredictions()

  • currently stops if input ‘mods’ has replicates

ecotrends 0.11

• getModels()

  • messages saying which variables removed by collinear()
  • constants checked before (rather than after) collin
  • added drop=FALSE to fix error when only one selected predictor

ecotrends 0.10

• getModels()

  • improved code to check ‘region’

• README

  • some more additions for improved clarity

ecotrends 0.9

• getTrend()

  • warning if no values produced due to small sample size
  • ‘occs’ can be of class ‘SpatVector’ or ‘sf’, in which case they aren’t converted to data.frame and their CRS is taken
  • ‘occs’ projected (with message) if not same CRS as ‘rasts’

• README

  • some additions for improved clarity

ecotrends 0.8

• getModels()

  • drop non-varying predictors (with message) to avoid maxnet() error
  • message if n pixels < nbg

• getPredictions()

  • ‘data’ CRS set to the same as ‘rasts’, to avoid warning “[mask] CRS do not match”
  • added bibliographic reference for type=“cloglog” recommended default

• getRegion()

  • removed in favour of a more complete version which was already being programmed in package {fuzzySim}

ecotrends 0.7

• getModels()

  • warning if input ‘rasts’ is not SpatRaster, which will work here but fail elsewhere

ecotrends 0.6

• getPerformance()

  • new function

• getModels()

  • output now includes three elements: $models, $replicates, $data (needed for getPerformance)

• getTrend()

  • added arguments ‘file’, ‘verbosity’

• getVariables(), getModels(), getPredictions(), getTrend(), README

  • implemented ‘file’ including a folder path, e.g. “outputs/models”
  • folder created if not in getwd()

• all functions

  • replaced instances of @import with @importFrom in roxygen skeleton

ecotrends 0.5

• getModels()

  • added argument ‘seed = 1’ for the background sample
  • added arguments ‘maxcor’ and ‘maxvif’ to pass to collinear::collinear()
  • added argument ‘classes’ to pass to maxnet::maxnet.formula()
  • added argument ‘regmult’ to pass to maxnet::maxnet()
  • default ‘nreps’ currently 0
  • added argument ‘test = 0.2’ for the test data proportion [STILL PENDING IMPLEMENTATION]

• getPredictions()

  • added arguments ‘clamp’ and ‘type’ to pass to maxnet::predict()

ecotrends 0.4

• getVariables()

  • changed url, following TerraClimate Batch Downloads instructions (https://www.climatologylab.org/wget-terraclimate.html)
  • set vsi=FALSE if not on unix platform, to prevent download fail

• getVariables(), getModels(), getPredictions()

  • object imported from ‘file’, if it exists in getwd()

ecotrends 0.3

• getTrend()

  • dealt with NA pixels to avoid numerous Kendall::MannKendall() warnings (thanks to Spacedman at https://gis.stackexchange.com/a/464198)
  • bonus: increased efficiency, as mannkendall outputs an unlisted vector (still thanks to Spacedman at https://gis.stackexchange.com/a/464198)

ecotrends 0.2

• getPredictions()

  • added argument ‘region’ (to get predictions only within modelled polygon)

• getTrend()

  • added argument ‘occs’ (to get trend only within presence pixels)
  • added Mann-Kendall outputs besides tau: p_value, S, S_variance

ecotrends 0.1

• Added the following package functions, together with documentation and users guide:

  • getRegion()
  • varsAvailable()
  • getVariables()
  • pixelArea()
  • getModels()
  • getPredictions()
  • getTrend()

ecotrends 0.0.0.9000

• Added a NEWS.md file to track changes to the package.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.