NEWS.md

In ecotrends: Temporal Trends in Ecological Niche Models

ecotrends 1.1

• getPerformance()

  • added 'kappa' to implemented metrics

  • create columns before they are populated

  • renamed and reordered some threshold columns for better readability

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

  • removed LICENSE file for not having additional restrictions

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.

ecotrends documentation built on Aug. 8, 2025, 6:11 p.m.