fixed - sample_balanced() & sample_existing_balanded - Updated to match BalancedSampling v2.0.6 changes to lcubsestratified. Thanks to Anton Grafström.
fixed - sample_strat() - Was not taking samples from other strata into account when calculating mindist between sample units. This has now been corrected for both Queinnec and random methods. From Tommasso Trotto #33
enhanced - calculate_distance() - added slope parameter to allow for calculation of slope distance. From Nic #32
enhanced - sample_ahels() - If attributes in existing contain numeric data – and match columns in mraster – these data will be used instead of extracting from mraster.
added - utils-write - made writing functions for samples, rasters, and tables to make code more succinct.
enhanced - sample_existing - A major change to sample_existing() has been implemented. Prior to sgsR v1.4.2, sample_existing() only leveraged sample_clhs() functionality. New functionality has been added to allow users to define the sub-sampling method of their choice out of (sample_srs(), sample_balanced(), sample_strat(), sample_clhs()). To do so, additional internal functions (sample_existing_strat(), sample_existing_srs(), sample_existing_balanced(), sample_existing_srs()) have been added that take in existing data and perform sampling based on those data. For sample_existing_strat(), new allocation algorithms that take existing as inputs needed to be written that are found in utils-allocation-existing(). Additionally, more utility functions that check existing data, and prepare existing data for sub-sampling have been developed and implemented in utils-existing(). Unit tests for all functions have been added. The plot parameter has been removed from sample_existing() for now. Likely to be added again later.
enhanced - Sampling Vignette - Added content about sample_existing()
fixed - strat_map() - Fixed improper use of terra::hasValues. From Robert Hijmans #31
fixed - sample_ahels() - gave an erroneous error when matrices was provided and nQuant did not match. Changed to allow only matrices to be provided.
fixed - extract_strata() - added error message if sraster had multiple layers #28
fixed - extract_metrics() - removed code where mraster layers with ID as name were removed. From Tommasso Trotto #27
enhanced - calculate_representation() - Added parameter drop = NULL. If !=NULL then filtering is applied where strata with under drop frequency are dropped from resulting dataframe and plot. #28
added - sample_sys_strat() - Systematic stratified sampling. Using same functionality as sample_systematic() but takes an sraster as input and performs sampling on each stratum iteratively.
enhanced - strat_breaks() - Vectorized function to allow for any number of input mraster layers and a corresponding number of breaks vectors (as list in respective order as mraster layers). Removed mraster2 & breaks2. Users can now supply an mraster with as many layers as they wish. Added map to allow for creating a combined (mapped) stratification output (strata). Internal function calculate_breaks() was added that facilitates vectorization.
enhanced - strat_quantiles() - Vectorized function to allow for any number of input mraster layers and a corresponding number of breaks vectors (as list in respective order as mraster layers). Removed mraster2 & nStrata2. Users can now supply an mraster with as many layers as they wish along side nStrata as a list with length(nStrata) == terra::nlyr(mraster). nStrata can be either a scalar integer representing the number of desired output strata, or a numeric vector of probabilities between 0-1 demarcating quantile break points. The nStrata list can be a mix of these (e.g. nStrata = list(c(0.1,0.8,1), 4, 9) where mraster would have 3 layers) to allow users to define both explicit quantile breaks or a desired strata number that is converted to quantiles breaks internally. Added map to allow for creating a combined (mapped) stratification output (strata). Internal functions calculate_quantile_breaks() / quantile_breaks_integer() / quantile_breaks() were added that facilitate vectorization.
enhanced - strat_map() - Vectorized function to allow for any number of input mraster layers and a corresponding number of breaks vectors (as list in respective order as mraster layers). Removed raster2. Users can now supply an sraster with as many layers as they wish. Thank you, Tommaso Trotto.
enhanced - Updated vignettes and documentation to account for vectorized functionality of the above functions.
enhanced - plot_scatter() - now visualizes with viridis colour scheme.
fixed - Added new citation information for upcoming manuscript release.
fixed - extract_strata() / extract_metrics() - CRS for existing will now be maintained when provided as an sf and the mraster CRS will be assigned otherwise. In addition, all sampling functions will maintain CRS from existing if possible, otherwise CRS from sraster/mraster are used for output samples.
fixed - sample_srs() / sample_strat(method = "random") - First sample unit was always duplicated From Tommaso Trotto.
added - plot_scatter() - Internal function. Scatter plot visualizing relationship between 2 mraster metrics with existing samples superimposed.
fixed - sample_strat() - srasters with categorical values were crashing the algorithm due to inability to combine facter and non-factor values from Evan Muise.
fixed - sample_systematic() - Added more contingency for cellsize values that resulted in empty sample output.
fixed - strat_map() - stratamapped was outputting as character and not as integer or character depending on input strata type as intended from Tommaso Trotto.
enchancement - calculate_pcomp() - Added maxcells parameter based on suggestion from R. Hijmans.
fixed - sample_systematic() - Fixed issue related to ATLAS Blas and CRAN errors with suggestions and support from R. Hijmans.
fixed - CRAN issue where errors were encountered when run on ATLAS instances.
enhancement - Edited vignettes and documentation for clarity.
enhancement - sample_srs() - Added message to tell users when nSamp sample units were unable to be allocated. From Evan Muise.
fixed - strat_quantiles() / strat_kmeans() - solved issue where correct number of strata & float strata values were being output.
enhancement - sample_existing() - made it so extra attributes are passed to output when raster is provided. Added additional unit tests and updated documentation.
enhancement - README.Rmd and vignettes have been updated.
enhancement - sample_systematic() - changed how tessellation was used internally and visualized during plotting.
fixed - strat_map() - #20 greatly simplified algorithm using suggestion from R. Hijmans (added as author to algorithm). Issue was related to level matching with categorical variables.
fixed - sample_ahels() - swapped plot marker icons to be consistent with other functions.
fixed - sample_systematic() - added random translation to sampling grid to ensure unbiased sampling.
new - sample_existing() - has been added. This algorithm sub-samples and existing sample using internal latin hypercube sampling. Constraints in the form of the cost parameter akin to sample_clhs() exist. Sub-sampling can be performed on existing samples alone, or using population level mraster distributions.
new - mask_existing() - internal function for masking exising samples using access buffers.
fixed - sample_systematic() - bug where cellsize values that caused no samples to intersect with the raster would cause extract_metrics() to provide an error about existing not having any samples. Added a check for intersection and corresponding error message.
enhancement - Added quiet to extract_metrics() & extract_strata() to allow internal use without messages.
fixed - strat_kmeans() bug related to terra where the re-assignment of values to the output raster was causing issues. R Hijmans kindly suggested the edit made.
fixed - sample_ahels() - bug where extra attributes in existing would cause the algorithm to crash when re-merging after sampling.
fixed - strat_quantiles() - no longer plots histogram / scatter plot when using plot = TRUE. Now correctly adds this to details list when details = TRUE.
new sampling method - Added sample_nc() based on the algorithm described in Melville & Stone (2016).
k parameter). These nearest neighbours are the output samples. Visualization of the centers and samples can be dispayed if details = TRUE is used and $kplot is plotted.fixed - sample_systematic() - now has inherent randomness for lower left corner of the tessellation.
fixed - strat_kmeans() - solved issue where only first raster layer was being involved in stratification.
enhanced - sample_strat() - added parameter method that allows users to choose between "Queinnec" (default method implemented in previous sgsR versions) and "random" (stratified random sampling). The random method ignores much of the functionality of the algorithm to allow users to use standard stratified random sampling approaches without the use of a focal window to locate contiguous stratum cells.
fixed - sample_strat() - factor handling improvement - GitHub issue #18.
enhanced - calculate_allocation() - improved documentation for output data frame to make attributes more clear.
fixed - calculate_representation() - will now not plot bar chart twice & NA values in existing will not be removed.
fixed - existing samples with other attributes will now not break sampling using sample_ahels() / sample_clhs() if values are NA. Variables are also added back to the sample output.
Added comprehensive tests using testthat for most functions and covr reporting.
Changed forceSamp to force in sample_systematic().
Removed details from sample_coob().
Improved ability to use data.frames() of samples as inputs for numerous algorithms.
Improve consistency in error messages and call. = FALSE across the package.
Added existingna.shp for example data where point are in NA locations.
strat_map() can now map categorical srasters (gave an error before). Now also returns the categories associated with the categorical rasters in the lookup table with details = TRUE.
Altered error handling for raster masking to be within mask_access() instead of individual sampling functions.
Changes to terra::distance() & terra::classify() required slight modifications to calculate_distance() and strat_breaks().
sample_strat
strat_rule1() and strat_rule2() functions to make code more concise. Fixed issue with mindist not setting distances between strata.sample_ahels()
tolerance parameter to sample_ahels() to allow users to define a tolerance around the desired sampling ratio (max tolerance = 0.1). This will allow the user to say “I ideally want the ratio to be XX but I’m OK if the ratio is XX - threshold if it means I don’t need to add more samples”.existing was a data frame.sample_ahels made ahels_nSamp() and ahels_threshold() functions to make code more concise.
Altered how existing (crosses) and new (circles) samples are plotted in sample_strat() and sample_ahels().
Added internal utility functions allocate_prop / allocate_optim / allocate_manual / allocate_equal / allocate_existing / allocate_force and integrated them into calculate_allocation() to make code more succinct and purposeful.
Fixed issue in calculate_allocation() where too many samples would be allocated (compared to the user-defined nSamp) due to using ceiling() instead of round() during proportional and optimal allocation.
Added allocation = "manual" to calculate_allocation(). The parameter weights was added (mandatory for allocation = "manual"), where users can provide a numeric vector of relative weightings to strata. sum(weights) must equal 1.
Added weights parameter to sample_strat() to allow for "manual" allocation.
Allow buff_inner to be NULL when providing access to isolate samples. This allows users to define only a maximum distance (should they wish to) that samples can be from access but not specify a minimum distance.
Updates names for internal package data in inst/exdata and corresponding examples and vignettes.
Added contingencies for sample_ahels, sample_strat, calculate_allocation, calculate_coobs to allow existing samples to fall in areas of NA and not cause algorithms to fail or bug.
extract_metrics & extract_strata produce more robust error messages & will now generate a message if existing samples are co-located with strata or metric values that are NA.
sample_clhs updated to fix issue where existing samples would not be appended to output.
strat_quantiles now provides a stratum look-up table when details = TRUE to allow user to see exact metric break points.
Updated documentation for many algorithms to fix grammatical and spelling errors.
Removed dependencies for stringr, tidyselect, rlang, RColorBrewer, magrittr, glue, Rcpp.
Improved documentation examples to have read speeds in line with <5 seconds for CRAN submission.
Improve processing speed for sample_coobs() and utils-mat.R courtesy of Jean-Romain Roussel.
Added example subset file to inst/extdata to improve example processing speeds for certain algorithms.
NEWS.md file to track changes to the package.