R Under development (unstable) (2024-07-05 r86874 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(bamm) > > test_check("bamm") Set A of the BAM digram it contains 8 slots @niche_model: a niche model: class : RasterLayer dimensions : 91, 159, 14469 (nrow, ncol, ncell) resolution : 0.2, 0.2 (x, y) extent : -118.4042, -86.60417, 14.51846, 32.71846 (xmin, xmax, ymin, ymax) crs : +proj=longlat +datum=WGS84 +no_defs source : memory names : layer values : 0, 1 (min, max) @suit_threshold: Threshold value used to binarize model@cellIDs: ids of the cells that have values (4281 pixels) @suit_values: Suitability values of the continuous model @sparse_model: A sparse square matrix of 4281 x 4281 entries @coordinates: Pixel centroid coordinates of the model Set M of the BAM digram it contains 7 slots @coordinates: A matrix with longitude and latitude values of each cell of the raster area x y [1,] -115.9042 32.61846 [2,] -115.7042 32.61846 [3,] -115.5042 32.61846 [4,] -115.3042 32.61846 [5,] -115.1042 32.61846 [6,] -114.9042 32.61846 @eigen_val: Eigen values of the connectivity matrix M @eigen_vec: Eigen vector of the connectivity matrix M Object of class csd it contains 3 slots: @connections: Geographic clusters data.frame x y clusterID cluster_size 1 -116.3042 32.41846 1 37 2 -116.7042 32.21846 1 37 3 -116.5042 32.21846 1 37 4 -116.3042 32.21846 1 37 @interactive_map: A leaflet map showing the geographic clusters @raster_map: A raster map of the clusters | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |====== | 9% | |============= | 18% | |=================== | 27% | |========================= | 36% | 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the BAM digram it contains 7 slots @coordinates: A matrix with longitude and latitude values of each cell of the raster area x y [1,] -115.9042 32.61846 [2,] -115.7042 32.61846 [3,] -115.5042 32.61846 [4,] -115.3042 32.61846 [5,] -115.1042 32.61846 [6,] -114.9042 32.61846 @eigen_val: Eigen values of the connectivity matrix M [1] 7.975459 @eigen_vec: Eigen vector of the connectivity matrix M [,1] [1,] -8.640620e-11 [2,] -1.555028e-10 [3,] -2.564191e-10 [4,] -4.169028e-10 [5,] -6.556495e-10 [6,] -8.733471e-10 | | | 0% | |====== | 9% | |============= | 18% | |=================== | 27% | |========================= | 36% | |================================ | 45% | |====================================== | 55% | |============================================= | 64% | |=================================================== | 73% | |========================================================= | 82% | |================================================================ | 91% | |======================================================================| 100% | | | 0% Attaching package: 'purrr' The following object is masked from 'package:testthat': is_null | | | 0% | |====== | 9% | |============= | 18% | |=================== | 27% | |========================= | 36% | |================================ | 45% | |====================================== | 55% | |============================================= | 64% | |=================================================== | 73% | |========================================================= | 82% | |================================================================ | 91% | |======================================================================| 100% | |============== | 20% | | | 0% | |====== | 9% | |============= | 18% | |=================== | 27% | |========================= | 36% | |================================ | 45% | |====================================== | 55% | |============================================= | 64% | 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|======================================================================| 100% | |======================================================================| 100%Object of class pam it contains 5 slots: @pams: A list of sparse PAM matrices 6 x 7 sparse Matrix of class "dgCMatrix" x y 77 -91.66667 82.66667 . . . . . 78 -90.66667 82.66667 . . . . . 79 -89.66667 82.66667 . . . . . 80 -88.66667 82.66667 . . . . . 81 -87.66667 82.66667 . . . . . 82 -86.66667 82.66667 . . . . . @sp_names: the species in the pam with 5 species: Brachylagus_idahoensis, Lepus_alleni, Lepus_americanus, Lepus_arcticus, Lepus_californicus @which_steps: time steps 1 2 3 4 5 6 7 8 9 10 @grid: raster grid of the studied area class : RasterLayer dimensions : 75, 112, 8400 (nrow, ncol, ncell) resolution : 1, 1 (x, y) extent : -168.1667, -56.16667, 8.166667, 83.16667 (xmin, xmax, ymin, ymax) crs : +proj=longlat +datum=WGS84 +no_defs source : memory names : layer values : 0, 1 (min, max) @cellIDs: site ids regarding the raster grid | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100% Progress: ─────────────────────────────────── 100% Progress: ─────────────────────────────────────── 100% Progress: ─────────────────────────────────────────── 100% Progress: ──────────────────────────────────────────────── 100% Progress: ──────────────────────────────────────────────────── 100% Progress: ──────────────────────────────────────────────────────── 100% Progress: ──────────────────────────────────────────────────────────── 100%New names: * `dfield` -> `dfield...1` * `dfield` -> `dfield...2` * `dfield` -> `dfield...3` * `dfield` -> `dfield...4` * `dfield` -> `dfield...5` * `dfield` -> `dfield...6` * `dfield` -> `dfield...7` * `dfield` -> `dfield...8` * `dfield` -> `dfield...9` * `dfield` -> `dfield...10` * `dfield` -> `dfield...11` * `dfield` -> `dfield...12` * `dfield` -> `dfield...13` * `dfield` -> `dfield...14` * `dfield` -> `dfield...15` * `dfield` -> `dfield...16` * `dfield` -> `dfield...17` * `dfield` -> `dfield...18` * `dfield` -> `dfield...19` * `dfield` -> `dfield...20` * `dfield` -> `dfield...21` * `dfield` -> `dfield...22` * `dfield` -> `dfield...23` * `dfield` -> `dfield...24` * `dfield` -> `dfield...25` * `dfield` -> `dfield...26` * `dfield` -> `dfield...27` * `dfield` -> `dfield...28` * `dfield` -> `dfield...29` * `dfield` -> `dfield...30` * `dfield` -> `dfield...31` * `dfield` -> `dfield...32` * `dfield` -> `dfield...33` * `dfield` -> `dfield...34` * `dfield` -> `dfield...35` * `dfield` -> `dfield...36` * `dfield` -> `dfield...37` * `dfield` -> `dfield...38` * `dfield` -> `dfield...39` * `dfield` -> `dfield...40` * `dfield` -> `dfield...41` * `dfield` -> `dfield...42` * `dfield` -> `dfield...43` * `dfield` -> `dfield...44` * `dfield` -> `dfield...45` * `dfield` -> `dfield...46` * `dfield` -> `dfield...47` * `dfield` -> `dfield...48` * `dfield` -> `dfield...49` * `dfield` -> `dfield...50` * `dfield` -> `dfield...51` * `dfield` -> `dfield...52` * `dfield` -> `dfield...53` * `dfield` -> `dfield...54` * `dfield` -> `dfield...55` * `dfield` -> `dfield...56` * `dfield` -> `dfield...57` * `dfield` -> `dfield...58` * `dfield` -> `dfield...59` * `dfield` -> `dfield...60` * `dfield` -> `dfield...61` * `dfield` -> `dfield...62` * `dfield` -> `dfield...63` * `dfield` -> `dfield...64` * `dfield` -> `dfield...65` * `dfield` -> `dfield...66` * `dfield` -> `dfield...67` * `dfield` -> `dfield...68` * `dfield` -> `dfield...69` * `dfield` -> `dfield...70` * `dfield` -> `dfield...71` * `dfield` -> `dfield...72` * `dfield` -> `dfield...73` * `dfield` -> `dfield...74` * `dfield` -> `dfield...75` * `dfield` -> `dfield...76` * `dfield` -> `dfield...77` * `dfield` -> `dfield...78` * `dfield` -> `dfield...79` * `dfield` -> `dfield...80` * `dfield` -> `dfield...81` * `dfield` -> `dfield...82` * `dfield` -> `dfield...83` * `dfield` -> `dfield...84` * `dfield` -> `dfield...85` * `dfield` -> `dfield...86` * `dfield` -> `dfield...87` * `dfield` -> `dfield...88` * `dfield` -> `dfield...89` * `dfield` -> `dfield...90` * `dfield` -> `dfield...91` * `dfield` -> `dfield...92` * `dfield` -> `dfield...93` * `dfield` -> `dfield...94` * `dfield` -> `dfield...95` * `dfield` -> `dfield...96` * `dfield` -> `dfield...97` * `dfield` -> `dfield...98` * `dfield` -> `dfield...99` * `dfield` -> `dfield...100` Progress: ────────────────────────────────── 100% Progress: ────────────────────────────────────── 100% Progress: ────────────────────────────────────────── 100% Progress: ─────────────────────────────────────────────── 100% Progress: ─────────────────────────────────────────────────── 100% Progress: ─────────────────────────────────────────────────────── 100% Progress: ─────────────────────────────────────────────────────────── 100% Progress: ──────────────────────────────────────────────────────────────── 100%New names: * `dfield` -> `dfield...1` * `dfield` -> `dfield...2` * `dfield` -> `dfield...3` * `dfield` -> `dfield...4` * `dfield` -> `dfield...5` * `dfield` -> `dfield...6` * `dfield` -> `dfield...7` * `dfield` -> `dfield...8` * `dfield` -> `dfield...9` * `dfield` -> `dfield...10` * `dfield` -> `dfield...11` * `dfield` -> `dfield...12` * `dfield` -> `dfield...13` * `dfield` -> `dfield...14` * `dfield` -> `dfield...15` * `dfield` -> `dfield...16` * `dfield` -> `dfield...17` * `dfield` -> `dfield...18` * `dfield` -> `dfield...19` * `dfield` -> `dfield...20` * `dfield` -> `dfield...21` * `dfield` -> `dfield...22` * `dfield` -> `dfield...23` * `dfield` -> `dfield...24` * `dfield` -> `dfield...25` * `dfield` -> `dfield...26` * `dfield` -> `dfield...27` * `dfield` -> `dfield...28` * `dfield` -> `dfield...29` * `dfield` -> `dfield...30` * `dfield` -> `dfield...31` * `dfield` -> `dfield...32` * `dfield` -> `dfield...33` * `dfield` -> `dfield...34` * `dfield` -> `dfield...35` * `dfield` -> `dfield...36` * `dfield` -> `dfield...37` * `dfield` -> `dfield...38` * `dfield` -> `dfield...39` * `dfield` -> `dfield...40` * `dfield` -> `dfield...41` * `dfield` -> `dfield...42` * `dfield` -> `dfield...43` * `dfield` -> `dfield...44` * `dfield` -> `dfield...45` * `dfield` -> `dfield...46` * `dfield` -> `dfield...47` * `dfield` -> `dfield...48` * `dfield` -> `dfield...49` * `dfield` -> `dfield...50` * `dfield` -> `dfield...51` * `dfield` -> `dfield...52` * `dfield` -> `dfield...53` * `dfield` -> `dfield...54` * `dfield` -> `dfield...55` * `dfield` -> `dfield...56` * `dfield` -> `dfield...57` * `dfield` -> `dfield...58` * `dfield` -> `dfield...59` * `dfield` -> `dfield...60` * `dfield` -> `dfield...61` * `dfield` -> `dfield...62` * `dfield` -> `dfield...63` * `dfield` -> `dfield...64` * `dfield` -> `dfield...65` * `dfield` -> `dfield...66` * `dfield` -> `dfield...67` * `dfield` -> `dfield...68` * `dfield` -> `dfield...69` * `dfield` -> `dfield...70` * `dfield` -> `dfield...71` * `dfield` -> `dfield...72` * `dfield` -> `dfield...73` * `dfield` -> `dfield...74` * `dfield` -> `dfield...75` * `dfield` -> `dfield...76` * `dfield` -> `dfield...77` * `dfield` -> `dfield...78` * `dfield` -> `dfield...79` * `dfield` -> `dfield...80` * `dfield` -> `dfield...81` * `dfield` -> `dfield...82` * `dfield` -> `dfield...83` * `dfield` -> `dfield...84` * `dfield` -> `dfield...85` * `dfield` -> `dfield...86` * `dfield` -> `dfield...87` * `dfield` -> `dfield...88` * `dfield` -> `dfield...89` * `dfield` -> `dfield...90` * `dfield` -> `dfield...91` * `dfield` -> `dfield...92` * `dfield` -> `dfield...93` * `dfield` -> `dfield...94` * `dfield` -> `dfield...95` * `dfield` -> `dfield...96` * `dfield` -> `dfield...97` * `dfield` -> `dfield...98` * `dfield` -> `dfield...99` * `dfield` -> `dfield...100` New names: * `dfield` -> `dfield...1` * `dfield` -> `dfield...2` * `dfield` -> `dfield...3` * `dfield` -> `dfield...4` * `dfield` -> `dfield...5` * `dfield` -> `dfield...6` * `dfield` -> `dfield...7` * `dfield` -> `dfield...8` * `dfield` -> `dfield...9` * `dfield` -> `dfield...10` New names: * `dfield` -> `dfield...1` * `dfield` -> `dfield...2` * `dfield` -> `dfield...3` * `dfield` -> `dfield...4` * `dfield` -> `dfield...5` * `dfield` -> `dfield...6` * `dfield` -> `dfield...7` * `dfield` -> `dfield...8` * `dfield` -> `dfield...9` * `dfield` -> `dfield...10` Object of class bioindex it contains 8 slots: @alpha: A sparse matrix with the richness of species per site attr(,"Dim") [1] 10 1 attr(,"Dimnames") attr(,"Dimnames")[[1]] NULL attr(,"Dimnames")[[2]] NULL attr(,"x") [1] 2 3 0 1 4 1 1 5 3 5 attr(,"factors") list() attr(,"class") [1] "dgeMatrix" attr(,"class")attr(,"package") [1] "Matrix" @omega: A sparse matrix with the range size of every species attr(,"Dim") [1] 10 1 attr(,"Dimnames") attr(,"Dimnames")[[1]] NULL attr(,"Dimnames")[[2]] NULL attr(,"x") [1] 1 1 2 3 3 3 1 3 3 5 attr(,"factors") list() attr(,"class") [1] "dgeMatrix" attr(,"class")attr(,"package") [1] "Matrix" @dispersion_field: A sparse with the set of ranges of all species that occur in at each locality attr(,"Dim") [1] 10 1 attr(,"Dimnames") attr(,"Dimnames")[[1]] NULL attr(,"Dimnames")[[2]] NULL attr(,"x") [1] 1 1 2 3 3 3 1 3 3 5 attr(,"factors") list() attr(,"class") [1] "dgeMatrix" attr(,"class")attr(,"package") [1] "Matrix" | | | 0% | |====== | 9% | |============= | 18% | |=================== | 27% | |========================= | 36% | |================================ | 45% | |====================================== | 55% | |============================================= | 64% | |=================================================== | 73% | |========================================================= | 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