R Under development (unstable) (2026-01-20 r89309 ucrt) -- "Unsuffered Consequences" Copyright (C) 2026 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/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(FishDiveR) FishDiveR version 1.1.0. Facilitating classification of aquatic animal behaviours from vertical movement data. Type 'citation("FishDiveR")' for citing this R package in publications. > > test_check("FishDiveR") Maximum depth is 262.2 Data sampling interval is 60 seconds Plotting every 10 records There are less than 2 representatives available for cluster 2 Cluster 1 dates 2000-01-08 Tag: dataCluster 1 dates 2000-01-09 Tag: data Cluster 2 dates 2000-01-10 Tag: data Cluster 3 dates 2000-01-03 Tag: dataCluster 3 dates 2000-01-02 Tag: data Cluster 4 dates 2000-01-04 Tag: dataCluster 4 dates 2000-01-05 Tag: data Output folder: D:\temp\2026_01_21_16_40_17_7836\RtmpeGA30Q/data/6_Cluster-plots.K=4 Maximum depth is 262.2 Data sampling interval is 60 seconds Plotting every 600 seconds There are less than 2 representatives available for cluster 2 Cluster 1 dates 2000-01-08 Tag: dataCluster 1 dates 2000-01-09 Tag: data Cluster 2 dates 2000-01-10 Tag: data Cluster 3 dates 2000-01-03 Tag: dataCluster 3 dates 2000-01-02 Tag: data Cluster 4 dates 2000-01-04 Tag: dataCluster 4 dates 2000-01-05 Tag: data Output folder: D:\temp\2026_01_21_16_40_17_7836\RtmpeGA30Q/data/6_Cluster-plots.K=4_shaded Tag ID = data Depth sampling interval is 60 seconds Number of depth values corrected (above 0):0 Mean depth = 81.5 SD = 87.6 Maximum depth = 262.2 Number of full days in dataset: 10 Output file: D:\temp\2026_01_21_16_40_17_7836\RtmpeGA30Q/data/archive_days.rds Data sampling interval is 60 seconds Plotting every 10 records Maximum depth is 256.6 meters Output file:D:\temp\2026_01_21_16_40_17_7836\RtmpeGA30Q/data/tag_archive.png Data has been filtered between X-axis limits Data sampling interval is 60 seconds Plotting every 600 seconds Maximum depth is 252.5 meters Output file:D:\temp\2026_01_21_16_40_17_7836\RtmpeGA30Q/data/tag_archive.png Starting wavelet transformation... ... and simulations... | | | 0% | |= | 1% | |= | 2% | |== | 3% | |=== | 4% | |==== | 5% | |==== | 6% | |===== | 7% | |====== | 8% | |====== | 9% | |======= | 10% | |======== | 11% | |======== | 12% | |========= | 13% | |========== | 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|=================================================================== | 96% | |==================================================================== | 97% | |===================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 100% Class attributes are accessible through following names: series loess.span dt dj Wave Phase Ampl Power Power.avg Power.pval Power.avg.pval Ridge Period Scale nc nr coi.1 coi.2 axis.1 axis.2 date.format date.tz Analysing tag ID data Creating new wavelet. Starting wavelet transformation... Class attributes are accessible through following names: series loess.span dt dj Wave Phase Ampl Power Power.avg Power.pval Power.avg.pval Ridge Period Scale nc nr coi.1 coi.2 axis.1 axis.2 date.format date.tz Wavelet saved to D:\temp\2026_01_21_16_40_17_7836\RtmpeGA30Q/data/1_Wavelets/data_wavelet.rds Output folder: D:\temp\2026_01_21_16_40_17_7836\RtmpeGA30Q/data/2_Wavelet_Figures/ Running create_wavelet_stats() on tag ID data Output file: D:\temp\2026_01_21_16_40_17_7836\RtmpeGA30Q/data/3_Stats/data_waveStats.csv Running create_depth_stats() on tag ID data Output folder: D:\temp\2026_01_21_16_40_17_7836\RtmpeGA30Q/data/3_Stats/data_depthStats.csv Running create_depth_stats() on tag ID data Using fixed sunrise and sunset times to calculate diel statistics Archive updated with diel periods Output folder: D:\temp\2026_01_21_16_40_17_7836\RtmpeGA30Q/data/3_Stats/data_depthStats.csv Running create_depth_stats() on tag ID data Reading in GPS locations. Using actual sunrise and sunset times to calculate diel statistics Archive updated with diel periods based on GPS calculated times Output folder: D:\temp\2026_01_21_16_40_17_7836\RtmpeGA30Q/data/3_Stats/data_depthStats.csv Output file: D:\temp\2026_01_21_16_40_17_7836\RtmpeGA30Q/data/4_PCA/pc_data.rds Output file: D:\temp\2026_01_21_16_40_17_7836\RtmpeGA30Q/data/4_PCA/pc_data.rds Non-numerical columns being excluded: tag_ID, date_only 9 principal components of 9 have eigenvalues >= 1 Output file: D:\temp\2026_01_21_16_40_17_7836\RtmpeGA30Q/data/4_PCA/eigenvalues_cum_var.csv Using cumulative variance threshold: Keeping 4 principal components to reach 99% variance Output file: D:\temp\2026_01_21_16_40_17_7836\RtmpeGA30Q/data/4_PCA/pc_results.rds contains the selected number of principal components. Non-numerical columns being excluded: tag_ID, date_only 7 principal components of 9 have eigenvalues >= 1 Output file: D:\temp\2026_01_21_16_40_17_7836\RtmpeGA30Q/data/4_PCA/eigenvalues_cum_var.csv Keeping 3 PC's contributing to a cumulative 91.6918728473569% of variance Output folder: D:\temp\2026_01_21_16_40_17_7836\RtmpeGA30Q/data/4_PCA Output file: D:\temp\2026_01_21_16_40_17_7836\RtmpeGA30Q/data/4_PCA/pc_results.rds contains the selected number of principal components. Output file: D:\temp\2026_01_21_16_40_17_7836\RtmpeGA30Q/data/4_PCA/pc_scores.rds Output folder: D:\temp\2026_01_21_16_40_17_7836\RtmpeGA30Q/data/4_PCA Output file: D:\temp\2026_01_21_16_40_17_7836\RtmpeGA30Q/data/4_PCA/pc_scores.rds Saving combined metrics to:D:\temp\2026_01_21_16_40_17_7836\RtmpeGA30Q/data/5_k-means/combined_stats.rds If kmeans_data is a combination of PC scores and depth data. Please standardise the data as this can greatly impact the reliability of the results. K = 2 Average silhouette width = 0.523 K = 3 Average silhouette width = 0.49 K = 4 Average silhouette width = 0.437 K = 5 Average silhouette width = 0.362 K = 6 Average silhouette width = 0.376 K = 7 Average silhouette width = 0.314 K = 8 Average silhouette width = 0.219 Optimal number of clusters according to gap statistic: 2 Single tag output file: D:\temp\2026_01_21_16_40_17_7836\RtmpeGA30Q/data/5_k-means/Select_k.3_PCs.png Standardising k-means input. K = 2 Average silhouette width = 0.499 K = 3 Average silhouette width = 0.586 K = 4 Average silhouette width = 0.642 K = 5 Average silhouette width = 0.518 K = 6 Average silhouette width = 0.392 K = 7 Average silhouette width = 0.243 K = 8 Average silhouette width = 0.154 Single tag output file: D:\temp\2026_01_21_16_40_17_7836\RtmpeGA30Q/data/5_k-means/Select_k.3_PCs.png If kmeans_data is a combination of PC scores and depth data. Please standardise the data as this can greatly impact the reliability of the results. Total of 10 days of data Output folder: D:\temp\2026_01_21_16_40_17_7836\RtmpeGA30Q/data/5_k-means Standardising k-means input. Total of 10 days of data Output folder: D:\temp\2026_01_21_16_40_17_7836\RtmpeGA30Q/data/5_k-means Loading tag data TDR Single tag k-means loaded Maximum depth is 262.2 Data sampling interval is 60 seconds Plotting every 10 records Output file: D:\temp\2026_01_21_16_40_17_7836\RtmpeGA30Q/data/data_TDR_k=4.png Loading tag data TDR Single tag k-means loaded Maximum depth is 262.2 Data sampling interval is 60 seconds Data has been filtered between X-axis limits Plotting every 600 seconds Output file: D:\temp\2026_01_21_16_40_17_7836\RtmpeGA30Q/data/data_TDR_k=4.png [ FAIL 0 | WARN 0 | SKIP 0 | PASS 36 ] > > proc.time() user system elapsed 68.93 17.46 91.28