Fix memory leak #41
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Fix memory leak #41
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…alues. It is much faster and will finish the computation for the human sequences also.
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* Create Rproj file * Change Clustur to clustur * PDS edits from going through vignette * Fix for test! * Fixed check and documentation, and other issues that caused failures with the check. * Fix for lintr, url issues, and wrong badges * Removing data not wihtin the cutoff for get_distance_df functionality. This function will now only show data that is within the cutoff. * Fix for test * fix for lintr and pkgdown * Removing unused code. * Improved test coverage to 90.86%, added error checking for when users pass incorrect parameters, and improved the validity of current test. * Update data files and issues * Update data files and issues, #38 * Fixing lingering issues (#40) * unstable, fixing reading so that it reads as a sparse * Fixing unit test after making changes to column, phylip, and sparse matrix reading * All the test are working! * Changed named of files, and allowed read_dist to remove data that is not in the cutoff. * Updated parameters for cluster to include cutoff and made proper modifications to the vignette file following the changes. * Fixed issue with time, and added a paramters to change the name of the feature and bin columns * Reorder the cluster_metric columns to be equal to that of mothur! * Fix for column read erroring and adding testing for it. * Fix for build warnings. Fixing type deduction. * Fixed the phylip file reading error out. It will now error immediately when the name isnt in the count. * Fix for linter * Fix memory leak (#41) * Adding function for profiling, and going to implement the fix. * Added todos * Removing RowData Vector from the code base * Added changes to matrix creation * Unstable push, but removing variables that store large amounts of data. * Optimization for optimatrix adapter * Update to optimatric adapter * Fix for clustering not working * Using unordered set over sets, lets see how much memory this takes. * Increased the speed of opticluster by 400% * Fixed test, still working to fix the get_distance_df function. * Fixed get_distance_df, so that it will not create bidirectional row values. It is much faster and will finish the computation for the human sequences also. * Revising the test to fit the new structure of clustur of the optimizations. * Fixed optimatrix-adapter test * All test should now work with the new structure! * Removing fluff(zombie code), and check works fine! * Check works, everything is documented and linted as well! * Removing old comments --------- Co-authored-by: GregJohnsonJr <[email protected]> Co-authored-by: Gregory Johnson <[email protected]>
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commit cc13093da588de1481222098e02163994324cdd8 Author: Pat Schloss <[email protected]> Date: Wed Nov 6 13:46:19 2024 -0500 First pass edits from going through vignettes (#38) * Create Rproj file * Change Clustur to clustur * PDS edits from going through vignette * Fix for test! * Fixed check and documentation, and other issues that caused failures with the check. * Fix for lintr, url issues, and wrong badges * Removing data not wihtin the cutoff for get_distance_df functionality. This function will now only show data that is within the cutoff. * Fix for test * fix for lintr and pkgdown * Removing unused code. * Improved test coverage to 90.86%, added error checking for when users pass incorrect parameters, and improved the validity of current test. * Update data files and issues * Update data files and issues, #38 * Fixing lingering issues (#40) * unstable, fixing reading so that it reads as a sparse * Fixing unit test after making changes to column, phylip, and sparse matrix reading * All the test are working! * Changed named of files, and allowed read_dist to remove data that is not in the cutoff. * Updated parameters for cluster to include cutoff and made proper modifications to the vignette file following the changes. * Fixed issue with time, and added a paramters to change the name of the feature and bin columns * Reorder the cluster_metric columns to be equal to that of mothur! * Fix for column read erroring and adding testing for it. * Fix for build warnings. Fixing type deduction. * Fixed the phylip file reading error out. It will now error immediately when the name isnt in the count. * Fix for linter * Fix memory leak (#41) * Adding function for profiling, and going to implement the fix. * Added todos * Removing RowData Vector from the code base * Added changes to matrix creation * Unstable push, but removing variables that store large amounts of data. * Optimization for optimatrix adapter * Update to optimatric adapter * Fix for clustering not working * Using unordered set over sets, lets see how much memory this takes. * Increased the speed of opticluster by 400% * Fixed test, still working to fix the get_distance_df function. * Fixed get_distance_df, so that it will not create bidirectional row values. It is much faster and will finish the computation for the human sequences also. * Revising the test to fit the new structure of clustur of the optimizations. * Fixed optimatrix-adapter test * All test should now work with the new structure! * Removing fluff(zombie code), and check works fine! * Check works, everything is documented and linted as well! * Removing old comments --------- Co-authored-by: GregJohnsonJr <[email protected]> Co-authored-by: Gregory Johnson <[email protected]> commit e474c5b2890a7c0a358e93ae5daebadd5d128ac7 Author: Gregory Johnson <[email protected]> Date: Mon Oct 21 14:39:15 2024 -0400 Dev (#37) * Added unit test and created a easy opticluster function * Release v0.0.1 (#1) * Fixed the wrapper for Calling Opticluster! * Fixing the .RD file * Fixed issue where opticluster was returning a matrix array and not a data.frame. * Changing documentation * Fixing the warnings from building the code. * Update to the test * Updating the gitignore * Add cpp test (#3) * Added Cpp testing structure! * Added Test Fixture Class * Forced the cluster to only return OTU data, and created the fix test fixture with test! * Created all of the test for the optimatrix adapter and removed the .dll from being tracked! * Created all the test in the testfixture for listvectors and now I am adding them to the test files. * Created base test for listVector * Basic test for listVector are completed! * Created the basic structure and test fixture for cluster commands * Cluster Testing suite being pushed up! * Fix cluster algorithm (#2) * Fixed a slew of issues by adding bidirection distances. * Fixed the clustering issue, clustering should be working correctly now! * Generated Definitions for OptiCluster Test * Finished creating unit test of the cluster command and opticluster * Added OptiData test fixture * Started creating the unit test for utils * Utils command cluster and test work as expected!! * Removed old code from one of the testing suites. * Added another test in utils. * Clustor has a 89% test coverage! Everything should be tested and ready to merge back! * RMD Check is able to run successfully! * Correcting the paths of my cpp files, should fix the action errors. * Update to the cluster command test fixture * Modifying the test for opticluster * Ensuring everything works with c++11 * Removing code issues from cluster command * Adding the build ignore * Founds some issue where I am using c++ 17 syntax and not 11. * Github action fixes, needed to update syntax towards cpp 11 * Modified the testing structure by removing the "Opticluster returns proper stats". I appears it is returning incorrect data on different computer architectures. It is also not needed in the code. * Fix cluster unit test (#5) * This should be the fix for the failing cluster test. * Changed the test to look for equivalence rows instead of equal dataframes. Gives the same results, the only differences is that the cluster have different numbers. * Printing out the metrics after you perform a cluster and added a true/false condition for shuffling * Release polish (#6) * Added to build ignore and properly documented the new R code. * Unstable, have to fix the mismatch header situation, but was able to return a vector with all the metrics! * Cluster now returns test metrics and added test to support it. * Added a depends for lazy-loading and other R related issues. * More cluster features (#7) * Adding a single, complete, average, and weighted linkage algorithms * Adding cluster functions * Added the new clustering methods, but am getting issues when trying to format them. * Unstable cannot create proper phylip file with matrix data.. * More unstable code, but we are getting closer. The phylip file is correct for a small dataset * STABLE, the cluster does not fail and will actually cluster. However I am getting incorrect results. Will refactor the code to work. * All Clusters (Furthest, Nearest, average, and weighted) all work as they should! I just need to clean it up and add test! * Created R-facing function in R from cpp and cleaned up a bit of the code. * Cleaning up the main function * Small optimization to cluster (x2 speed_up) * Added optimization and cleaned up functions * Modifications to the namespace file and test! * Cluster works with windows now! * Fixing the round point error on windows and in R. It has something to do with the compilation of the objects...most likely it is related to the conversions of data. * Fixed the floating point issue, now I have to fix an issue where the cutoff amounts are decreasing. * Fixed the floating point issue! My adjust was not set! Now I need to figure out why the nearest algorithm is not returning any data. * Small code style changes * Cluster works as expected! Everything clusters. Now to add tests * Started adding more test for Clustor * Created Test fixtures for the new code * Completed the sparse distance matrix and read phylip test, need to fix some test errors. * Added test for phylip reader and matrix adapter. Adding the final test for rAbund now. * Added all the rAbund test, and the cluster feature should be working properly! * Adding include statements for windows and other operating systems, this should work as expected. RCMD check works. * The fix for github actions. * Change to the include file. * Removing srand from Utils, going to attempt to set seeds inside of R. * Fix for race condition issue. * Fix for RCMD check warnings * The fix for the windows version of RMD Check! * Adding dependency for time. * Make shared (#9) * Adding a count table variation * Update Makevars * Preparation to Create a Shared File for the clustering output. * Added a simple make shared functionality. It works without the group information. Count_table + list_file = shared_file * Small changes, going to need to modify the make shared code soon. * Modifying the way cluster result data is stored. * Add a datastructure for returning and generating cluster data. * Cluster export works for Traditional Cluster Methods * Progress on making a shared file without a group. Have to make test soon. * Created a pseudo shared file successfully! * Changes to the abundance output * Delete F:\Opticluster\output_rabund.txt * Delete tests/testthat/F:\Opticluster\output_rabund.txt Removing werid paths. * Some example data and count table creation * Pushing lots of temp test files, and small changes * Adding the count table! * Count table structure has been created * Shared File with count tables and without work! * Count table can now be added to the cluster functions and will produce an output of abundance and clusters in dataframes. - Removed the exchanged of strings and read table between r and c++ and added a more modifiable approach. * Fixed test, now we have to add more test. * Fixes for linux and other computer architectures. * Removing dependencies that are not used. * Created test fixtures for unit test * Removed all of the negligent files that are not needed and added test to all of the new functions! --------- Co-authored-by: YoungKrug <[email protected]> * Forgot a unit test. (#10) * Fix results (#11) * Adding example data for mothur results. * Added support for similarity matrix functionality * Updates to phylip writing, and fixes to incorrect clustering! * Stable, Classic cluster and opticluster both are identical to that of mothur! + Names can be added * Results are the same as they are in mothur! * All the unit test work, and clustur prints out expected results! * Removing and fixing check issues. * Fix compilation warnings (#12) * No warnings on mac! * Still fixing clang-tidy errors. Lots of comparisons between longs and ints that will cause problems. * Half way done, modified a lot of deduced type conversions. May need to go back in the future to remove them. * Should fix all the warnings on linux and windows. * Pushing through more deduced type fixes. * Should be the final fix for linux. * Fix for negative index value * Cleaning up build notes. * lintr fixes * Fix for lintr * Read phylip files (#14) * Looking to add a function to replace the entry point. * Added support for phylip file reading! * Initial push * Adding r documentation about mothur and clustur * Added functionality for column distance file reading! * Column distance files work! * Adding read column feature (#15) * Added reading of column files, but result arent correct. * Correct Column file * Column Reader works as expected! * Added test for column reading, and it all works as expected. * Fixed check issues * Documentation (#16) * Initial push * Adding r documentation about mothur and clustur * Added functionality for column distance file reading! * Column distance files work! * Adding read column feature (#15) * Added reading of column files, but result arent correct. * Correct Column file * Column Reader works as expected! * Added test for column reading, and it all works as expected. * Fixed check issues * Fix for opticluster clustering. * Fixing up the documentation * I am getting the same number of bins! * example data * Fix for test error * Testing values to RMD file * Small changes * Added sorting by bin size to cluster output and fixed the clustering issue! * Modification to the test! * Updates to test file * Cleaning up test * Small change * Method to check if each cluster exist in the dataframe * Using content paths instead of absolutes * Create 96_sq_column_results_mac.list * Pushing results for different operating systems * Updating documentation * Added inst folders * Update Cluster.R * Pushing the temporary fix! * Pushing spare_matrix data file * Squashed commit of the following: commit dfd9b2d83c4ab60a95b1585995482ac176fc1114 Author: YoungKrug <[email protected]> Date: Tue Sep 24 15:42:56 2024 -0400 Big error in readPhylip matrix. I was never checking whether the matrix was a square or not! * Creating vignettes * Created base pkgdown structure * Base structure of documentation and website * Small optimzation to clustur * Fixing unit test * Removing comments * Changed the name of the package to clustur * Removing unneeded data and fixing issue to validate count_table * Fixing check errors. * Consistent randomization (#17) * Have to fix test, but this is the basic framework for randomization * Squashed commit of the following: commit 3f2d3995c30894a457bd860379243aa5329f52cd Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:52:00 2024 -0400 Fixing check errors. commit 3f04170d4897e243a2a87847f39d8f4fe1307be0 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:43:06 2024 -0400 Removing unneeded data and fixing issue to validate count_table commit 2c642f300cf9fedb6ade3b46eab053c691c26f45 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:31:56 2024 -0400 Changed the name of the package to clustur commit 1251c3c63a7d6fca99ddf1373633e3281d0472e2 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 16:53:16 2024 -0400 Removing comments * Changes to the utils class to allow for randomization and added a seed to the functions * Adding another test * Fix for note * Randomization has been added and we changed the way we create sparse matrices! * Consistent randomization (#18) * Have to fix test, but this is the basic framework for randomization * Squashed commit of the following: commit 3f2d3995c30894a457bd860379243aa5329f52cd Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:52:00 2024 -0400 Fixing check errors. commit 3f04170d4897e243a2a87847f39d8f4fe1307be0 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:43:06 2024 -0400 Removing unneeded data and fixing issue to validate count_table commit 2c642f300cf9fedb6ade3b46eab053c691c26f45 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:31:56 2024 -0400 Changed the name of the package to clustur commit 1251c3c63a7d6fca99ddf1373633e3281d0472e2 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 16:53:16 2024 -0400 Removing comments * Changes to the utils class to allow for randomization and added a seed to the functions * Adding another test * Fix for note * Randomization has been added and we changed the way we create sparse matrices! * Forgot to include the updated namesapce! * Squashed commit of the following: commit 45ba179f6b2e63687229c042be92a6f4cae2c786 Author: Gregory Johnson <[email protected]> Date: Thu Sep 26 18:17:22 2024 -0400 Consistent randomization (#18) * Have to fix test, but this is the basic framework for randomization * Squashed commit of the following: commit 3f2d3995c30894a457bd860379243aa5329f52cd Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:52:00 2024 -0400 Fixing check errors. commit 3f04170d4897e243a2a87847f39d8f4fe1307be0 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:43:06 2024 -0400 Removing unneeded data and fixing issue to validate count_table commit 2c642f300cf9fedb6ade3b46eab053c691c26f45 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:31:56 2024 -0400 Changed the name of the package to clustur commit 1251c3c63a7d6fca99ddf1373633e3281d0472e2 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 16:53:16 2024 -0400 Removing comments * Changes to the utils class to allow for randomization and added a seed to the functions * Adding another test * Fix for note * Randomization has been added and we changed the way we create sparse matrices! * Forgot to include the updated namesapce! commit 10c2ad9915d63dac5fee47d5385b91e711a8b16a Author: Gregory Johnson <[email protected]> Date: Thu Sep 26 18:15:33 2024 -0400 Consistent randomization (#17) * Have to fix test, but this is the basic framework for randomization * Squashed commit of the following: commit 3f2d3995c30894a457bd860379243aa5329f52cd Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:52:00 2024 -0400 Fixing check errors. commit 3f04170d4897e243a2a87847f39d8f4fe1307be0 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:43:06 2024 -0400 Removing unneeded data and fixing issue to validate count_table commit 2c642f300cf9fedb6ade3b46eab053c691c26f45 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:31:56 2024 -0400 Changed the name of the package to clustur commit 1251c3c63a7d6fca99ddf1373633e3281d0472e2 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 16:53:16 2024 -0400 Removing comments * Changes to the utils class to allow for randomization and added a seed to the functions * Adding another test * Fix for note * Randomization has been added and we changed the way we create sparse matrices! commit 3f2d3995c30894a457bd860379243aa5329f52cd Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:52:00 2024 -0400 Fixing check errors. commit 3f04170d4897e243a2a87847f39d8f4fe1307be0 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:43:06 2024 -0400 Removing unneeded data and fixing issue to validate count_table commit 2c642f300cf9fedb6ade3b46eab053c691c26f45 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:31:56 2024 -0400 Changed the name of the package to clustur commit 1251c3c63a7d6fca99ddf1373633e3281d0472e2 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 16:53:16 2024 -0400 Removing comments commit e87319e3bfdb1c1657fc399af778e1c6bd17fc37 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 12:04:03 2024 -0400 Fixing unit test commit 8c648bd5dce04613d5fb11b2f8133dda762d8507 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 11:51:15 2024 -0400 Small optimzation to clustur commit 05c8a0738991359f6ef9f69f3de180fd6173ee44 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 11:38:43 2024 -0400 Base structure of documentation and website commit 4a4fcfa4ed154804a9574323d1a56f76d958c24f Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 10:43:40 2024 -0400 Created base pkgdown structure commit a714b7d0a7c9390c30eb723d4135b980a052d387 Author: YoungKrug <[email protected]> Date: Tue Sep 24 23:01:44 2024 -0400 Creating vignettes commit 6a5df2035a1de3f206a1bcd9ddc0d4bb9b763a83 Author: YoungKrug <[email protected]> Date: Tue Sep 24 15:43:09 2024 -0400 Squashed commit of the following: commit dfd9b2d83c4ab60a95b1585995482ac176fc1114 Author: YoungKrug <[email protected]> Date: Tue Sep 24 15:42:56 2024 -0400 Big error in readPhylip matrix. I was never checking whether the matrix was a square or not! commit 63d515ed9dac7370abd579ec1a3d9c3a69f589d2 Author: GregJohnsonJr <[email protected]> Date: Tue Sep 24 15:02:02 2024 -0400 Pushing spare_matrix data file commit 7eec4fbf6ba4b4c881d65cabf86eb9c4b344ca1b Author: GregJohnsonJr <[email protected]> Date: Tue Sep 24 14:43:12 2024 -0400 Pushing the temporary fix! commit 0b5a145cc3ee1db43d4c7472940568324f48cacf Author: YoungKrug <[email protected]> Date: Tue Sep 24 13:56:47 2024 -0400 Update Cluster.R commit 7c694e39687ccd62d63fbaa6f3d8713606f5b633 Author: YoungKrug <[email protected]> Date: Tue Sep 24 12:51:01 2024 -0400 Added inst folders commit 3cb0ba458c6fb35c963a4ee2b6000ee4137a6442 Author: YoungKrug <[email protected]> Date: Tue Sep 24 12:02:56 2024 -0400 Updating documentation commit 5af269d6bf15db5c96e1c6b676ad57a9b9793eeb Author: YoungKrug <[email protected]> Date: Mon Sep 23 19:45:19 2024 -0400 Pushing results for different operating systems commit a745510b856aa3259400c65a4566e98d61a643a8 Author: GregJohnsonJr <[email protected]> Date: Mon Sep 23 19:36:29 2024 -0400 Create 96_sq_column_results_mac.list commit d08a209b9ac4419e64313312497be6a83acd562f Author: YoungKrug <[email protected]> Date: Sat Sep 21 12:03:56 2024 -0400 Using content paths instead of absolutes commit 1623601703cf96bf75a0dd36ecee49c75b2084f9 Author: YoungKrug <[email protected]> Date: Sat Sep 21 09:49:11 2024 -0400 Method to check if each cluster exist in the dataframe commit 585736ef751b407d397925269788600c83521942 Author: YoungKrug <[email protected]> Date: Wed Sep 18 13:51:36 2024 -0400 Small change commit acfbc9a008e215a4822265d89a224ff9973a475f Author: YoungKrug <[email protected]> Date: Wed Sep 18 13:50:29 2024 -0400 Cleaning up test commit 60d16f54feff027ecdfa641ff99f65399781a1b3 Author: YoungKrug <[email protected]> Date: Wed Sep 18 13:49:41 2024 -0400 Updates to test file commit d89afb52f6e2daf8ab6491fbcadde43a96147914 Author: YoungKrug <[email protected]> Date: Wed Sep 18 13:47:32 2024 -0400 Modification to the test! commit d48660439a99d0352960e00eb060228fa6293c3f Author: GregJohnsonJr <[email protected]> Date: Wed Sep 18 13:21:11 2024 -0400 Added sorting by bin size to cluster output and fixed the clustering issue! commit 3bddc53b063b8439a0485cc31e3064f7082d7a2a Author: GregJohnsonJr <[email protected]> Date: Tue Sep 17 20:05:22 2024 -0400 Small changes commit 0d3e798422ff9d11e2bc0dee51d741263f6d2a9b Author: GregJohnsonJr <[email protected]> Date: Tue Sep 17 15:20:47 2024 -0400 Testing values to RMD file commit 58a7e8e612730f991c10e17f5629120899a71caf Author: GregJohnsonJr <[email protected]> Date: Tue Sep 17 13:55:31 2024 -0400 Fix for test error commit 4c63f8ca1fe110d484914c0663a12bac7273240b Author: GregJohnsonJr <[email protected]> Date: Tue Sep 17 13:06:52 2024 -0400 example data commit 48a0f38462b12e3cc1ca4c3c2b11c7d672643f61 Author: GregJohnsonJr <[email protected]> Date: Mon Sep 16 19:21:22 2024 -0400 I am getting the same number of bins! commit 37cdb7e40373f455f3497f019d80d1baace40762 Author: GregJohnsonJr <[email protected]> Date: Mon Sep 16 17:29:51 2024 -0400 Fixing up the documentation commit d7dc2948ca5adc2f7033348492549d277db2e3c4 Author: GregJohnsonJr <[email protected]> Date: Mon Sep 16 16:43:10 2024 -0400 Fix for opticluster clustering. commit 3d8015fe6918bc3c36047abe0551596f51927726 Author: Gregory Johnson <[email protected]> Date: Mon Sep 16 15:01:11 2024 -0400 Adding read column feature (#15) * Added reading of column files, but result arent correct. * Correct Column file * Column Reader works as expected! * Added test for column reading, and it all works as expected. * Fixed check issues commit 6f830c6aa435260c84627946281b10f5a8d03353 Author: GregJohnsonJr <[email protected]> Date: Fri Sep 13 17:02:03 2024 -0400 Column distance files work! commit e6f00a816e9778b1dd4a8b9c1ec92818c93e3249 Author: GregJohnsonJr <[email protected]> Date: Fri Sep 13 12:38:20 2024 -0400 Added functionality for column distance file reading! commit 25a357dccce0f4d0b9e1ec198ced4f98a3653163 Author: GregJohnsonJr <[email protected]> Date: Thu Sep 12 17:37:58 2024 -0400 Adding r documentation about mothur and clustur commit fa25af7f600e7feb97aa97b963ec27ae6f0abdac Author: GregJohnsonJr <[email protected]> Date: Thu Sep 12 16:44:32 2024 -0400 Initial push * Documentation (#16) (#19) (#20) * Documentation (#16) * Initial push * Adding r documentation about mothur and clustur * Added functionality for column distance file reading! * Column distance files work! * Adding read column feature (#15) * Added reading of column files, but result arent correct. * Correct Column file * Column Reader works as expected! * Added test for column reading, and it all works as expected. * Fixed check issues * Squashed commit of the following: commit 45ba179f6b2e63687229c042be92a6f4cae2c786 Author: Gregory Johnson <[email protected]> Date: Thu Sep 26 18:17:22 2024 -0400 Consistent randomization (#18) * Have to fix test, but this is the basic framework for randomization * Squashed commit of the following: commit 3f2d3995c30894a457bd860379243aa5329f52cd Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:52:00 2024 -0400 Fixing check errors. commit 3f04170d4897e243a2a87847f39d8f4fe1307be0 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:43:06 2024 -0400 Removing unneeded data and fixing issue to validate count_table commit 2c642f300cf9fedb6ade3b46eab053c691c26f45 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:31:56 2024 -0400 Changed the name of the package to clustur commit 1251c3c63a7d6fca99ddf1373633e3281d0472e2 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 16:53:16 2024 -0400 Removing comments * Changes to the utils class to allow for randomization and added a seed to the functions * Adding another test * Fix for note * Randomization has been added and we changed the way we create sparse matrices! * Forgot to include the updated namesapce! commit 10c2ad9915d63dac5fee47d5385b91e711a8b16a Author: Gregory Johnson <[email protected]> Date: Thu Sep 26 18:15:33 2024 -0400 Consistent randomization (#17) * Have to fix test, but this is the basic framework for randomization * Squashed commit of the following: commit 3f2d3995c30894a457bd860379243aa5329f52cd Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:52:00 2024 -0400 Fixing check errors. commit 3f04170d4897e243a2a87847f39d8f4fe1307be0 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:43:06 2024 -0400 Removing unneeded data and fixing issue to validate count_table commit 2c642f300cf9fedb6ade3b46eab053c691c26f45 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:31:56 2024 -0400 Changed the name of the package to clustur commit 1251c3c63a7d6fca99ddf1373633e3281d0472e2 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 16:53:16 2024 -0400 Removing comments * Changes to the utils class to allow for randomization and added a seed to the functions * Adding another test * Fix for note * Randomization has been added and we changed the way we create sparse matrices! commit 3f2d3995c30894a457bd860379243aa5329f52cd Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:52:00 2024 -0400 Fixing check errors. commit 3f04170d4897e243a2a87847f39d8f4fe1307be0 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:43:06 2024 -0400 Removing unneeded data and fixing issue to validate count_table commit 2c642f300cf9fedb6ade3b46eab053c691c26f45 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:31:56 2024 -0400 Changed the name of the package to clustur commit 1251c3c63a7d6fca99ddf1373633e3281d0472e2 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 16:53:16 2024 -0400 Removing comments commit e87319e3bfdb1c1657fc399af778e1c6bd17fc37 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 12:04:03 2024 -0400 Fixing unit test commit 8c648bd5dce04613d5fb11b2f8133dda762d8507 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 11:51:15 2024 -0400 Small optimzation to clustur commit 05c8a0738991359f6ef9f69f3de180fd6173ee44 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 11:38:43 2024 -0400 Base structure of documentation and website commit 4a4fcfa4ed154804a9574323d1a56f76d958c24f Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 10:43:40 2024 -0400 Created base pkgdown structure commit a714b7d0a7c9390c30eb723d4135b980a052d387 Author: YoungKrug <[email protected]> Date: Tue Sep 24 23:01:44 2024 -0400 Creating vignettes commit 6a5df2035a1de3f206a1bcd9ddc0d4bb9b763a83 Author: YoungKrug <[email protected]> Date: Tue Sep 24 15:43:09 2024 -0400 Squashed commit of the following: commit dfd9b2d83c4ab60a95b1585995482ac176fc1114 Author: YoungKrug <[email protected]> Date: Tue Sep 24 15:42:56 2024 -0400 Big error in readPhylip matrix. I was never checking whether the matrix was a square or not! commit 63d515ed9dac7370abd579ec1a3d9c3a69f589d2 Author: GregJohnsonJr <[email protected]> Date: Tue Sep 24 15:02:02 2024 -0400 Pushing spare_matrix data file commit 7eec4fbf6ba4b4c881d65cabf86eb9c4b344ca1b Author: GregJohnsonJr <[email protected]> Date: Tue Sep 24 14:43:12 2024 -0400 Pushing the temporary fix! commit 0b5a145cc3ee1db43d4c7472940568324f48cacf Author: YoungKrug <[email protected]> Date: Tue Sep 24 13:56:47 2024 -0400 Update Cluster.R commit 7c694e39687ccd62d63fbaa6f3d8713606f5b633 Author: YoungKrug <[email protected]> Date: Tue Sep 24 12:51:01 2024 -0400 Added inst folders commit 3cb0ba458c6fb35c963a4ee2b6000ee4137a6442 Author: YoungKrug <[email protected]> Date: Tue Sep 24 12:02:56 2024 -0400 Updating documentation commit 5af269d6bf15db5c96e1c6b676ad57a9b9793eeb Author: YoungKrug <[email protected]> Date: Mon Sep 23 19:45:19 2024 -0400 Pushing results for different operating systems commit a745510b856aa3259400c65a4566e98d61a643a8 Author: GregJohnsonJr <[email protected]> Date: Mon Sep 23 19:36:29 2024 -0400 Create 96_sq_column_results_mac.list commit d08a209b9ac4419e64313312497be6a83acd562f Author: YoungKrug <[email protected]> Date: Sat Sep 21 12:03:56 2024 -0400 Using content paths instead of absolutes commit 1623601703cf96bf75a0dd36ecee49c75b2084f9 Author: YoungKrug <[email protected]> Date: Sat Sep 21 09:49:11 2024 -0400 Method to check if each cluster exist in the dataframe commit 585736ef751b407d397925269788600c83521942 Author: YoungKrug <[email protected]> Date: Wed Sep 18 13:51:36 2024 -0400 Small change commit acfbc9a008e215a4822265d89a224ff9973a475f Author: YoungKrug <[email protected]> Date: Wed Sep 18 13:50:29 2024 -0400 Cleaning up test commit 60d16f54feff027ecdfa641ff99f65399781a1b3 Author: YoungKrug <[email protected]> Date: Wed Sep 18 13:49:41 2024 -0400 Updates to test file commit d89afb52f6e2daf8ab6491fbcadde43a96147914 Author: YoungKrug <[email protected]> Date: Wed Sep 18 13:47:32 2024 -0400 Modification to the test! commit d48660439a99d0352960e00eb060228fa6293c3f Author: GregJohnsonJr <[email protected]> Date: Wed Sep 18 13:21:11 2024 -0400 Added sorting by bin size to cluster output and fixed the clustering issue! commit 3bddc53b063b8439a0485cc31e3064f7082d7a2a Author: GregJohnsonJr <[email protected]> Date: Tue Sep 17 20:05:22 2024 -0400 Small changes commit 0d3e798422ff9d11e2bc0dee51d741263f6d2a9b Author: GregJohnsonJr <[email protected]> Date: Tue Sep 17 15:20:47 2024 -0400 Testing values to RMD file commit 58a7e8e612730f991c10e17f5629120899a71caf Author: GregJohnsonJr <[email protected]> Date: Tue Sep 17 13:55:31 2024 -0400 Fix for test error commit 4c63f8ca1fe110d484914c0663a12bac7273240b Author: GregJohnsonJr <[email protected]> Date: Tue Sep 17 13:06:52 2024 -0400 example data commit 48a0f38462b12e3cc1ca4c3c2b11c7d672643f61 Author: GregJohnsonJr <[email protected]> Date: Mon Sep 16 19:21:22 2024 -0400 I am getting the same number of bins! commit 37cdb7e40373f455f3497f019d80d1baace40762 Author: GregJohnsonJr <[email protected]> Date: Mon Sep 16 17:29:51 2024 -0400 Fixing up the documentation commit d7dc2948ca5adc2f7033348492549d277db2e3c4 Author: GregJohnsonJr <[email protected]> Date: Mon Sep 16 16:43:10 2024 -0400 Fix for opticluster clustering. commit 3d8015fe6918bc3c36047abe0551596f51927726 Author: Gregory Johnson <[email protected]> Date: Mon Sep 16 15:01:11 2024 -0400 Adding read column feature (#15) * Added reading of column files, but result arent correct. * Correct Column file * Column Reader works as expected! * Added test for column reading, and it all works as expected. * Fixed check issues commit 6f830c6aa435260c84627946281b10f5a8d03353 Author: GregJohnsonJr <[email protected]> Date: Fri Sep 13 17:02:03 2024 -0400 Column distance files work! commit e6f00a816e9778b1dd4a8b9c1ec92818c93e3249 Author: GregJohnsonJr <[email protected]> Date: Fri Sep 13 12:38:20 2024 -0400 Added functionality for column distance file reading! commit 25a357dccce0f4d0b9e1ec198ced4f98a3653163 Author: GregJohnsonJr <[email protected]> Date: Thu Sep 12 17:37:58 2024 -0400 Adding r documentation about mothur and clustur commit fa25af7f600e7feb97aa97b963ec27ae6f0abdac Author: GregJohnsonJr <[email protected]> Date: Thu Sep 12 16:44:32 2024 -0400 Initial push * Removing old vignette * Adding additional documentation * Adding links (#22) * Moving RDS file * Small changes to test * Adding a vignette, fixed the test that were failing, and removed old data. * Small change to test * Pushing lintr fixes * Distance files to sparse matrix (#23) * Added the conversion from distance files (phylip, column) to sparse matrix. * Removing unneeded data and cleaning up files. * Unify clustering (#25) * added documentation * Check works on mac-os * Edit getting started vignette * Small changes to the test and removing unneeded data. --------- Co-authored-by: Pat Schloss <[email protected]> * Refactor package methods (#26) * Added functionality to determine if the file is a phylip or column and allowed for the creation of a distance matrix object in r. * Getters and Setters for distance processing work! * Created a abstract class to unify the column and phylip reader class. * Process Sparse Data aswell! * Added cluster functionality! * Created R function for the c++ functionality * Added the copy constructors and fixed issues with data not being maintained. * Added documentation, need to fix read sparse matrices * Added new functions and removed old functionality * Count table can now read sparse data files * added documentation to all of the functions and created new 'light-weight' test for the clustering test. Im using smaller csv's. . * Test work, just need to fix check errors! * Added new functionality, created test and examples for all of the functions and refactored the current siting test to be faster and use smaller csv files. * Removing DS_Store object from tracking * Updating git ignore * Forgot to include the queue header! * Linted the package * Small Change to examples * Added tests for the validate_count_table function * Removing R profile from tracking * Delete .Rprofile * Fix lintr and pkgdown issues * Fix for pkgdown and lintr * Change to test in cluster_object-getters. * Squashed commit of the following: commit 744dfb7bad358dd57303fec4dd492e5320a6a3a9 Author: Gregory Johnson <[email protected]> Date: Sun Oct 13 11:18:40 2024 -0400 Update check-full.yml Removed devel tag from github action commit dcb9b49b790155ecaef76ca142c2210c86b587a6 Author: Gregory Johnson <[email protected]> Date: Sun Oct 13 10:54:44 2024 -0400 Dev (#28) * Added unit test and created a easy opticluster function * Release v0.0.1 (#1) * Fixed the wrapper for Calling Opticluster! * Fixing the .RD file * Fixed issue where opticluster was returning a matrix array and not a data.frame. * Changing documentation * Fixing the warnings from building the code. * Update to the test * Updating the gitignore * Add cpp test (#3) * Added Cpp testing structure! * Added Test Fixture Class * Forced the cluster to only return OTU data, and created the fix test fixture with test! * Created all of the test for the optimatrix adapter and removed the .dll from being tracked! * Created all the test in the testfixture for listvectors and now I am adding them to the test files. * Created base test for listVector * Basic test for listVector are completed! * Created the basic structure and test fixture for cluster commands * Cluster Testing suite being pushed up! * Fix cluster algorithm (#2) * Fixed a slew of issues by adding bidirection distances. * Fixed the clustering issue, clustering should be working correctly now! * Generated Definitions for OptiCluster Test * Finished creating unit test of the cluster command and opticluster * Added OptiData test fixture * Started creating the unit test for utils * Utils command cluster and test work as expected!! * Removed old code from one of the testing suites. * Added another test in utils. * Clustor has a 89% test coverage! Everything should be tested and ready to merge back! * RMD Check is able to run successfully! * Correcting the paths of my cpp files, should fix the action errors. * Update to the cluster command test fixture * Modifying the test for opticluster * Ensuring everything works with c++11 * Removing code issues from cluster command * Adding the build ignore * Founds some issue where I am using c++ 17 syntax and not 11. * Github action fixes, needed to update syntax towards cpp 11 * Modified the testing structure by removing the "Opticluster returns proper stats". I appears it is returning incorrect data on different computer architectures. It is also not needed in the code. * Fix cluster unit test (#5) * This should be the fix for the failing cluster test. * Changed the test to look for equivalence rows instead of equal dataframes. Gives the same results, the only differences is that the cluster have different numbers. * Printing out the metrics after you perform a cluster and added a true/false condition for shuffling * Release polish (#6) * Added to build ignore and properly documented the new R code. * Unstable, have to fix the mismatch header situation, but was able to return a vector with all the metrics! * Cluster now returns test metrics and added test to support it. * Added a depends for lazy-loading and other R related issues. * More cluster features (#7) * Adding a single, complete, average, and weighted linkage algorithms * Adding cluster functions * Added the new clustering methods, but am getting issues when trying to format them. * Unstable cannot create proper phylip file with matrix data.. * More unstable code, but we are getting closer. The phylip file is correct for a small dataset * STABLE, the cluster does not fail and will actually cluster. However I am getting incorrect results. Will refactor the code to work. * All Clusters (Furthest, Nearest, average, and weighted) all work as they should! I just need to clean it up and add test! * Created R-facing function in R from cpp and cleaned up a bit of the code. * Cleaning up the main function * Small optimization to cluster (x2 speed_up) * Added optimization and cleaned up functions * Modifications to the namespace file and test! * Cluster works with windows now! * Fixing the round point error on windows and in R. It has something to do with the compilation of the objects...most likely it is related to the conversions of data. * Fixed the floating point issue, now I have to fix an issue where the cutoff amounts are decreasing. * Fixed the floating point issue! My adjust was not set! Now I need to figure out why the nearest algorithm is not returning any data. * Small code style changes * Cluster works as expected! Everything clusters. Now to add tests * Started adding more test for Clustor * Created Test fixtures for the new code * Completed the sparse distance matrix and read phylip test, need to fix some test errors. * Added test for phylip reader and matrix adapter. Adding the final test for rAbund now. * Added all the rAbund test, and the cluster feature should be working properly! * Adding include statements for windows and other operating systems, this should work as expected. RCMD check works. * The fix for github actions. * Change to the include file. * Removing srand from Utils, going to attempt to set seeds inside of R. * Fix for race condition issue. * Fix for RCMD check warnings * The fix for the windows version of RMD Check! * Adding dependency for time. * Make shared (#9) * Adding a count table variation * Update Makevars * Preparation to Create a Shared File for the clustering output. * Added a simple make shared functionality. It works without the group information. Count_table + list_file = shared_file * Small changes, going to need to modify the make shared code soon. * Modifying the way cluster result data is stored. * Add a datastructure for returning and generating cluster data. * Cluster export works for Traditional Cluster Methods * Progress on making a shared file without a group. Have to make test soon. * Created a pseudo shared file successfully! * Changes to the abundance output * Delete F:\Opticluster\output_rabund.txt * Delete tests/testthat/F:\Opticluster\output_rabund.txt Removing werid paths. * Some example data and count table creation * Pushing lots of temp test files, and small changes * Adding the count table! * Count table structure has been created * Shared File with count tables and without work! * Count table can now be added to the cluster functions and will produce an output of abundance and clusters in dataframes. - Removed the exchanged of strings and read table between r and c++ and added a more modifiable approach. * Fixed test, now we have to add more test. * Fixes for linux and other computer architectures. * Removing dependencies that are not used. * Created test fixtures for unit test * Removed all of the negligent files that are not needed and added test to all of the new functions! --------- Co-authored-by: YoungKrug <[email protected]> * Forgot a unit test. (#10) * Fix results (#11) * Adding example data for mothur results. * Added support for similarity matrix functionality * Updates to phylip writing, and fixes to incorrect clustering! * Stable, Classic cluster and opticluster both are identical to that of mothur! + Names can be added * Results are the same as they are in mothur! * All the unit test work, and clustur prints out expected results! * Removing and fixing check issues. * Fix compilation warnings (#12) * No warnings on mac! * Still fixing clang-tidy errors. Lots of comparisons between longs and ints that will cause problems. * Half way done, modified a lot of deduced type conversions. May need to go back in the future to remove them. * Should fix all the warnings on linux and windows. * Pushing through more deduced type fixes. * Should be the final fix for linux. * Fix for negative index value * Cleaning up build notes. * lintr fixes * Fix for lintr * Read phylip files (#14) * Looking to add a function to replace the entry point. * Added support for phylip file reading! * Initial push * Adding r documentation about mothur and clustur * Added functionality for column distance file reading! * Column distance files work! * Adding read column feature (#15) * Added reading of column files, but result arent correct. * Correct Column file * Column Reader works as expected! * Added test for column reading, and it all works as expected. * Fixed check issues * Documentation (#16) * Initial push * Adding r documentation about mothur and clustur * Added functionality for column distance file reading! * Column distance files work! * Adding read column feature (#15) * Added reading of column files, but result arent correct. * Correct Column file * Column Reader works as expected! * Added test for column reading, and it all works as expected. * Fixed check issues * Fix for opticluster clustering. * Fixing up the documentation * I am getting the same number of bins! * example data * Fix for test error * Testing values to RMD file * Small changes * Added sorting by bin size to cluster output and fixed the clustering issue! * Modification to the test! * Updates to test file * Cleaning up test * Small change * Method to check if each cluster exist in the dataframe * Using content paths instead of absolutes * Create 96_sq_column_results_mac.list * Pushing results for different operating systems * Updating documentation * Added inst folders * Update Cluster.R * Pushing the temporary fix! * Pushing spare_matrix data file * Squashed commit of the following: commit dfd9b2d83c4ab60a95b1585995482ac176fc1114 Author: YoungKrug <[email protected]> Date: Tue Sep 24 15:42:56 2024 -0400 Big error in readPhylip matrix. I was never checking whether the matrix was a square or not! * Creating vignettes * Created base pkgdown structure * Base structure of documentation and website * Small optimzation to clustur * Fixing unit test * Removing comments * Changed the name of the package to clustur * Removing unneeded data and fixing issue to validate count_table * Fixing check errors. * Consistent randomization (#17) * Have to fix test, but this is the basic framework for randomization * Squashed commit of the following: commit 3f2d3995c30894a457bd860379243aa5329f52cd Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:52:00 2024 -0400 Fixing check errors. commit 3f04170d4897e243a2a87847f39d8f4fe1307be0 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:43:06 2024 -0400 Removing unneeded data and fixing issue to validate count_table commit 2c642f300cf9fedb6ade3b46eab053c691c26f45 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:31:56 2024 -0400 Changed the name of the package to clustur commit 1251c3c63a7d6fca99ddf1373633e3281d0472e2 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 16:53:16 2024 -0400 Removing comments * Changes to the utils class to allow for randomization and added a seed to the functions * Adding another test * Fix for note * Randomization has been added and we changed the way we create sparse matrices! * Consistent randomization (#18) * Have to fix test, but this is the basic framework for randomization * Squashed commit of the following: commit 3f2d3995c30894a457bd860379243aa5329f52cd Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:52:00 2024 -0400 Fixing check errors. commit 3f04170d4897e243a2a87847f39d8f4fe1307be0 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:43:06 2024 -0400 Removing unneeded data and fixing issue to validate count_table commit 2c642f300cf9fedb6ade3b46eab053c691c26f45 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:31:56 2024 -0400 Changed the name of the package to clustur commit 1251c3c63a7d6fca99ddf1373633e3281d0472e2 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 16:53:16 2024 -0400 Removing comments * Changes to the utils class to allow for randomization and added a seed to the functions * Adding another test * Fix for note * Randomization has been added and we changed the way we create sparse matrices! * Forgot to include the updated namesapce! * Squashed commit of the following: commit 45ba179f6b2e63687229c042be92a6f4cae2c786 Author: Gregory Johnson <[email protected]> Date: Thu Sep 26 18:17:22 2024 -0400 Consistent randomization (#18) * Have to fix test, but this is the basic framework for randomization * Squashed commit of the following: commit 3f2d3995c30894a457bd860379243aa5329f52cd Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:52:00 2024 -0400 Fixing check errors. commit 3f04170d4897e243a2a87847f39d8f4fe1307be0 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:43:06 2024 -0400 Removing unneeded data and fixing issue to validate count_table commit 2c642f300cf9fedb6ade3b46eab053c691c26f45 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:31:56 2024 -0400 Changed the name of the package to clustur commit 1251c3c63a7d6fca99ddf1373633e3281d0472e2 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 16:53:16 2024 -0400 Removing comments * Changes to the utils class to allow for randomization and added a seed to the functions * Adding another test * Fix for note * Randomization has been added and we changed the way we create sparse matrices! * Forgot to include the updated namesapce! commit 10c2ad9915d63dac5fee47d5385b91e711a8b16a Author: Gregory Johnson <[email protected]> Date: Thu Sep 26 18:15:33 2024 -0400 Consistent randomization (#17) * Have to fix test, but this is the basic framework for randomization * Squashed commit of the following: commit 3f2d3995c30894a457bd860379243aa5329f52cd Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:52:00 2024 -0400 Fixing check errors. commit 3f04170d4897e243a2a87847f39d8f4fe1307be0 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:43:06 2024 -0400 Removing unneeded data and fixing issue to validate count_table commit 2c642f300cf9fedb6ade3b46eab053c691c26f45 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:31:56 2024 -0400 Changed the name of the package to clustur commit 1251c3c63a7d6fca99ddf1373633e3281d0472e2 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 16:53:16 2024 -0400 Removing comments * Changes to the utils class to allow for randomization and added a seed to the functions * Adding another test * Fix for note * Randomization has been added and we changed the way we create sparse matrices! commit 3f2d3995c30894a457bd860379243aa5329f52cd Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:52:00 2024 -0400 Fixing check errors. commit 3f04170d4897e243a2a87847f39d8f4fe1307be0 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:43:06 2024 -0400 Removing unneeded data and fixing issue to validate count_table commit 2c642f300cf9fedb6ade3b46eab053c691c26f45 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:31:56 2024 -0400 Changed the name of the package to clustur commit 1251c3c63a7d6fca99ddf1373633e3281d0472e2 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 16:53:16 2024 -0400 Removing comments commit e87319e3bfdb1c1657fc399af778e1c6bd17fc37 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 12:04:03 2024 -0400 Fixing unit test commit 8c648bd5dce04613d5fb11b2f8133dda762d8507 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 11:51:15 2024 -0400 Small optimzation to clustur commit 05c8a0738991359f6ef9f69f3de180fd6173ee44 Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 11:38:43 2024 -0400 Base structure of documentation and website commit 4a4fcfa4ed154804a9574323d1a56f76d958c24f Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 10:43:40 2024 -0400 Created base pkgdown structure commit a714b7d0a7c9390c30eb723d4135b980a052d387 Author: YoungKrug <[email protected]> Date: Tue Sep 24 23:01:44 2024 -0400 Creating vignettes commit 6a5df2035a1de3f206a1bcd9ddc0d4bb9b763a83 Author: YoungKrug <[email protected]> Date: Tue Sep 24 15:43:09 2024 -0400 Squashed commit of the following: commit dfd9b2d83c4ab60a95b1585995482ac176fc1114 Author: YoungKrug <[email protected]> Date: Tue Sep 24 15:42:56 2024 -0400 Big error in readPhylip matrix. I was never checking whether the matrix was a square or not! commit 63d515ed9dac7370abd579ec1a3d9c3a69f589d2 Author: GregJohnsonJr <[email protected]> Date: Tue Sep 24 15:02:02 2024 -0400 Pushing spare_matrix data file commit 7eec4fbf6ba4b4c881d65cabf86eb9c4b344ca1b Author: GregJohnsonJr <[email protected]> Date: Tue Sep 24 14:43:12 2024 -0400 Pushing the temporary fix! commit 0b5a145cc3ee1db43d4c7472940568324f48cacf Author: YoungKrug <[email protected]> Date: Tue Sep 24 13:56:47 2024 -0400 Update Cluster.R commit 7c694e39687ccd62d63fbaa6f3d8713606f5b633 Author: YoungKrug <[email protected]> Date: Tue Sep 24 12:51:01 2024 -0400 Added inst folders commit 3cb0ba458c6fb35c963a4ee2b6000ee4137a6442 Author: YoungKrug <[email protected]> Date: Tue Sep 24 12:02:56 2024 -0400 Updating documentation commit 5af269d6bf15db5c96e1c6b676ad57a9b9793eeb Author: YoungKrug <[email protected]> Date: Mon Sep 23 19:45:19 2024 -0400 Pushing results for different operating systems commit a745510b856aa3259400c65a4566e98d61a643a8 Author: GregJohnsonJr <[email protected]> Date: Mon Sep 23 19:36:29 2024 -0400 Create 96_sq_column_results_mac.list commit d08a209b9ac4419e64313312497be6a83acd562f Author: YoungKrug <[email protected]> Date: Sat Sep 21 12:03:56 2024 -0400 Using content paths instead of absolutes commit 1623601703cf96bf75a0dd36ecee49c75b2084f9 Author: YoungKrug <[email protected]> Date: Sat Sep 21 09:49:11 2024 -0400 Method to check if each cluster exist in the dataframe commit 585736ef751b407d397925269788600c83521942 Author: YoungKrug <[email protected]> Date: Wed Sep 18 13:51:36 2024 -0400 Small change commit acfbc9a008e215a4822265d89a224ff9973a475f Author: YoungKrug <[email protected]> Date: Wed Sep 18 13:50:29 2024 -0400 Cleaning up test commit 60d16f54feff027ecdfa641ff99f65399781a1b3 Author: YoungKrug <[email protected]> Date: Wed Sep 18 13:49:41 2024 -0400 Updates to test file commit d89afb52f6e2daf8ab6491fbcadde43a96147914 Author: YoungKrug <[email protected]> Date: Wed Sep 18 13:47:32 2024 -0400 Modification to the test! commit d48660439a99d0352960e00eb060228fa6293c3f Author: GregJohnsonJr <[email protected]> Date: Wed Sep 18 13:21:11 2024 -0400 Added sorting by bin size to cluster output and fixed the clustering issue! commit 3bddc53b063b8439a0485cc31e3064f7082d7a2a Author: GregJohnsonJr <[email protected]> Date: Tue Sep 17 20:05:22 2024 -0400 Small changes commit 0d3e798422ff9d11e2bc0dee51d741263f6d2a9b Author: GregJohnsonJr <[email protected]> Date: Tue Sep 17 15:20:47 2024 -0400 Testing values to RMD file commit 58a7e8e612730f991c10e17f5629120899a71caf Author: GregJohnsonJr <[email protected]> Date: Tue Sep 17 13:55:31 2024 -0400 Fix for test error commit 4c63f8ca1fe110d484914c0663a12bac7273240b Author: GregJohnsonJr <[email protected]> Date: Tue Sep 17 13:06:52 2024 -0400 example data commit 48a0f38462b12e3cc1ca4c3c2b11c7d672643f61 Author: GregJohnsonJr <[email protected]> Date: Mon Sep 16 19:21:22 2024 -0400 I am getting the same number of bins! commit 37cdb7e40373f455f3497f019d80d1baace40762 Author: GregJohnsonJr <[email protected]> Date: Mon Sep 16 17:29:51 2024 -0400 Fixing up the documentation commit d7dc2948ca5adc2f7033348492549d277db2e3c4 Author: GregJohnsonJr <[email protected]> Date: Mon Sep 16 16:43:10 2024 -0400 Fix for opticluster clustering. commit 3d8015fe6918bc3c36047abe0551596f51927726 Author: Gregory Johnson <[email protected]> Date: Mon Sep 16 15:01:11 2024 -0400 Adding read column feature (#15) * Added reading of column files, but result arent correct. * Correct Column file * Column Reader works as expected! * Added test for column reading, and it all works as expected. * Fixed check issues commit 6f830c6aa435260c84627946281b10f5a8d03353 Author: GregJohnsonJr <[email protected]> Date: Fri Sep 13 17:02:03 2024 -0400 Column distance files work! commit e6f00a816e9778b1dd4a8b9c1ec92818c93e3249 Author: GregJohnsonJr <[email protected]> Date: Fri Sep 13 12:38:20 2024 -0400 Added functionality for column distance file reading! commit 25a357dccce0f4d0b9e1ec198ced4f98a3653163 Author: GregJohnsonJr <[email protected]> Date: Thu Sep 12 17:37:58 2024 -0400 Adding r documentation about mothur and clustur commit fa25af7f600e7feb97aa97b963ec27ae6f0abdac Author: GregJohnsonJr <[email protected]> Date: Thu Sep 12 16:44:32 2024 -0400 Initial push * Documentation (#16) (#19) (#20) * Documentation (#16) * Initial push * Adding r documentation about mothur and clustur * Added functionality for column distance file reading! * Column distance files work! * Adding read column feature (#15) * Added reading of column files, but result arent correct. * Correct Column file * Column Reader works as expected! * Added test for column reading, and it all works as expected. * Fixed check issues * Squashed commit of the following: commit 45ba179f6b2e63687229c042be92a6f4cae2c786 Author: Gregory Johnson <[email protected]> Date: Thu Sep 26 18:17:22 2024 -0400 Consistent randomization (#18) * Have to fix test, but this is the basic framework for randomization * Squashed commit of the following: commit 3f2d3995c30894a457bd860379243aa5329f52cd Author: GregJohnsonJr <[email protected]> Date: Wed Sep 25 17:52:00 2024 -0400 Fixing check errors. commit 3f04170d4897e243a2a87847f39d8f4fe13…
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Optimized memory usage by about 1000% 60gb -> 5-8gbs, and optimized speed by 400%. We also removed zombie code and other pieces of code that are not needed.