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* 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
* 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!
…roper stats". I appears it is returning incorrect data on different computer architectures. It is also not needed in the code.
* 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.
…/false condition for shuffling
* 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.
* 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.
* 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 <31873199+YoungKrug@users.noreply.github.com>
* 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!
commit dfd9b2d Author: YoungKrug <gregjohn456@gmail.com> 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!
* Have to fix test, but this is the basic framework for randomization * Squashed commit of the following: commit 3f2d399 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 17:52:00 2024 -0400 Fixing check errors. commit 3f04170 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 17:43:06 2024 -0400 Removing unneeded data and fixing issue to validate count_table commit 2c642f3 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 17:31:56 2024 -0400 Changed the name of the package to clustur commit 1251c3c Author: GregJohnsonJr <gregjohn456@gmail.com> 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!
* Have to fix test, but this is the basic framework for randomization * Squashed commit of the following: commit 3f2d399 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 17:52:00 2024 -0400 Fixing check errors. commit 3f04170 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 17:43:06 2024 -0400 Removing unneeded data and fixing issue to validate count_table commit 2c642f3 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 17:31:56 2024 -0400 Changed the name of the package to clustur commit 1251c3c Author: GregJohnsonJr <gregjohn456@gmail.com> 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 45ba179 Author: Gregory Johnson <31873199+GregJohnsonJr@users.noreply.github.com> 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 3f2d399 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 17:52:00 2024 -0400 Fixing check errors. commit 3f04170 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 17:43:06 2024 -0400 Removing unneeded data and fixing issue to validate count_table commit 2c642f3 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 17:31:56 2024 -0400 Changed the name of the package to clustur commit 1251c3c Author: GregJohnsonJr <gregjohn456@gmail.com> 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 10c2ad9 Author: Gregory Johnson <31873199+GregJohnsonJr@users.noreply.github.com> 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 3f2d399 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 17:52:00 2024 -0400 Fixing check errors. commit 3f04170 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 17:43:06 2024 -0400 Removing unneeded data and fixing issue to validate count_table commit 2c642f3 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 17:31:56 2024 -0400 Changed the name of the package to clustur commit 1251c3c Author: GregJohnsonJr <gregjohn456@gmail.com> 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 3f2d399 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 17:52:00 2024 -0400 Fixing check errors. commit 3f04170 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 17:43:06 2024 -0400 Removing unneeded data and fixing issue to validate count_table commit 2c642f3 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 17:31:56 2024 -0400 Changed the name of the package to clustur commit 1251c3c Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 16:53:16 2024 -0400 Removing comments commit e87319e Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 12:04:03 2024 -0400 Fixing unit test commit 8c648bd Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 11:51:15 2024 -0400 Small optimzation to clustur commit 05c8a07 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 11:38:43 2024 -0400 Base structure of documentation and website commit 4a4fcfa Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 10:43:40 2024 -0400 Created base pkgdown structure commit a714b7d Author: YoungKrug <gregjohn456@gmail.com> Date: Tue Sep 24 23:01:44 2024 -0400 Creating vignettes commit 6a5df20 Author: YoungKrug <gregjohn456@gmail.com> Date: Tue Sep 24 15:43:09 2024 -0400 Squashed commit of the following: commit dfd9b2d Author: YoungKrug <gregjohn456@gmail.com> 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 63d515e Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Tue Sep 24 15:02:02 2024 -0400 Pushing spare_matrix data file commit 7eec4fb Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Tue Sep 24 14:43:12 2024 -0400 Pushing the temporary fix! commit 0b5a145 Author: YoungKrug <gregjohn456@gmail.com> Date: Tue Sep 24 13:56:47 2024 -0400 Update Cluster.R commit 7c694e3 Author: YoungKrug <gregjohn456@gmail.com> Date: Tue Sep 24 12:51:01 2024 -0400 Added inst folders commit 3cb0ba4 Author: YoungKrug <gregjohn456@gmail.com> Date: Tue Sep 24 12:02:56 2024 -0400 Updating documentation commit 5af269d Author: YoungKrug <gregjohn456@gmail.com> Date: Mon Sep 23 19:45:19 2024 -0400 Pushing results for different operating systems commit a745510 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Mon Sep 23 19:36:29 2024 -0400 Create 96_sq_column_results_mac.list commit d08a209 Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com> Date: Sat Sep 21 12:03:56 2024 -0400 Using content paths instead of absolutes commit 1623601 Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com> Date: Sat Sep 21 09:49:11 2024 -0400 Method to check if each cluster exist in the dataframe commit 585736e Author: YoungKrug <gregjohn456@gmail.com> Date: Wed Sep 18 13:51:36 2024 -0400 Small change commit acfbc9a Author: YoungKrug <gregjohn456@gmail.com> Date: Wed Sep 18 13:50:29 2024 -0400 Cleaning up test commit 60d16f5 Author: YoungKrug <gregjohn456@gmail.com> Date: Wed Sep 18 13:49:41 2024 -0400 Updates to test file commit d89afb5 Author: YoungKrug <gregjohn456@gmail.com> Date: Wed Sep 18 13:47:32 2024 -0400 Modification to the test! commit d486604 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 18 13:21:11 2024 -0400 Added sorting by bin size to cluster output and fixed the clustering issue! commit 3bddc53 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Tue Sep 17 20:05:22 2024 -0400 Small changes commit 0d3e798 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Tue Sep 17 15:20:47 2024 -0400 Testing values to RMD file commit 58a7e8e Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Tue Sep 17 13:55:31 2024 -0400 Fix for test error commit 4c63f8c Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Tue Sep 17 13:06:52 2024 -0400 example data commit 48a0f38 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Mon Sep 16 19:21:22 2024 -0400 I am getting the same number of bins! commit 37cdb7e Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Mon Sep 16 17:29:51 2024 -0400 Fixing up the documentation commit d7dc294 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Mon Sep 16 16:43:10 2024 -0400 Fix for opticluster clustering. commit 3d8015f Author: Gregory Johnson <31873199+GregJohnsonJr@users.noreply.github.com> 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 6f830c6 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Fri Sep 13 17:02:03 2024 -0400 Column distance files work! commit e6f00a8 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Fri Sep 13 12:38:20 2024 -0400 Added functionality for column distance file reading! commit 25a357d Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Thu Sep 12 17:37:58 2024 -0400 Adding r documentation about mothur and clustur commit fa25af7 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Thu Sep 12 16:44:32 2024 -0400 Initial push
* 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 45ba179 Author: Gregory Johnson <31873199+GregJohnsonJr@users.noreply.github.com> 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 3f2d399 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 17:52:00 2024 -0400 Fixing check errors. commit 3f04170 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 17:43:06 2024 -0400 Removing unneeded data and fixing issue to validate count_table commit 2c642f3 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 17:31:56 2024 -0400 Changed the name of the package to clustur commit 1251c3c Author: GregJohnsonJr <gregjohn456@gmail.com> 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 10c2ad9 Author: Gregory Johnson <31873199+GregJohnsonJr@users.noreply.github.com> 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 3f2d399 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 17:52:00 2024 -0400 Fixing check errors. commit 3f04170 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 17:43:06 2024 -0400 Removing unneeded data and fixing issue to validate count_table commit 2c642f3 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 17:31:56 2024 -0400 Changed the name of the package to clustur commit 1251c3c Author: GregJohnsonJr <gregjohn456@gmail.com> 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 3f2d399 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 17:52:00 2024 -0400 Fixing check errors. commit 3f04170 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 17:43:06 2024 -0400 Removing unneeded data and fixing issue to validate count_table commit 2c642f3 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 17:31:56 2024 -0400 Changed the name of the package to clustur commit 1251c3c Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 16:53:16 2024 -0400 Removing comments commit e87319e Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 12:04:03 2024 -0400 Fixing unit test commit 8c648bd Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 11:51:15 2024 -0400 Small optimzation to clustur commit 05c8a07 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 11:38:43 2024 -0400 Base structure of documentation and website commit 4a4fcfa Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 25 10:43:40 2024 -0400 Created base pkgdown structure commit a714b7d Author: YoungKrug <gregjohn456@gmail.com> Date: Tue Sep 24 23:01:44 2024 -0400 Creating vignettes commit 6a5df20 Author: YoungKrug <gregjohn456@gmail.com> Date: Tue Sep 24 15:43:09 2024 -0400 Squashed commit of the following: commit dfd9b2d Author: YoungKrug <gregjohn456@gmail.com> 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 63d515e Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Tue Sep 24 15:02:02 2024 -0400 Pushing spare_matrix data file commit 7eec4fb Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Tue Sep 24 14:43:12 2024 -0400 Pushing the temporary fix! commit 0b5a145 Author: YoungKrug <gregjohn456@gmail.com> Date: Tue Sep 24 13:56:47 2024 -0400 Update Cluster.R commit 7c694e3 Author: YoungKrug <gregjohn456@gmail.com> Date: Tue Sep 24 12:51:01 2024 -0400 Added inst folders commit 3cb0ba4 Author: YoungKrug <gregjohn456@gmail.com> Date: Tue Sep 24 12:02:56 2024 -0400 Updating documentation commit 5af269d Author: YoungKrug <gregjohn456@gmail.com> Date: Mon Sep 23 19:45:19 2024 -0400 Pushing results for different operating systems commit a745510 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Mon Sep 23 19:36:29 2024 -0400 Create 96_sq_column_results_mac.list commit d08a209 Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com> Date: Sat Sep 21 12:03:56 2024 -0400 Using content paths instead of absolutes commit 1623601 Author: YoungKrug <31873199+YoungKrug@users.noreply.github.com> Date: Sat Sep 21 09:49:11 2024 -0400 Method to check if each cluster exist in the dataframe commit 585736e Author: YoungKrug <gregjohn456@gmail.com> Date: Wed Sep 18 13:51:36 2024 -0400 Small change commit acfbc9a Author: YoungKrug <gregjohn456@gmail.com> Date: Wed Sep 18 13:50:29 2024 -0400 Cleaning up test commit 60d16f5 Author: YoungKrug <gregjohn456@gmail.com> Date: Wed Sep 18 13:49:41 2024 -0400 Updates to test file commit d89afb5 Author: YoungKrug <gregjohn456@gmail.com> Date: Wed Sep 18 13:47:32 2024 -0400 Modification to the test! commit d486604 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Wed Sep 18 13:21:11 2024 -0400 Added sorting by bin size to cluster output and fixed the clustering issue! commit 3bddc53 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Tue Sep 17 20:05:22 2024 -0400 Small changes commit 0d3e798 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Tue Sep 17 15:20:47 2024 -0400 Testing values to RMD file commit 58a7e8e Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Tue Sep 17 13:55:31 2024 -0400 Fix for test error commit 4c63f8c Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Tue Sep 17 13:06:52 2024 -0400 example data commit 48a0f38 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Mon Sep 16 19:21:22 2024 -0400 I am getting the same number of bins! commit 37cdb7e Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Mon Sep 16 17:29:51 2024 -0400 Fixing up the documentation commit d7dc294 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Mon Sep 16 16:43:10 2024 -0400 Fix for opticluster clustering. commit 3d8015f Author: Gregory Johnson <31873199+GregJohnsonJr@users.noreply.github.com> 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 6f830c6 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Fri Sep 13 17:02:03 2024 -0400 Column distance files work! commit e6f00a8 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Fri Sep 13 12:38:20 2024 -0400 Added functionality for column distance file reading! commit 25a357d Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Thu Sep 12 17:37:58 2024 -0400 Adding r documentation about mothur and clustur commit fa25af7 Author: GregJohnsonJr <gregjohn456@gmail.com> Date: Thu Sep 12 16:44:32 2024 -0400 Initial push
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We will merge this, the only issue is related to the lintr. It does not like explicit returns, but that is apart of our coding standards. |
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Everything including the site should be added, we will need to add the pkgdown GitHub stuff to create the actual site.