Squashed commit of the following:

commit 8ad307cd6c55690b556d76f720192e76bc70e81c
Author: GregJohnsonJr <[email protected]>
Date:   Mon Oct 14 15:28:36 2024 -0400

    removing data files

commit 3d7cddb9fd310878f026445f8bd928fc9a1f5ddb
Author: GregJohnsonJr <[email protected]>
Date:   Mon Oct 14 13:28:36 2024 -0400

    Fix for reading column and phylip files.

commit 8e509d96120f84c2208e3283ece44d1a7ef461ce
Author: Gregory Johnson <[email protected]>
Date:   Sun Oct 13 22:24:57 2024 -0400

    Sync branches (#29)

    * 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.

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        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.

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    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

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    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
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    Date:   Tue Sep 24 23:01:44 2024 -0400

        Creating vignettes

    commit 6a5df2035a1de3f206a1bcd9ddc0d4bb9b763a83
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    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

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        Pushing the temporary fix!

    commit 0b5a145cc3ee1db43d4c7472940568324f48cacf
    Author: YoungKrug <[email protected]>
    Date:   Tue Sep 24 13:56:47 2024 -0400

        Update Cluster.R

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    Date:   Tue Sep 24 12:51:01 2024 -0400

        Added inst folders

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    Date:   Tue Sep 24 12:02:56 2024 -0400

        Updating documentation

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    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

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    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

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    Author: YoungKrug <[email protected]>
    Date:   Wed Sep 18 13:51:36 2024 -0400

        Small change

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    Date:   Wed Sep 18 13:50:29 2024 -0400

        Cleaning up test

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    Date:   Wed Sep 18 13:49:41 2024 -0400

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    Date:   Wed Sep 18 13:47:32 2024 -0400

        Modification to the test!

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    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!

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    Date:   Tue Sep 17 20:05:22 2024 -0400

        Small changes

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        Testing values to RMD file

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    Date:   Tue Sep 17 13:55:31 2024 -0400

        Fix for test error

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    Date:   Tue Sep 17 13:06:52 2024 -0400

        example data

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    Date:   Mon Sep 16 19:21:22 2024 -0400

        I am getting the same number of bins!

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    Date:   Mon Sep 16 17:29:51 2024 -0400

        Fixing up the documentation

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    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!

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    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:

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    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:

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        Author: GregJohnsonJr <[email protected]>
        Date:   Wed Sep 25 17:52:00 2024 -0400

            Fixing check errors.

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        Date:   Wed Sep 25 17:43:06 2024 -0400

            Removing unneeded data and fixing issue to validate count_table

        commit 2c642f300cf9fedb6ade3b46eab053c691c26f45
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        Date:   Wed Sep 25 17:31:56 2024 -0400

            Changed the name of the package to clustur

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        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
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    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:

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        Author: GregJohnsonJr <[email protected]>
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            Fixing check errors.

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        Date:   Wed Sep 25 17:43:06 2024 -0400

            Removing unneeded data and fixing issue to validate count_table

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        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.

    ---------

    Co-authored-by: YoungKrug <[email protected]>
    Co-authored-by: Pat Schloss <[email protected]>

    * Update check-full.yml

    Removed devel tag from github action

    ---------

    Co-authored-by: YoungKrug <[email protected]>
    Co-authored-by: Pat Schloss <[email protected]>

commit 4a5b787ac4c78ac7dcbca4da79766ec2407ebde1
Author: YoungKrug <[email protected]>
Date:   Sun Oct 13 22:23:57 2024 -0400

    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 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…

.Rbuildignore

@@ -5,3 +5,11 @@
 ^cmake-build-release$
 ^CMakeLists\.txt$
 ^\.idea$
+^doc$
+^Meta$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^vignettes/articles$
+^\.vscode$
+^\.lintr$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/lintr.yml

@@ -1,11 +1,18 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
     branches: [main, master]
   pull_request:
     branches: [main, master]
+  workflow_dispatch:
+  schedule: [{cron: '0 4 * * 1'}]
+  # run every monday at 4 am.
 
 name: lint
 
+permissions: read-all
+
 jobs:
   lint:
     runs-on: ubuntu-latest
@@ -20,14 +27,11 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: |
-            any::cyclocomp
-            r-lib/lintr
-            local::.
+          extra-packages: any::lintr, local::.
           needs: lint
 
       - name: Lint
         run: lintr::lint_package()
         shell: Rscript {0}
         env:
-          LINTR_ERROR_ON_LINT: true
+          LINTR_ERROR_ON_LINT: true

.github/workflows/pkgdown.yaml

@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yml

@@ -38,7 +38,7 @@ jobs:
           covr::to_cobertura(cov)
         shell: Rscript {0}
 
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v3
         with:
           fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
           file: ./cobertura.xml

.gitignore

@@ -193,3 +193,15 @@ fabric.properties
 .idea
 src/.DS_Store
 /.vscode
+inst/doc
+/doc/
+/Meta/
+docs
+
+#R Profile files
+.Rprofile
+
+
+# DS Store files
+
+.DS_Store

.lintr

@@ -0,0 +1,5 @@
+linters: linters_with_defaults() # see vignette("lintr")
+encoding: "UTF-8"
+exclusions: list(
+    "vignettes/clustur.Rmd"
+  )

DESCRIPTION

@@ -1,4 +1,4 @@
-Package: Opticluster
+Package: clustur
 Type: Package
 Title: What the Package Does in One 'Title Case' Line
 Version: 1.0
@@ -8,13 +8,20 @@ Maintainer: Gregory Johnson <[email protected]>
 Description: One paragraph description of what the package does as one
         or more full sentences.
 License: GPL (>= 2)
-Imports: Rcpp (>= 1.0.12)
+Imports: 
+    Matrix,
+    Rcpp (>= 1.0.12),
+    utils
 Depends:
     R (>= 3.5.0)
 LinkingTo: Rcpp,
     testthat
 Suggests: 
+    knitr,
+    rmarkdown,
     testthat (>= 3.0.0),
     xml2
 Config/testthat/edition: 3
 RoxygenNote: 7.3.1
+VignetteBuilder: knitr
+URL: http://www.schlosslab.org/Clustur/

NAMESPACE

@@ -1,5 +1,17 @@
-useDynLib(Opticluster, .registration=TRUE)
-importFrom(Rcpp, evalCpp)
-importFrom("utils", "read.table")
+# Generated by roxygen2: do not edit by hand
+
 export(cluster)
-export(opti_cluster)
+export(example_path)
+export(get_clusters)
+export(get_count_table)
+export(get_cutoff)
+export(get_distance_data_frame)
+export(get_metrics)
+export(get_shared)
+export(read_count)
+export(read_dist)
+export(validate_count_table)
+importFrom(Matrix,spMatrix)
+importFrom(Rcpp,evalCpp)
+importFrom(utils,read.delim)
+useDynLib(clustur)