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 dfd9b2d
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 3f2d399
Author: GregJohnsonJr <[email protected]>
Date:   Wed Sep 25 17:52:00 2024 -0400

    Fixing check errors.

commit 3f04170
Author: GregJohnsonJr <[email protected]>
Date:   Wed Sep 25 17:43:06 2024 -0400

    Removing unneeded data and fixing issue to validate count_table

commit 2c642f3
Author: GregJohnsonJr <[email protected]>
Date:   Wed Sep 25 17:31:56 2024 -0400

    Changed the name of the package to clustur

commit 1251c3c
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 3f2d399
Author: GregJohnsonJr <[email protected]>
Date:   Wed Sep 25 17:52:00 2024 -0400

    Fixing check errors.

commit 3f04170
Author: GregJohnsonJr <[email protected]>
Date:   Wed Sep 25 17:43:06 2024 -0400

    Removing unneeded data and fixing issue to validate count_table

commit 2c642f3
Author: GregJohnsonJr <[email protected]>
Date:   Wed Sep 25 17:31:56 2024 -0400

    Changed the name of the package to clustur

commit 1251c3c
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 45ba179
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 3f2d399
    Author: GregJohnsonJr <[email protected]>
    Date:   Wed Sep 25 17:52:00 2024 -0400

        Fixing check errors.

    commit 3f04170
    Author: GregJohnsonJr <[email protected]>
    Date:   Wed Sep 25 17:43:06 2024 -0400

        Removing unneeded data and fixing issue to validate count_table

    commit 2c642f3
    Author: GregJohnsonJr <[email protected]>
    Date:   Wed Sep 25 17:31:56 2024 -0400

        Changed the name of the package to clustur

    commit 1251c3c
    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 10c2ad9
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 3f2d399
    Author: GregJohnsonJr <[email protected]>
    Date:   Wed Sep 25 17:52:00 2024 -0400

        Fixing check errors.

    commit 3f04170
    Author: GregJohnsonJr <[email protected]>
    Date:   Wed Sep 25 17:43:06 2024 -0400

        Removing unneeded data and fixing issue to validate count_table

    commit 2c642f3
    Author: GregJohnsonJr <[email protected]>
    Date:   Wed Sep 25 17:31:56 2024 -0400

        Changed the name of the package to clustur

    commit 1251c3c
    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 3f2d399
Author: GregJohnsonJr <[email protected]>
Date:   Wed Sep 25 17:52:00 2024 -0400

    Fixing check errors.

commit 3f04170
Author: GregJohnsonJr <[email protected]>
Date:   Wed Sep 25 17:43:06 2024 -0400

    Removing unneeded data and fixing issue to validate count_table

commit 2c642f3
Author: GregJohnsonJr <[email protected]>
Date:   Wed Sep 25 17:31:56 2024 -0400

    Changed the name of the package to clustur

commit 1251c3c
Author: GregJohnsonJr <[email protected]>
Date:   Wed Sep 25 16:53:16 2024 -0400

    Removing comments

commit e87319e
Author: GregJohnsonJr <[email protected]>
Date:   Wed Sep 25 12:04:03 2024 -0400

    Fixing unit test

commit 8c648bd
Author: GregJohnsonJr <[email protected]>
Date:   Wed Sep 25 11:51:15 2024 -0400

    Small optimzation to clustur

commit 05c8a07
Author: GregJohnsonJr <[email protected]>
Date:   Wed Sep 25 11:38:43 2024 -0400

    Base structure of documentation and website

commit 4a4fcfa
Author: GregJohnsonJr <[email protected]>
Date:   Wed Sep 25 10:43:40 2024 -0400

    Created base pkgdown structure

commit a714b7d
Author: YoungKrug <[email protected]>
Date:   Tue Sep 24 23:01:44 2024 -0400

    Creating vignettes

commit 6a5df20
Author: YoungKrug <[email protected]>
Date:   Tue Sep 24 15:43:09 2024 -0400

    Squashed commit of the following:

    commit dfd9b2d
    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 63d515e
Author: GregJohnsonJr <[email protected]>
Date:   Tue Sep 24 15:02:02 2024 -0400

    Pushing spare_matrix data file

commit 7eec4fb
Author: GregJohnsonJr <[email protected]>
Date:   Tue Sep 24 14:43:12 2024 -0400

    Pushing the temporary fix!

commit 0b5a145
Author: YoungKrug <[email protected]>
Date:   Tue Sep 24 13:56:47 2024 -0400

    Update Cluster.R

commit 7c694e3
Author: YoungKrug <[email protected]>
Date:   Tue Sep 24 12:51:01 2024 -0400

    Added inst folders

commit 3cb0ba4
Author: YoungKrug <[email protected]>
Date:   Tue Sep 24 12:02:56 2024 -0400

    Updating documentation

commit 5af269d
Author: YoungKrug <[email protected]>
Date:   Mon Sep 23 19:45:19 2024 -0400

    Pushing results for different operating systems

commit a745510
Author: GregJohnsonJr <[email protected]>
Date:   Mon Sep 23 19:36:29 2024 -0400

    Create 96_sq_column_results_mac.list

commit d08a209
Author: YoungKrug <[email protected]>
Date:   Sat Sep 21 12:03:56 2024 -0400

    Using content paths instead of absolutes

commit 1623601
Author: YoungKrug <[email protected]>
Date:   Sat Sep 21 09:49:11 2024 -0400

    Method to check if each cluster exist in the dataframe

commit 585736e
Author: YoungKrug <[email protected]>
Date:   Wed Sep 18 13:51:36 2024 -0400

    Small change

commit acfbc9a
Author: YoungKrug <[email protected]>
Date:   Wed Sep 18 13:50:29 2024 -0400

    Cleaning up test

commit 60d16f5
Author: YoungKrug <[email protected]>
Date:   Wed Sep 18 13:49:41 2024 -0400

    Updates to test file

commit d89afb5
Author: YoungKrug <[email protected]>
Date:   Wed Sep 18 13:47:32 2024 -0400

    Modification to the test!

commit d486604
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 3bddc53
Author: GregJohnsonJr <[email protected]>
Date:   Tue Sep 17 20:05:22 2024 -0400

    Small changes

commit 0d3e798
Author: GregJohnsonJr <[email protected]>
Date:   Tue Sep 17 15:20:47 2024 -0400

    Testing values to RMD file

commit 58a7e8e
Author: GregJohnsonJr <[email protected]>
Date:   Tue Sep 17 13:55:31 2024 -0400

    Fix for test error

commit 4c63f8c
Author: GregJohnsonJr <[email protected]>
Date:   Tue Sep 17 13:06:52 2024 -0400

    example data

commit 48a0f38
Author: GregJohnsonJr <[email protected]>
Date:   Mon Sep 16 19:21:22 2024 -0400

    I am getting the same number of bins!

commit 37cdb7e
Author: GregJohnsonJr <[email protected]>
Date:   Mon Sep 16 17:29:51 2024 -0400

    Fixing up the documentation

commit d7dc294
Author: GregJohnsonJr <[email protected]>
Date:   Mon Sep 16 16:43:10 2024 -0400

    Fix for opticluster clustering.

commit 3d8015f
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 6f830c6
Author: GregJohnsonJr <[email protected]>
Date:   Fri Sep 13 17:02:03 2024 -0400

    Column distance files work!

commit e6f00a8
Author: GregJohnsonJr <[email protected]>
Date:   Fri Sep 13 12:38:20 2024 -0400

    Added functionality for column distance file reading!

commit 25a357d
Author: GregJohnsonJr <[email protected]>
Date:   Thu Sep 12 17:37:58 2024 -0400

    Adding r documentation about mothur and clustur

commit fa25af7
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 45ba179
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 3f2d399
    Author: GregJohnsonJr <[email protected]>
    Date:   Wed Sep 25 17:52:00 2024 -0400

        Fixing check errors.

    commit 3f04170
    Author: GregJohnsonJr <[email protected]>
    Date:   Wed Sep 25 17:43:06 2024 -0400

        Removing unneeded data and fixing issue to validate count_table

    commit 2c642f3
    Author: GregJohnsonJr <[email protected]>
    Date:   Wed Sep 25 17:31:56 2024 -0400

        Changed the name of the package to clustur

    commit 1251c3c
    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 10c2ad9
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 3f2d399
    Author: GregJohnsonJr <[email protected]>
    Date:   Wed Sep 25 17:52:00 2024 -0400

        Fixing check errors.

    commit 3f04170
    Author: GregJohnsonJr <[email protected]>
    Date:   Wed Sep 25 17:43:06 2024 -0400

        Removing unneeded data and fixing issue to validate count_table

    commit 2c642f3
    Author: GregJohnsonJr <[email protected]>
    Date:   Wed Sep 25 17:31:56 2024 -0400

        Changed the name of the package to clustur

    commit 1251c3c
    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 3f2d399
Author: GregJohnsonJr <[email protected]>
Date:   Wed Sep 25 17:52:00 2024 -0400

    Fixing check errors.

commit 3f04170
Author: GregJohnsonJr <[email protected]>
Date:   Wed Sep 25 17:43:06 2024 -0400

    Removing unneeded data and fixing issue to validate count_table

commit 2c642f3
Author: GregJohnsonJr <[email protected]>
Date:   Wed Sep 25 17:31:56 2024 -0400

    Changed the name of the package to clustur

commit 1251c3c
Author: GregJohnsonJr <[email protected]>
Date:   Wed Sep 25 16:53:16 2024 -0400

    Removing comments

commit e87319e
Author: GregJohnsonJr <[email protected]>
Date:   Wed Sep 25 12:04:03 2024 -0400

    Fixing unit test

commit 8c648bd
Author: GregJohnsonJr <[email protected]>
Date:   Wed Sep 25 11:51:15 2024 -0400

    Small optimzation to clustur

commit 05c8a07
Author: GregJohnsonJr <[email protected]>
Date:   Wed Sep 25 11:38:43 2024 -0400

    Base structure of documentation and website

commit 4a4fcfa
Author: GregJohnsonJr <[email protected]>
Date:   Wed Sep 25 10:43:40 2024 -0400

    Created base pkgdown structure

commit a714b7d
Author: YoungKrug <[email protected]>
Date:   Tue Sep 24 23:01:44 2024 -0400

    Creating vignettes

commit 6a5df20
Author: YoungKrug <[email protected]>
Date:   Tue Sep 24 15:43:09 2024 -0400

    Squashed commit of the following:

    commit dfd9b2d
    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 63d515e
Author: GregJohnsonJr <[email protected]>
Date:   Tue Sep 24 15:02:02 2024 -0400

    Pushing spare_matrix data file

commit 7eec4fb
Author: GregJohnsonJr <[email protected]>
Date:   Tue Sep 24 14:43:12 2024 -0400

    Pushing the temporary fix!

commit 0b5a145
Author: YoungKrug <[email protected]>
Date:   Tue Sep 24 13:56:47 2024 -0400

    Update Cluster.R

commit 7c694e3
Author: YoungKrug <[email protected]>
Date:   Tue Sep 24 12:51:01 2024 -0400

    Added inst folders

commit 3cb0ba4
Author: YoungKrug <[email protected]>
Date:   Tue Sep 24 12:02:56 2024 -0400

    Updating documentation

commit 5af269d
Author: YoungKrug <[email protected]>
Date:   Mon Sep 23 19:45:19 2024 -0400

    Pushing results for different operating systems

commit a745510
Author: GregJohnsonJr <[email protected]>
Date:   Mon Sep 23 19:36:29 2024 -0400

    Create 96_sq_column_results_mac.list

commit d08a209
Author: YoungKrug <[email protected]>
Date:   Sat Sep 21 12:03:56 2024 -0400

    Using content paths instead of absolutes

commit 1623601
Author: YoungKrug <[email protected]>
Date:   Sat Sep 21 09:49:11 2024 -0400

    Method to check if each cluster exist in the dataframe

commit 585736e
Author: YoungKrug <[email protected]>
Date:   Wed Sep 18 13:51:36 2024 -0400

    Small change

commit acfbc9a
Author: YoungKrug <[email protected]>
Date:   Wed Sep 18 13:50:29 2024 -0400

    Cleaning up test

commit 60d16f5
Author: YoungKrug <[email protected]>
Date:   Wed Sep 18 13:49:41 2024 -0400

    Updates to test file

commit d89afb5
Author: YoungKrug <[email protected]>
Date:   Wed Sep 18 13:47:32 2024 -0400

    Modification to the test!

commit d486604
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 3bddc53
Author: GregJohnsonJr <[email protected]>
Date:   Tue Sep 17 20:05:22 2024 -0400

    Small changes

commit 0d3e798
Author: GregJohnsonJr <[email protected]>
Date:   Tue Sep 17 15:20:47 2024 -0400

    Testing values to RMD file

commit 58a7e8e
Author: GregJohnsonJr <[email protected]>
Date:   Tue Sep 17 13:55:31 2024 -0400

    Fix for test error

commit 4c63f8c
Author: GregJohnsonJr <[email protected]>
Date:   Tue Sep 17 13:06:52 2024 -0400

    example data

commit 48a0f38
Author: GregJohnsonJr <[email protected]>
Date:   Mon Sep 16 19:21:22 2024 -0400

    I am getting the same number of bins!

commit 37cdb7e
Author: GregJohnsonJr <[email protected]>
Date:   Mon Sep 16 17:29:51 2024 -0400

    Fixing up the documentation

commit d7dc294
Author: GregJohnsonJr <[email protected]>
Date:   Mon Sep 16 16:43:10 2024 -0400

    Fix for opticluster clustering.

commit 3d8015f
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 6f830c6
Author: GregJohnsonJr <[email protected]>
Date:   Fri Sep 13 17:02:03 2024 -0400

    Column distance files work!

commit e6f00a8
Author: GregJohnsonJr <[email protected]>
Date:   Fri Sep 13 12:38:20 2024 -0400

    Added functionality for column distance file reading!

commit 25a357d
Author: GregJohnsonJr <[email protected]>
Date:   Thu Sep 12 17:37:58 2024 -0400

    Adding r documentation about mothur and clustur

commit fa25af7
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.

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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]>