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SchlossLab / clustur

Cluster algorithms from mothur in R
http://www.schlosslab.org/clustur/
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Documentation (#16) (#19) #20

Closed GregJohnsonJr closed 1 month ago

GregJohnsonJr commented 1 month ago

commit 45ba179f6b2e63687229c042be92a6f4cae2c786 Author: Gregory Johnson 31873199+GregJohnsonJr@users.noreply.github.com Date: Thu Sep 26 18:17:22 2024 -0400

Consistent randomization (#18)

* Have to fix test, but this is the basic framework for randomization

* Squashed commit of the following:

commit 3f2d3995c30894a457bd860379243aa5329f52cd
Author: GregJohnsonJr <gregjohn456@gmail.com>
Date:   Wed Sep 25 17:52:00 2024 -0400

    Fixing check errors.

commit 3f04170d4897e243a2a87847f39d8f4fe1307be0
Author: GregJohnsonJr <gregjohn456@gmail.com>
Date:   Wed Sep 25 17:43:06 2024 -0400

    Removing unneeded data and fixing issue to validate count_table

commit 2c642f300cf9fedb6ade3b46eab053c691c26f45
Author: GregJohnsonJr <gregjohn456@gmail.com>
Date:   Wed Sep 25 17:31:56 2024 -0400

    Changed the name of the package to clustur

commit 1251c3c63a7d6fca99ddf1373633e3281d0472e2
Author: GregJohnsonJr <gregjohn456@gmail.com>
Date:   Wed Sep 25 16:53:16 2024 -0400

    Removing comments

* Changes to the utils class to allow for randomization and added a seed to the functions

* Adding another test

* Fix for note

* Randomization has been added and we changed the way we create sparse matrices!

* Forgot to include the updated namesapce!

commit 10c2ad9915d63dac5fee47d5385b91e711a8b16a Author: Gregory Johnson 31873199+GregJohnsonJr@users.noreply.github.com Date: Thu Sep 26 18:15:33 2024 -0400

Consistent randomization (#17)

* Have to fix test, but this is the basic framework for randomization

* Squashed commit of the following:

commit 3f2d3995c30894a457bd860379243aa5329f52cd
Author: GregJohnsonJr <gregjohn456@gmail.com>
Date:   Wed Sep 25 17:52:00 2024 -0400

    Fixing check errors.

commit 3f04170d4897e243a2a87847f39d8f4fe1307be0
Author: GregJohnsonJr <gregjohn456@gmail.com>
Date:   Wed Sep 25 17:43:06 2024 -0400

    Removing unneeded data and fixing issue to validate count_table

commit 2c642f300cf9fedb6ade3b46eab053c691c26f45
Author: GregJohnsonJr <gregjohn456@gmail.com>
Date:   Wed Sep 25 17:31:56 2024 -0400

    Changed the name of the package to clustur

commit 1251c3c63a7d6fca99ddf1373633e3281d0472e2
Author: GregJohnsonJr <gregjohn456@gmail.com>
Date:   Wed Sep 25 16:53:16 2024 -0400

    Removing comments

* Changes to the utils class to allow for randomization and added a seed to the functions

* Adding another test

* Fix for note

* Randomization has been added and we changed the way we create sparse matrices!

commit 3f2d3995c30894a457bd860379243aa5329f52cd Author: GregJohnsonJr gregjohn456@gmail.com Date: Wed Sep 25 17:52:00 2024 -0400

Fixing check errors.

commit 3f04170d4897e243a2a87847f39d8f4fe1307be0 Author: GregJohnsonJr gregjohn456@gmail.com Date: Wed Sep 25 17:43:06 2024 -0400

Removing unneeded data and fixing issue to validate count_table

commit 2c642f300cf9fedb6ade3b46eab053c691c26f45 Author: GregJohnsonJr gregjohn456@gmail.com Date: Wed Sep 25 17:31:56 2024 -0400

Changed the name of the package to clustur

commit 1251c3c63a7d6fca99ddf1373633e3281d0472e2 Author: GregJohnsonJr gregjohn456@gmail.com Date: Wed Sep 25 16:53:16 2024 -0400

Removing comments

commit e87319e3bfdb1c1657fc399af778e1c6bd17fc37 Author: GregJohnsonJr gregjohn456@gmail.com Date: Wed Sep 25 12:04:03 2024 -0400

Fixing unit test

commit 8c648bd5dce04613d5fb11b2f8133dda762d8507 Author: GregJohnsonJr gregjohn456@gmail.com Date: Wed Sep 25 11:51:15 2024 -0400

Small optimzation to clustur

commit 05c8a0738991359f6ef9f69f3de180fd6173ee44 Author: GregJohnsonJr gregjohn456@gmail.com Date: Wed Sep 25 11:38:43 2024 -0400

Base structure of documentation and website

commit 4a4fcfa4ed154804a9574323d1a56f76d958c24f Author: GregJohnsonJr gregjohn456@gmail.com Date: Wed Sep 25 10:43:40 2024 -0400

Created base pkgdown structure

commit a714b7d0a7c9390c30eb723d4135b980a052d387 Author: YoungKrug gregjohn456@gmail.com Date: Tue Sep 24 23:01:44 2024 -0400

Creating vignettes

commit 6a5df2035a1de3f206a1bcd9ddc0d4bb9b763a83 Author: YoungKrug gregjohn456@gmail.com Date: Tue Sep 24 15:43:09 2024 -0400

Squashed commit of the following:

commit dfd9b2d83c4ab60a95b1585995482ac176fc1114
Author: YoungKrug <gregjohn456@gmail.com>
Date:   Tue Sep 24 15:42:56 2024 -0400

    Big error in readPhylip matrix. I was never checking whether the matrix was a square or not!

commit 63d515ed9dac7370abd579ec1a3d9c3a69f589d2 Author: GregJohnsonJr gregjohn456@gmail.com Date: Tue Sep 24 15:02:02 2024 -0400

Pushing spare_matrix data file

commit 7eec4fbf6ba4b4c881d65cabf86eb9c4b344ca1b Author: GregJohnsonJr gregjohn456@gmail.com Date: Tue Sep 24 14:43:12 2024 -0400

Pushing the temporary fix!

commit 0b5a145cc3ee1db43d4c7472940568324f48cacf Author: YoungKrug gregjohn456@gmail.com Date: Tue Sep 24 13:56:47 2024 -0400

Update Cluster.R

commit 7c694e39687ccd62d63fbaa6f3d8713606f5b633 Author: YoungKrug gregjohn456@gmail.com Date: Tue Sep 24 12:51:01 2024 -0400

Added inst folders

commit 3cb0ba458c6fb35c963a4ee2b6000ee4137a6442 Author: YoungKrug gregjohn456@gmail.com Date: Tue Sep 24 12:02:56 2024 -0400

Updating documentation

commit 5af269d6bf15db5c96e1c6b676ad57a9b9793eeb Author: YoungKrug gregjohn456@gmail.com Date: Mon Sep 23 19:45:19 2024 -0400

Pushing results for different operating systems

commit a745510b856aa3259400c65a4566e98d61a643a8 Author: GregJohnsonJr gregjohn456@gmail.com Date: Mon Sep 23 19:36:29 2024 -0400

Create 96_sq_column_results_mac.list

commit d08a209b9ac4419e64313312497be6a83acd562f Author: YoungKrug 31873199+YoungKrug@users.noreply.github.com Date: Sat Sep 21 12:03:56 2024 -0400

Using content paths instead of absolutes

commit 1623601703cf96bf75a0dd36ecee49c75b2084f9 Author: YoungKrug 31873199+YoungKrug@users.noreply.github.com Date: Sat Sep 21 09:49:11 2024 -0400

Method to check if each cluster exist in the dataframe

commit 585736ef751b407d397925269788600c83521942 Author: YoungKrug gregjohn456@gmail.com Date: Wed Sep 18 13:51:36 2024 -0400

Small change

commit acfbc9a008e215a4822265d89a224ff9973a475f Author: YoungKrug gregjohn456@gmail.com Date: Wed Sep 18 13:50:29 2024 -0400

Cleaning up test

commit 60d16f54feff027ecdfa641ff99f65399781a1b3 Author: YoungKrug gregjohn456@gmail.com Date: Wed Sep 18 13:49:41 2024 -0400

Updates to test file

commit d89afb52f6e2daf8ab6491fbcadde43a96147914 Author: YoungKrug gregjohn456@gmail.com Date: Wed Sep 18 13:47:32 2024 -0400

Modification to the test!

commit d48660439a99d0352960e00eb060228fa6293c3f Author: GregJohnsonJr gregjohn456@gmail.com Date: Wed Sep 18 13:21:11 2024 -0400

Added sorting by bin size to cluster output and fixed the clustering issue!

commit 3bddc53b063b8439a0485cc31e3064f7082d7a2a Author: GregJohnsonJr gregjohn456@gmail.com Date: Tue Sep 17 20:05:22 2024 -0400

Small changes

commit 0d3e798422ff9d11e2bc0dee51d741263f6d2a9b Author: GregJohnsonJr gregjohn456@gmail.com Date: Tue Sep 17 15:20:47 2024 -0400

Testing values to RMD file

commit 58a7e8e612730f991c10e17f5629120899a71caf Author: GregJohnsonJr gregjohn456@gmail.com Date: Tue Sep 17 13:55:31 2024 -0400

Fix for test error

commit 4c63f8ca1fe110d484914c0663a12bac7273240b Author: GregJohnsonJr gregjohn456@gmail.com Date: Tue Sep 17 13:06:52 2024 -0400

example data

commit 48a0f38462b12e3cc1ca4c3c2b11c7d672643f61 Author: GregJohnsonJr gregjohn456@gmail.com Date: Mon Sep 16 19:21:22 2024 -0400

I am getting the same number of bins!

commit 37cdb7e40373f455f3497f019d80d1baace40762 Author: GregJohnsonJr gregjohn456@gmail.com Date: Mon Sep 16 17:29:51 2024 -0400

Fixing up the documentation

commit d7dc2948ca5adc2f7033348492549d277db2e3c4 Author: GregJohnsonJr gregjohn456@gmail.com Date: Mon Sep 16 16:43:10 2024 -0400

Fix for opticluster clustering.

commit 3d8015fe6918bc3c36047abe0551596f51927726 Author: Gregory Johnson 31873199+GregJohnsonJr@users.noreply.github.com Date: Mon Sep 16 15:01:11 2024 -0400

Adding read column feature (#15)

* Added reading of column files, but result arent correct.

* Correct Column file

* Column Reader works as expected!

* Added test for column reading, and it all works as expected.

* Fixed check issues

commit 6f830c6aa435260c84627946281b10f5a8d03353 Author: GregJohnsonJr gregjohn456@gmail.com Date: Fri Sep 13 17:02:03 2024 -0400

Column distance files work!

commit e6f00a816e9778b1dd4a8b9c1ec92818c93e3249 Author: GregJohnsonJr gregjohn456@gmail.com Date: Fri Sep 13 12:38:20 2024 -0400

Added functionality for column distance file reading!

commit 25a357dccce0f4d0b9e1ec198ced4f98a3653163 Author: GregJohnsonJr gregjohn456@gmail.com Date: Thu Sep 12 17:37:58 2024 -0400

Adding r documentation about mothur and clustur

commit fa25af7f600e7feb97aa97b963ec27ae6f0abdac Author: GregJohnsonJr gregjohn456@gmail.com Date: Thu Sep 12 16:44:32 2024 -0400

Initial push
GregJohnsonJr commented 1 month ago

Merged the wrong branch ahah