From e20b9b59dc4b766d09e8415d7978fd59cfd42912 Mon Sep 17 00:00:00 2001 From: sdgamboa <53412049+sdgamboa@users.noreply.github.com> Date: Tue, 2 Apr 2024 19:06:33 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20waldronl?= =?UTF-8?q?ab/taxPPro@4ffb7087c0277cc439703d8aa228672165e695d0=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- 404.html | 2 +- articles/add_singletons.html | 6 ++-- articles/figure_example.html | 10 +++--- articles/index.html | 2 +- articles/internal_nodes.html | 6 ++-- articles/nsti.html | 10 +++--- .../figure-html/unnamed-chunk-5-1.png | Bin 19631 -> 20712 bytes .../figure-html/unnamed-chunk-6-1.png | Bin 19173 -> 20569 bytes articles/smaller_example.html | 8 ++--- articles/taxPPro.html | 8 ++--- articles/uncertainty_binary.html | 6 ++-- articles/uncertainty_multistate.html | 6 ++-- authors.html | 12 +++---- index.html | 13 ++++---- pkgdown.yml | 2 +- reference/addRankPrefix.html | 2 +- reference/classif2Table.html | 2 +- reference/completeBinaryData.html | 2 +- reference/conf2Fct.html | 2 +- reference/filterData.html | 10 +++--- reference/filterDataDiscrete.html | 14 +++++--- reference/filterDataNumeric.html | 18 +++++------ reference/freq2Scores.html | 2 +- reference/getDataReady.html | 2 +- reference/getNsti.html | 4 +-- reference/getSetWithIDs.html | 2 +- reference/getSetWithoutIDs.html | 2 +- reference/index.html | 30 ++---------------- reference/ltp.html | 2 +- reference/roundDec.html | 2 +- reference/scores2Freq.html | 2 +- sitemap.xml | 24 -------------- 32 files changed, 85 insertions(+), 128 deletions(-) diff --git a/404.html b/404.html index e1b27a5..5a53dad 100644 --- a/404.html +++ b/404.html @@ -32,7 +32,7 @@ taxPPro - 0.1.0 + 0.99.0 diff --git a/articles/add_singletons.html b/articles/add_singletons.html index 26f55a3..10e4793 100644 --- a/articles/add_singletons.html +++ b/articles/add_singletons.html @@ -33,7 +33,7 @@ taxPPro - 0.1.0 + 0.99.0 @@ -236,13 +236,13 @@

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Session info#> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Etc/UTC -#> date 2024-03-26 +#> date 2024-04-02 #> pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> ape * 5.7-1 2023-03-13 [1] RSPM (R 4.3.0) #> aplot 0.2.2 2023-10-06 [1] RSPM (R 4.3.0) -#> bslib 0.6.2 2024-03-22 [1] RSPM (R 4.3.0) +#> bslib 0.7.0 2024-03-29 [1] RSPM (R 4.3.0) #> cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0) #> castor * 1.8.0 2024-01-09 [1] RSPM (R 4.3.0) #> cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0) @@ -268,7 +268,7 @@

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Session information#> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Etc/UTC -#> date 2024-03-26 +#> date 2024-04-02 #> pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> ape * 5.7-1 2023-03-13 [1] RSPM (R 4.3.0) -#> bslib 0.6.2 2024-03-22 [1] RSPM (R 4.3.0) +#> bslib 0.7.0 2024-03-29 [1] RSPM (R 4.3.0) #> cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0) #> cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0) #> clusterGeneration 1.3.8 2023-08-16 [1] RSPM (R 4.3.0) diff --git a/articles/nsti.html b/articles/nsti.html index 108bd5f..000b557 100644 --- a/articles/nsti.html +++ b/articles/nsti.html @@ -33,7 +33,7 @@ taxPPro - 0.1.0 + 0.99.0 @@ -167,13 +167,13 @@

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Session info#> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Etc/UTC -#> date 2024-03-26 +#> date 2024-04-02 #> pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── @@ -473,7 +473,7 @@

Session info#> aplot 0.2.2 2023-10-06 [1] RSPM (R 4.3.0) #> backports 1.4.1 2021-12-13 [1] RSPM (R 4.3.0) #> broom 1.0.5 2023-06-09 [1] RSPM (R 4.3.0) -#> bslib 0.6.2 2024-03-22 [1] RSPM (R 4.3.0) +#> bslib 0.7.0 2024-03-29 [1] RSPM (R 4.3.0) #> cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0) #> car 3.1-2 2023-03-30 [1] RSPM (R 4.3.0) #> carData 3.0-5 2022-01-06 [1] RSPM (R 4.3.0) @@ -525,7 +525,7 @@

Session info#> Matrix 1.6-1.1 2023-09-18 [2] CRAN (R 4.3.2) #> memoise 2.0.1 2021-11-26 [1] RSPM (R 4.3.0) #> mnormt 2.1.1 2022-09-26 [1] RSPM (R 4.3.0) -#> munsell 0.5.0 2018-06-12 [1] RSPM (R 4.3.0) +#> munsell 0.5.1 2024-04-01 [1] RSPM (R 4.3.0) #> nlme 3.1-163 2023-08-09 [2] CRAN (R 4.3.2) #> numDeriv 2016.8-1.1 2019-06-06 [1] RSPM (R 4.3.0) #> optimParallel 1.0-2 2021-02-11 [1] RSPM (R 4.3.0) diff --git a/articles/taxPPro.html b/articles/taxPPro.html index cab6490..5bde97c 100644 --- a/articles/taxPPro.html +++ b/articles/taxPPro.html @@ -33,7 +33,7 @@ taxPPro - 0.1.0 + 0.99.0 @@ -141,13 +141,13 @@

Session information#> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Etc/UTC -#> date 2024-03-26 +#> date 2024-04-02 #> pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> ape 5.7-1 2023-03-13 [1] RSPM (R 4.3.0) -#> bslib 0.6.2 2024-03-22 [1] RSPM (R 4.3.0) +#> bslib 0.7.0 2024-03-29 [1] RSPM (R 4.3.0) #> cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0) #> cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0) #> data.tree * 1.1.0 2023-11-12 [1] RSPM (R 4.3.0) @@ -182,7 +182,7 @@

Session information#> sessioninfo 1.2.2 2021-12-06 [1] RSPM (R 4.3.0) #> stringi 1.8.3 2023-12-11 [1] RSPM (R 4.3.0) #> systemfonts 1.0.5 2023-10-09 [1] RSPM (R 4.3.0) -#> taxPPro * 0.1.0 2024-03-26 [1] local +#> taxPPro * 0.99.0 2024-04-02 [1] local #> textshaping 0.3.7 2023-10-09 [1] RSPM (R 4.3.0) #> tibble 3.2.1 2023-03-20 [1] RSPM (R 4.3.0) #> tidyselect 1.2.1 2024-03-11 [1] RSPM (R 4.3.0) diff --git a/articles/uncertainty_binary.html b/articles/uncertainty_binary.html index 63362cd..ed99fc7 100644 --- a/articles/uncertainty_binary.html +++ b/articles/uncertainty_binary.html @@ -33,7 +33,7 @@ taxPPro - 0.1.0 + 0.99.0 @@ -228,13 +228,13 @@

Session information#> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Etc/UTC -#> date 2024-03-26 +#> date 2024-04-02 #> pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> ape * 5.7-1 2023-03-13 [1] RSPM (R 4.3.0) -#> bslib 0.6.2 2024-03-22 [1] RSPM (R 4.3.0) +#> bslib 0.7.0 2024-03-29 [1] RSPM (R 4.3.0) #> cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0) #> cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0) #> clusterGeneration 1.3.8 2023-08-16 [1] RSPM (R 4.3.0) diff --git a/articles/uncertainty_multistate.html b/articles/uncertainty_multistate.html index c07933b..195cd01 100644 --- a/articles/uncertainty_multistate.html +++ b/articles/uncertainty_multistate.html @@ -33,7 +33,7 @@ taxPPro - 0.1.0 + 0.99.0 @@ -234,13 +234,13 @@

Session information#> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Etc/UTC -#> date 2024-03-26 +#> date 2024-04-02 #> pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> ape * 5.7-1 2023-03-13 [1] RSPM (R 4.3.0) -#> bslib 0.6.2 2024-03-22 [1] RSPM (R 4.3.0) +#> bslib 0.7.0 2024-03-29 [1] RSPM (R 4.3.0) #> cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0) #> cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0) #> clusterGeneration 1.3.8 2023-08-16 [1] RSPM (R 4.3.0) diff --git a/authors.html b/authors.html index b22ae87..f880e35 100644 --- a/authors.html +++ b/authors.html @@ -17,7 +17,7 @@ taxPPro - 0.1.0 + 0.99.0 @@ -77,7 +77,7 @@

Authors

  • -

    Samuel Gamboa. Maintainer. +

    Samuel Gamboa. Author, maintainer.

@@ -90,14 +90,14 @@

Citation

Gamboa S (2024). -taxPPro: Taxonomic and phylogenetic propagation. -R package version 0.1.0, https://github.com/sdgamboa/taxPPro. +taxPPro: Taxonomic and phylogenetic propagation for bugphyzz. +R package version 0.99.0, https://github.com/sdgamboa/taxPPro. 

@Manual{,
-  title = {taxPPro: Taxonomic and phylogenetic propagation},
+  title = {taxPPro: Taxonomic and phylogenetic propagation for bugphyzz},
   author = {Samuel Gamboa},
   year = {2024},
-  note = {R package version 0.1.0},
+  note = {R package version 0.99.0},
   url = {https://github.com/sdgamboa/taxPPro},
 }
diff --git a/index.html b/index.html index 673aa20..a6fa100 100644 --- a/index.html +++ b/index.html @@ -5,14 +5,14 @@ -Taxonomic and phylogenetic propagation • taxPPro +Taxonomic and phylogenetic propagation for bugphyzz • taxPPro - - + + Filter data — filterData • taxPProFilter data — filterData • taxPPro @@ -17,7 +18,7 @@ taxPPro - 0.1.0 + 0.99.0 @@ -77,7 +78,8 @@

Filter data

-

filterData

+

filterData is the first step in the propagation process. +It ensures that only data that can be used for propagation is retained.

@@ -94,7 +96,7 @@

Arguments

Value

-

A data.frame

+

A data.frame.

diff --git a/reference/filterDataDiscrete.html b/reference/filterDataDiscrete.html index b445a96..f5026eb 100644 --- a/reference/filterDataDiscrete.html +++ b/reference/filterDataDiscrete.html @@ -1,5 +1,7 @@ -Filter attributes with discrete type — filterDataDiscrete • taxPProFilter data with discrete attributes — filterDataDiscrete • taxPPro @@ -17,7 +19,7 @@ taxPPro - 0.1.0 + 0.99.0 @@ -71,13 +73,15 @@
-

Filter attributes with discrete type

+

Filter data with discrete attributes

Source: R/taxPPro.R
-

filterDataDiscrete filters discrete data.

+

filterDataDiscrete filters data that could be used for propagation +of discrete attributes. It also creates a Scores column based on +the Frequency column.

@@ -87,7 +91,7 @@

Filter attributes with discrete type

Arguments

tbl
-

A data.frame.

+

A data.frame imported with bugphyzz::physiologies

diff --git a/reference/filterDataNumeric.html b/reference/filterDataNumeric.html index ec698ad..e10cae3 100644 --- a/reference/filterDataNumeric.html +++ b/reference/filterDataNumeric.html @@ -1,8 +1,8 @@ -Filter data of numeric attributes — filterDataNumeric • taxPProFilter data with numeric attributes — filterDataNumeric • taxPPro @@ -20,7 +20,7 @@ taxPPro - 0.1.0 + 0.99.0
@@ -74,16 +74,16 @@
-

Filter data of numeric attributes

+

Filter data with numeric attributes

Source: R/taxPPro.R

filterDataNumeric filters data that could be used for propagation -of numeric attributes. Attribute type is numeric because all numeric -attributes are converted to range when they're imported with the physiologies -function.

+of numeric attributes. These are labeled as "range" when being imported +with the physiologies function. It also creates a Score column +based on the Frequency column.

diff --git a/reference/freq2Scores.html b/reference/freq2Scores.html index cfcb533..3d52cc9 100644 --- a/reference/freq2Scores.html +++ b/reference/freq2Scores.html @@ -19,7 +19,7 @@ taxPPro - 0.1.0 + 0.99.0
diff --git a/reference/getDataReady.html b/reference/getDataReady.html index 1bcea43..21a551f 100644 --- a/reference/getDataReady.html +++ b/reference/getDataReady.html @@ -17,7 +17,7 @@ taxPPro - 0.1.0 + 0.99.0
diff --git a/reference/getNsti.html b/reference/getNsti.html index 9ad30f4..8176748 100644 --- a/reference/getNsti.html +++ b/reference/getNsti.html @@ -19,7 +19,7 @@ taxPPro - 0.1.0 + 0.99.0
@@ -74,7 +74,7 @@

Get NSTI

- Source: R/utils.R + Source: R/trees.R
diff --git a/reference/getSetWithIDs.html b/reference/getSetWithIDs.html index d2cc09e..ddfe6e6 100644 --- a/reference/getSetWithIDs.html +++ b/reference/getSetWithIDs.html @@ -17,7 +17,7 @@ taxPPro - 0.1.0 + 0.99.0
diff --git a/reference/getSetWithoutIDs.html b/reference/getSetWithoutIDs.html index bb0f872..c9a9c82 100644 --- a/reference/getSetWithoutIDs.html +++ b/reference/getSetWithoutIDs.html @@ -17,7 +17,7 @@ taxPPro - 0.1.0 + 0.99.0
diff --git a/reference/index.html b/reference/index.html index f018583..1667cd3 100644 --- a/reference/index.html +++ b/reference/index.html @@ -17,7 +17,7 @@ taxPPro - 0.1.0 + 0.99.0
@@ -86,10 +86,6 @@

All functions classif2Table()

Taxize classification to data frame

- -

cleanNode()

- -

Clean node

completeBinaryData()

@@ -105,11 +101,11 @@

All functions

filterDataDiscrete()

-

Filter attributes with discrete type

+

Filter data with discrete attributes

filterDataNumeric()

-

Filter data of numeric attributes

+

Filter data with numeric attributes

freq2Scores()

@@ -118,10 +114,6 @@

All functions getDataReady()

Get data ready for propagation

- -

getMRCATaxPPro()

- -

Get Most Recent Common Ancestor

getNsti()

@@ -134,22 +126,10 @@

All functions getSetWithoutIDs()

Get set without IDs

- -

inh1()

- -

Inheritance first round

- -

inh2()

- -

Inheritance second round

ltp()

Get living tree project (LTP) tree and data

- -

mpa()

- -

Get metphlan tree or data v31

roundDec()

@@ -158,10 +138,6 @@

All functions scores2Freq()

Scores to frequency

- -

taxPool()

- -

Perform taxonomic pooling

diff --git a/reference/roundDec.html b/reference/roundDec.html index 1ec2bdd..ee401d2 100644 --- a/reference/roundDec.html +++ b/reference/roundDec.html @@ -18,7 +18,7 @@ taxPPro - 0.1.0 + 0.99.0 diff --git a/reference/scores2Freq.html b/reference/scores2Freq.html index 91caba9..ea5a09a 100644 --- a/reference/scores2Freq.html +++ b/reference/scores2Freq.html @@ -18,7 +18,7 @@ taxPPro - 0.1.0 + 0.99.0 diff --git a/sitemap.xml b/sitemap.xml index 26b5f6f..a286ffe 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -3,12 +3,6 @@ https://waldronlab.io/taxPPro/404.html - - https://waldronlab.io/taxPPro/LICENSE-text.html - - - https://waldronlab.io/taxPPro/LICENSE.html - https://waldronlab.io/taxPPro/articles/add_singletons.html @@ -48,9 +42,6 @@ https://waldronlab.io/taxPPro/reference/classif2Table.html - - https://waldronlab.io/taxPPro/reference/cleanNode.html - https://waldronlab.io/taxPPro/reference/completeBinaryData.html @@ -72,9 +63,6 @@ https://waldronlab.io/taxPPro/reference/getDataReady.html - - https://waldronlab.io/taxPPro/reference/getMRCATaxPPro.html - https://waldronlab.io/taxPPro/reference/getNsti.html @@ -87,25 +75,13 @@ https://waldronlab.io/taxPPro/reference/index.html - - https://waldronlab.io/taxPPro/reference/inh1.html - - - https://waldronlab.io/taxPPro/reference/inh2.html - https://waldronlab.io/taxPPro/reference/ltp.html - - https://waldronlab.io/taxPPro/reference/mpa.html - https://waldronlab.io/taxPPro/reference/roundDec.html https://waldronlab.io/taxPPro/reference/scores2Freq.html - - https://waldronlab.io/taxPPro/reference/taxPool.html -