diff --git a/404.html b/404.html index 2b538cf..7cd2172 100644 --- a/404.html +++ b/404.html @@ -18,7 +18,7 @@ - +
- +
@@ -121,16 +121,16 @@

Page not found (404)

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/articles/add_singletons.html b/articles/add_singletons.html index d36c98a..6254c9b 100644 --- a/articles/add_singletons.html +++ b/articles/add_singletons.html @@ -12,14 +12,13 @@ - - +
- +
@@ -102,7 +101,7 @@

add_singletons

- Source: vignettes/articles/add_singletons.Rmd + Source: vignettes/articles/add_singletons.Rmd
@@ -229,99 +228,97 @@

Session information
 sessioninfo::session_info()
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+ @@ -334,16 +331,16 @@

Session information

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/articles/figure_example.html b/articles/figure_example.html index 6bfec41..0f3a981 100644 --- a/articles/figure_example.html +++ b/articles/figure_example.html @@ -12,14 +12,13 @@ - - +
- +
@@ -102,7 +101,7 @@

Example numeric

- Source: vignettes/articles/figure_example.Rmd + Source: vignettes/articles/figure_example.Rmd
@@ -208,120 +207,119 @@

Session info
 sessioninfo::session_info()
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Session info

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Site built with pkgdown 2.0.9.

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Site built with pkgdown 2.1.0.

- - + + diff --git a/articles/index.html b/articles/index.html index c52a1db..b840b33 100644 --- a/articles/index.html +++ b/articles/index.html @@ -3,7 +3,7 @@ - +
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@@ -107,15 +107,15 @@

All vignettes

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Site built with pkgdown 2.0.9.

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Site built with pkgdown 2.1.0.

- - + + diff --git a/articles/internal_nodes.html b/articles/internal_nodes.html index b48cf6a..5ffe4a4 100644 --- a/articles/internal_nodes.html +++ b/articles/internal_nodes.html @@ -12,14 +12,13 @@ - - +
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@@ -102,7 +101,7 @@

internal_nodes

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@@ -349,99 +348,97 @@

Session information
 sessioninfo::session_info()
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Session information

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- +
@@ -103,7 +102,7 @@

weighted Nearest Sequenced Taxon Index (wNSTI)

- Source: vignettes/articles/nsti.Rmd + Source: vignettes/articles/nsti.Rmd
@@ -161,90 +160,87 @@

System information
 sessioninfo::session_info()
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 #> 
-#> ------------------------------------------------------------------------------

+#> ──────────────────────────────────────────────────────────────────────────────
+ @@ -257,16 +253,16 @@

System information

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/articles/nsti_files/figure-html/unnamed-chunk-5-1.png b/articles/nsti_files/figure-html/unnamed-chunk-5-1.png index 44b358e..d645ada 100644 Binary files a/articles/nsti_files/figure-html/unnamed-chunk-5-1.png and b/articles/nsti_files/figure-html/unnamed-chunk-5-1.png differ diff --git a/articles/nsti_files/figure-html/unnamed-chunk-6-1.png b/articles/nsti_files/figure-html/unnamed-chunk-6-1.png index 991c7d7..b4cdb65 100644 Binary files a/articles/nsti_files/figure-html/unnamed-chunk-6-1.png and b/articles/nsti_files/figure-html/unnamed-chunk-6-1.png differ diff --git a/articles/smaller_example.html b/articles/smaller_example.html index 729387b..4095dac 100644 --- a/articles/smaller_example.html +++ b/articles/smaller_example.html @@ -12,14 +12,13 @@ - - +
- +
@@ -102,7 +101,7 @@

Examples with a single annotation

- Source: vignettes/articles/smaller_example.Rmd + Source: vignettes/articles/smaller_example.Rmd
@@ -456,132 +455,131 @@

Session info
 sessioninfo::session_info()
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-#> ------------------------------------------------------------------------------

+#> ──────────────────────────────────────────────────────────────────────────────
+ @@ -594,16 +592,16 @@

Session info

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

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taxPPro

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Session information
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Session information

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Uncertainty in tips with binary attributes

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Session information
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Uncertainty in tips with multistate(-intersection) annotations

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@@ -227,99 +226,97 @@

Session information
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-#>  pkgdown             2.0.9      2024-04-18 [1] RSPM (R 4.4.0)
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-#>  quadprog            1.5-8      2019-11-20 [1] CRAN (R 4.4.0)
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-#>  rmarkdown           2.26       2024-03-05 [1] RSPM (R 4.4.0)
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-#>  yaml                2.3.8      2023-12-11 [1] RSPM (R 4.4.0)
+#>  xfun                0.46       2024-07-18 [1] RSPM (R 4.4.0)
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 #> 
 #>  [1] /usr/local/lib/R/site-library
 #>  [2] /usr/local/lib/R/library
 #> 
-#> ------------------------------------------------------------------------------

+#> ──────────────────────────────────────────────────────────────────────────────
+ @@ -332,16 +329,16 @@

Session information

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/authors.html b/authors.html index 9aa6c90..74686fa 100644 --- a/authors.html +++ b/authors.html @@ -3,7 +3,7 @@ - +
- +
@@ -78,7 +78,7 @@

Authors and Citation

- +
-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/index.html b/index.html index 13c8fdd..7d7478f 100644 --- a/index.html +++ b/index.html @@ -19,7 +19,7 @@ - +
- +
@@ -158,16 +158,16 @@

Developers

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/news/index.html b/news/index.html index e764ea3..2ffd88e 100644 --- a/news/index.html +++ b/news/index.html @@ -3,7 +3,7 @@ - +
- +

Changelog

- Source: NEWS.md + Source: NEWS.md
@@ -96,15 +96,15 @@

taxPPro 1.0.0
-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/pkgdown.yml b/pkgdown.yml index 4faa379..9a2eca8 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -1,17 +1,16 @@ -pandoc: 3.1.13 -pkgdown: 2.0.9 +pandoc: '3.2' +pkgdown: 2.1.0 pkgdown_sha: ~ articles: - add_singletons: add_singletons.html - figure_example: figure_example.html - internal_nodes: internal_nodes.html - nsti: nsti.html - smaller_example: smaller_example.html + articles/add_singletons: add_singletons.html + articles/figure_example: figure_example.html + articles/internal_nodes: internal_nodes.html + articles/nsti: nsti.html + articles/smaller_example: smaller_example.html taxPPro: taxPPro.html - uncertainty_binary: uncertainty_binary.html - uncertainty_multistate: uncertainty_multistate.html -last_built: 2024-05-09T15:31Z + articles/uncertainty_binary: uncertainty_binary.html + articles/uncertainty_multistate: uncertainty_multistate.html +last_built: 2024-07-23T20:08Z urls: reference: https://waldronlab.io/taxPPro/reference article: https://waldronlab.io/taxPPro/articles - diff --git a/reference/addRankPrefix.html b/reference/addRankPrefix.html index 0f5ec91..6646938 100644 --- a/reference/addRankPrefix.html +++ b/reference/addRankPrefix.html @@ -3,7 +3,7 @@ - +
- +

Add rank prefix to NCBI_ID

- Source: R/utils.R + Source: R/utils.R
@@ -89,19 +89,19 @@

Add rank prefix to NCBI_ID

Arguments

-
id
+ + +
id

A character vector of NCBI IDs (taxids).

-
rank
+
rank

A character vector of ranks

Value

- - -

A character vector of IDs with prefix.

+

A character vector of IDs with prefix.

@@ -116,15 +116,15 @@

Value

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/reference/classif2Table.html b/reference/classif2Table.html index 848c3ec..4418ea9 100644 --- a/reference/classif2Table.html +++ b/reference/classif2Table.html @@ -4,7 +4,7 @@ - +
- +

Taxize classification to data frame

- Source: R/utils.R + Source: R/utils.R
@@ -91,19 +91,19 @@

Taxize classification to data frame

Arguments

-
x
+ + +
x

Output from the `taxize::classification` function.

-
ranks
+
ranks

Ranks to be selected. Default is given by `.validRanks()`.

Value

- - -

A data frame.

+

A data frame.

@@ -118,15 +118,15 @@

Value

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/reference/completeBinaryData.html b/reference/completeBinaryData.html index e0e5922..da8b2cb 100644 --- a/reference/completeBinaryData.html +++ b/reference/completeBinaryData.html @@ -4,7 +4,7 @@ - +
- +

Complete binary data

- Source: R/taxPPro.R + Source: R/taxPPro.R
@@ -91,15 +91,15 @@

Complete binary data

Arguments

-
tbl
+ + +
tbl

A data.frame.

Value

- - -

A data.frame.

+

A data.frame.

@@ -114,15 +114,15 @@

Value

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/reference/conf2Fct.html b/reference/conf2Fct.html index 2017587..6a6a34f 100644 --- a/reference/conf2Fct.html +++ b/reference/conf2Fct.html @@ -4,7 +4,7 @@ - +
- +

Confidence in curation to factor

- Source: R/utils.R + Source: R/utils.R
@@ -91,15 +91,15 @@

Confidence in curation to factor

Arguments

-
x
+ + +
x

A character vector.

Value

- - -

A factor.

+

A factor.

@@ -114,15 +114,15 @@

Value

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/reference/filterData.html b/reference/filterData.html index daeaf3c..cc87f86 100644 --- a/reference/filterData.html +++ b/reference/filterData.html @@ -4,7 +4,7 @@ - +
- +

Filter data

- Source: R/taxPPro.R + Source: R/taxPPro.R
@@ -91,15 +91,15 @@

Filter data

Arguments

-
tbl
+ + +
tbl

A data.frame.

Value

- - -

A data.frame.

+

A data.frame.

@@ -114,15 +114,15 @@

Value

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/reference/filterDataDiscrete.html b/reference/filterDataDiscrete.html index b180815..4374e00 100644 --- a/reference/filterDataDiscrete.html +++ b/reference/filterDataDiscrete.html @@ -5,7 +5,7 @@ - +
- +

Filter data with discrete attributes

- Source: R/taxPPro.R + Source: R/taxPPro.R
@@ -93,15 +93,15 @@

Filter data with discrete attributes

Arguments

-
tbl
+ + +
tbl

A data.frame imported with bugphyzz::physiologies

Value

- - -

A data.frame.

+

A data.frame.

@@ -116,15 +116,15 @@

Value

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/reference/filterDataNumeric.html b/reference/filterDataNumeric.html index fd2a055..14c2e27 100644 --- a/reference/filterDataNumeric.html +++ b/reference/filterDataNumeric.html @@ -6,7 +6,7 @@ - +
- +

Filter data with numeric attributes

- Source: R/taxPPro.R + Source: R/taxPPro.R
@@ -95,15 +95,15 @@

Filter data with numeric attributes

Arguments

-
tbl
+ + +
tbl

A data.frame imported with bugphyzz::physiologies

Value

- - -

A data.frame.

+

A data.frame.

@@ -118,15 +118,15 @@

Value

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/reference/freq2Scores.html b/reference/freq2Scores.html index 8f760de..da01fa2 100644 --- a/reference/freq2Scores.html +++ b/reference/freq2Scores.html @@ -5,7 +5,7 @@ - +
- +

Frequency to scores

- Source: R/utils.R + Source: R/utils.R
@@ -93,15 +93,15 @@

Frequency to scores

Arguments

-
x
+ + +
x

A character vector.

Value

- - -

A numeric vector.

+

A numeric vector.

@@ -116,15 +116,15 @@

Value

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/reference/freq2Scores2.html b/reference/freq2Scores2.html index 20e89c5..04315ff 100644 --- a/reference/freq2Scores2.html +++ b/reference/freq2Scores2.html @@ -6,7 +6,7 @@ - +
- +

Frequency to scores 2

- Source: R/utils.R + Source: R/utils.R
@@ -95,15 +95,15 @@

Frequency to scores 2

Arguments

-
x
+ + +
x

A character vector.

Value

- - -

A numeric vector.

+

A numeric vector.

@@ -118,15 +118,15 @@

Value

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/reference/getDataReady.html b/reference/getDataReady.html index 1e1a0f2..4991717 100644 --- a/reference/getDataReady.html +++ b/reference/getDataReady.html @@ -3,7 +3,7 @@ - +
- +

Get data ready for propagation

- Source: R/taxPPro.R + Source: R/taxPPro.R
@@ -89,15 +89,15 @@

Get data ready for propagation

Arguments

-
tbl
+ + +
tbl

A data.frame.

Value

- - -

A data.frame.

+

A data.frame.

@@ -112,15 +112,15 @@

Value

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/reference/getNsti.html b/reference/getNsti.html index d05ebef..083e2a6 100644 --- a/reference/getNsti.html +++ b/reference/getNsti.html @@ -5,7 +5,7 @@ - +
- +

Get NSTI

- Source: R/trees.R + Source: R/trees.R
@@ -93,24 +93,24 @@

Get NSTI

Arguments

-
tree
+ + +
tree

A phylo object

-
annotated_tip_labels
+
annotated_tip_labels

A character vector with the names of the tips

-
nodes
+
nodes

A character vector with the names of nodes in the tree that are annotated.

Value

- - -

A data.frame with two columns: tip_label and nsti.

+

A data.frame with two columns: tip_label and nsti.

@@ -125,15 +125,15 @@

Value

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/reference/getSetWithIDs.html b/reference/getSetWithIDs.html index adff8e8..3c1045e 100644 --- a/reference/getSetWithIDs.html +++ b/reference/getSetWithIDs.html @@ -3,7 +3,7 @@ - +
- +

Get set with IDs

- Source: R/taxPPro.R + Source: R/taxPPro.R
@@ -89,15 +89,15 @@

Get set with IDs

Arguments

-
tbl
+ + +
tbl

A data.frame.

Value

- - -

A data.frame.

+

A data.frame.

@@ -112,15 +112,15 @@

Value

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/reference/getSetWithoutIDs.html b/reference/getSetWithoutIDs.html index b409508..7edad83 100644 --- a/reference/getSetWithoutIDs.html +++ b/reference/getSetWithoutIDs.html @@ -3,7 +3,7 @@ - +
- +

Get set without IDs

- Source: R/taxPPro.R + Source: R/taxPPro.R
@@ -89,19 +89,19 @@

Get set without IDs

Arguments

-
tbl
+ + +
tbl

A data.frame.

-
set_with_ids
+
set_with_ids

A data.frame

Value

- - -

A data.frame.

+

A data.frame.

@@ -116,15 +116,15 @@

Value

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/reference/index.html b/reference/index.html index 81f3046..66800a1 100644 --- a/reference/index.html +++ b/reference/index.html @@ -1,9 +1,9 @@ -Function reference • taxPProPackage index • taxPPro - +
- +
@@ -162,15 +162,15 @@

All functions
-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/reference/ltp.html b/reference/ltp.html index b763ebc..49e7ca2 100644 --- a/reference/ltp.html +++ b/reference/ltp.html @@ -4,7 +4,7 @@ - +
- +

Get living tree project (LTP) tree and data

- Source: R/trees.R + Source: R/trees.R
@@ -91,21 +91,21 @@

Get living tree project (LTP) tree and data

Arguments

-
remove_gn_nodes
+ + +
remove_gn_nodes

Remove rows from node_data with genus taxids. Default is TRUE, which removes them. These are already in tip_data.

-
node_names
+
node_names

Add names to unnamed nodes (n + node number). This will only be in the tree (not in node_data).

Value

- - -

A list with a the LTP tree (phylo), tips and node data (data.frames), +

A list with a the LTP tree (phylo), tips and node data (data.frames), and the names of the genera added to the original tree (character vector). .

@@ -122,15 +122,15 @@

Value

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/reference/nsti2Freq.html b/reference/nsti2Freq.html index d28bbab..8dc138e 100644 --- a/reference/nsti2Freq.html +++ b/reference/nsti2Freq.html @@ -3,7 +3,7 @@ - +
- +

NSTI to Frequency

- Source: R/utils.R + Source: R/utils.R
@@ -89,15 +89,15 @@

NSTI to Frequency

Arguments

-
x
+ + +
x

A numeric vectir of nsti values

Value

- - -

A character vector of frequency keywords.

+

A character vector of frequency keywords.

@@ -112,15 +112,15 @@

Value

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/reference/roundDec.html b/reference/roundDec.html index e9bfc10..3721f9a 100644 --- a/reference/roundDec.html +++ b/reference/roundDec.html @@ -4,7 +4,7 @@ - +
- +

Round up to nearest decimal

- Source: R/utils.R + Source: R/utils.R
@@ -91,15 +91,15 @@

Round up to nearest decimal

Arguments

-
A
+ + +
A

character vector (of attributes).

Value

- - -

A double.

+

A double.

@@ -114,15 +114,15 @@

Value

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/reference/scores2Freq.html b/reference/scores2Freq.html index ce1e19c..e9f1d48 100644 --- a/reference/scores2Freq.html +++ b/reference/scores2Freq.html @@ -4,7 +4,7 @@ - +
- +

Scores to frequency

- Source: R/utils.R + Source: R/utils.R
@@ -91,15 +91,15 @@

Scores to frequency

Arguments

-
x
+ + +
x

A numeric vector.

Value

- - -

A character vector.

+

A character vector.

@@ -114,15 +114,15 @@

Value

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

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