From 4ee70290951598c5d8f6bdf75584db3e1000a426 Mon Sep 17 00:00:00 2001 From: danro9685 Date: Mon, 22 Jul 2024 09:54:10 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20BIMIB-DI?= =?UTF-8?q?SCo/VERSO@ee1b8327b2f04e8dbbaa0c8124c7420c1b6360be=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 | 14 ++++---- LICENSE-text.html | 14 ++++---- articles/index.html | 14 ++++---- articles/v1_introduction.html | 23 ++++++------- articles/v2_running_VERSO.html | 23 ++++++------- authors.html | 26 +++++++-------- index.html | 14 ++++---- pkgdown.yml | 9 +++-- reference/VERSO.html | 56 ++++++++++++++++---------------- reference/index.html | 14 ++++---- reference/inference.html | 20 +++++------- reference/variants.html | 28 ++++++++-------- reference/write.newick.tree.html | 24 +++++++------- sitemap.xml | 52 ++++++++--------------------- 14 files changed, 148 insertions(+), 183 deletions(-) diff --git a/404.html b/404.html index d7120d0..a570f8e 100644 --- a/404.html +++ b/404.html @@ -18,7 +18,7 @@ - +
- +
@@ -100,16 +100,16 @@

Page not found (404)

-

Site built with pkgdown 2.0.9.9000.

+

Site built with pkgdown 2.1.0.9000.

- - + + diff --git a/LICENSE-text.html b/LICENSE-text.html index ac6dcf0..5813e18 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -3,7 +3,7 @@ - +
- +
@@ -274,15 +274,15 @@

License

-

Site built with pkgdown 2.0.9.9000.

+

Site built with pkgdown 2.1.0.9000.

- - + + diff --git a/articles/index.html b/articles/index.html index 9b03210..805e3a8 100644 --- a/articles/index.html +++ b/articles/index.html @@ -3,7 +3,7 @@ - +
- +
@@ -74,15 +74,15 @@

All vignettes

-

Site built with pkgdown 2.0.9.9000.

+

Site built with pkgdown 2.1.0.9000.

- - + + diff --git a/articles/v1_introduction.html b/articles/v1_introduction.html index 88f9cdd..eac17f1 100644 --- a/articles/v1_introduction.html +++ b/articles/v1_introduction.html @@ -12,14 +12,13 @@ - - +
- +
@@ -92,9 +91,9 @@

Luca De

Gianluca Ascolani

-

May 07, 2024

+

July 22, 2024

- Source: vignettes/v1_introduction.Rmd + Source: vignettes/v1_introduction.Rmd
@@ -133,9 +132,7 @@

Debug +

@@ -148,16 +145,16 @@

Debug

-

Site built with pkgdown 2.0.9.9000.

+

Site built with pkgdown 2.1.0.9000.

- - + + diff --git a/articles/v2_running_VERSO.html b/articles/v2_running_VERSO.html index 33b6523..0602704 100644 --- a/articles/v2_running_VERSO.html +++ b/articles/v2_running_VERSO.html @@ -12,14 +12,13 @@ - - +
- +
@@ -92,9 +91,9 @@

Luca De

Gianluca Ascolani

-

May 07, 2024

+

July 22, 2024

- Source: vignettes/v2_running_VERSO.Rmd + Source: vignettes/v2_running_VERSO.Rmd
@@ -175,9 +174,7 @@

Example of phylogenetic infe +

@@ -190,16 +187,16 @@

Example of phylogenetic infe

-

Site built with pkgdown 2.0.9.9000.

+

Site built with pkgdown 2.1.0.9000.

- - + + diff --git a/authors.html b/authors.html index 270b717..dcbb350 100644 --- a/authors.html +++ b/authors.html @@ -3,7 +3,7 @@ - +
- +
@@ -57,21 +57,21 @@

Authors and Citation

- +

  • Daniele Ramazzotti. Author.

  • -

    Fabrizio Angaroni. Author. +

    Fabrizio Angaroni. Author.

  • -

    Davide Maspero. Maintainer, author. +

    Davide Maspero. Maintainer, author.

  • -

    Alex Graudenzi. Author. +

    Alex Graudenzi. Author.

  • @@ -82,14 +82,14 @@

    Authors and Citation

    Citation

    - Source: DESCRIPTION + Source: DESCRIPTION

    Ramazzotti D, Angaroni F, Maspero D, Graudenzi A, De Sano L (2024). VERSO: Viral Evolution ReconStructiOn (VERSO). -R package version 1.14.0, https://github.com/BIMIB-DISCo/VERSO. +R package version 1.14.0, https://github.com/BIMIB-DISCo/VERSO. 

    @Manual{,
   title = {VERSO: Viral Evolution ReconStructiOn (VERSO)},
@@ -110,15 +110,15 @@ 
    Citation
-

Site built with pkgdown 2.0.9.9000.

+

Site built with pkgdown 2.1.0.9000.

- - + + diff --git a/index.html b/index.html index 6927d20..0d461cb 100644 --- a/index.html +++ b/index.html @@ -19,7 +19,7 @@ - +
- +
@@ -169,16 +169,16 @@

Developers

-

Site built with pkgdown 2.0.9.9000.

+

Site built with pkgdown 2.1.0.9000.

- - + + diff --git a/pkgdown.yml b/pkgdown.yml index 82e43a6..2d03e62 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -1,8 +1,7 @@ -pandoc: 3.1.13 -pkgdown: 2.0.9.9000 -pkgdown_sha: 7bc81933fa3e63252a109010ecf361f109a6744c +pandoc: '3.2' +pkgdown: 2.1.0.9000 +pkgdown_sha: 2841c0f994fda7f7c7da94034bd24e3882fc7a37 articles: v1_introduction: v1_introduction.html v2_running_VERSO: v2_running_VERSO.html -last_built: 2024-05-07T17:14Z - +last_built: 2024-07-22T09:53Z diff --git a/reference/VERSO.html b/reference/VERSO.html index 8eb3ead..afc7e4f 100644 --- a/reference/VERSO.html +++ b/reference/VERSO.html @@ -3,7 +3,7 @@ - +
- +

VERSO

- Source: R/frontend.R + Source: R/frontend.R
@@ -83,30 +83,32 @@

VERSO

Arguments

-
D
-

Input data for the inference reporting presence (as 1), absense (as 0) or missing + + +

D
+

Input data for the inference reporting presence (as 1), absense (as 0) or missing information (as NA) for a set of variants.

alpha
-

False positive error rate provided as a verctor; if a vector of alpha (and beta) -is provided, the inference is performed +

False positive error rate provided as a verctor; if a vector of alpha (and beta) +is provided, the inference is performed for multiple values and the solution at maximum-likelihood is returned.

beta
-

False negative error rate provided as a verctor; if a vector of beta (and alpha) -is provided, the inference is performed +

False negative error rate provided as a verctor; if a vector of beta (and alpha) +is provided, the inference is performed for multiple values and the solution at maximum-likelihood is returned.

initialization
-

Binary matrix representing a perfect philogeny tree; genotypes are rows and mutations are columns. +

Binary matrix representing a perfect philogeny tree; genotypes are rows and mutations are columns. This parameter overrides "random_tree".

random_tree
-

Boolean. Shall I start MCMC search from a random tree? If FALSE (default) and initialization is NULL, search +

Boolean. Shall I start MCMC search from a random tree? If FALSE (default) and initialization is NULL, search is started from a TRaIT tree (BMC Bioinformatics . 2019 Apr 25;20(1):210. doi: 10.1186/s12859-019-2795-4).

@@ -115,7 +117,7 @@

Arguments

check_indistinguishable
-

Boolean. Shall I remove any indistinguishable variant +

Boolean. Shall I remove any indistinguishable variant from input data prior inference?

@@ -136,7 +138,7 @@

Arguments

num_processes
-

Number of processes to be used during parallel execution. To execute in single process mode, +

Number of processes to be used during parallel execution. To execute in single process mode, this parameter needs to be set to either 1, NA or NULL.

@@ -150,16 +152,14 @@

Arguments

Value

- - -

A list of 9 elements: B, C, phylogenetic_tree, corrected_genotypes, genotypes_prevalence, -genotypes_summary, log_likelihood and error_rates. Here, B returns the maximum likelihood variants tree -(inner nodes of the phylogenetic tree), C the attachment of patients to genotypes and phylogenetic_tree VERSO -phylogenetic tree, including both variants tree and patients attachments to variants; corrected_genotypes is the -corrected genotypes, which corrects D given VERSO phylogenetic tree, genotypes_prevalence the number of patients -and observed prevalence of each genotype and genotypes_summary provide a summary of association of mutations -to genotypes. In equivalent_solutions, solutions (B and C) with likelihood equivalent to the best solution are returned. -Finally log_likelihood and error_rates return the likelihood of the inferred phylogenetic moldel and best values of alpha and beta +

A list of 9 elements: B, C, phylogenetic_tree, corrected_genotypes, genotypes_prevalence, +genotypes_summary, log_likelihood and error_rates. Here, B returns the maximum likelihood variants tree +(inner nodes of the phylogenetic tree), C the attachment of patients to genotypes and phylogenetic_tree VERSO +phylogenetic tree, including both variants tree and patients attachments to variants; corrected_genotypes is the +corrected genotypes, which corrects D given VERSO phylogenetic tree, genotypes_prevalence the number of patients +and observed prevalence of each genotype and genotypes_summary provide a summary of association of mutations +to genotypes. In equivalent_solutions, solutions (B and C) with likelihood equivalent to the best solution are returned. +Finally log_likelihood and error_rates return the likelihood of the inferred phylogenetic moldel and best values of alpha and beta as estimated by VERSO.

@@ -191,15 +191,15 @@

Examples

-

Site built with pkgdown 2.0.9.9000.

+

Site built with pkgdown 2.1.0.9000.

- - + + diff --git a/reference/index.html b/reference/index.html index 940de66..86e852d 100644 --- a/reference/index.html +++ b/reference/index.html @@ -3,7 +3,7 @@ - +
- +
@@ -89,15 +89,15 @@

All functions
-

Site built with pkgdown 2.0.9.9000.

+

Site built with pkgdown 2.1.0.9000.

- - + + diff --git a/reference/inference.html b/reference/inference.html index 1c7c90b..5976e3a 100644 --- a/reference/inference.html +++ b/reference/inference.html @@ -3,7 +3,7 @@ - +
- +

Results obtained running VERSO on the provided input dataset.

- Source: R/data.R + Source: R/data.R
@@ -72,9 +72,7 @@

Format

Value

- - -

results obtained running VERSO on the provided input dataset

+

results obtained running VERSO on the provided input dataset

@@ -89,15 +87,15 @@

Value

-

Site built with pkgdown 2.0.9.9000.

+

Site built with pkgdown 2.1.0.9000.

- - + + diff --git a/reference/variants.html b/reference/variants.html index 12a8845..dda3316 100644 --- a/reference/variants.html +++ b/reference/variants.html @@ -1,11 +1,11 @@ -Mutation data obtained by variant calling from raw data of a selected set of SARS-CoV-2 samples available from NCBI BioProject PRJNA610428. — variants • VERSOMutation data obtained by variant calling from raw data of a selected set of SARS-CoV-2 samples available from NCBI BioProject PRJNA610428. — variants • VERSO - +
- +

Mutation data obtained by variant calling from raw data of a selected set of SARS-CoV-2 samples available from NCBI BioProject PRJNA610428.

- Source: R/data.R + Source: R/data.R
-

The dataset includes variants for a selected set of 15 -SARS-CoV-2 samples obtained by variant calling from raw data +

The dataset includes variants for a selected set of 15 +SARS-CoV-2 samples obtained by variant calling from raw data available from NCBI BioProject PRJNA610428.

@@ -80,9 +80,7 @@

Source

Value

- - -

SARS-CoV-2 variants

+

SARS-CoV-2 variants

@@ -97,15 +95,15 @@

Value

-

Site built with pkgdown 2.0.9.9000.

+

Site built with pkgdown 2.1.0.9000.

- - + + diff --git a/reference/write.newick.tree.html b/reference/write.newick.tree.html index e1b6ced..67dfcdc 100644 --- a/reference/write.newick.tree.html +++ b/reference/write.newick.tree.html @@ -3,7 +3,7 @@ - +
- +

write.newick.tree

- Source: R/frontend.R + Source: R/frontend.R
@@ -68,7 +68,9 @@

write.newick.tree

Arguments

-
phylogenetic_tree
+ + +
phylogenetic_tree

Inference results by VERSO.

@@ -78,9 +80,7 @@

Arguments

Value

- - -

A phylogenetic tree as inferred by VERSO in newick format.

+

A phylogenetic tree as inferred by VERSO in newick format.

@@ -103,15 +103,15 @@

Examples

-

Site built with pkgdown 2.0.9.9000.

+

Site built with pkgdown 2.1.0.9000.

- - + + diff --git a/sitemap.xml b/sitemap.xml index c53b595..4aba931 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -1,39 +1,15 @@ - - - - /404.html - - - /LICENSE-text.html - - - /articles/index.html - - - /articles/v1_introduction.html - - - /articles/v2_running_VERSO.html - - - /authors.html - - - /index.html - - - /reference/VERSO.html - - - /reference/index.html - - - /reference/inference.html - - - /reference/variants.html - - - /reference/write.newick.tree.html - + +/404.html +/LICENSE-text.html +/articles/index.html +/articles/v1_introduction.html +/articles/v2_running_VERSO.html +/authors.html +/index.html +/reference/VERSO.html +/reference/index.html +/reference/inference.html +/reference/variants.html +/reference/write.newick.tree.html +