cran submission

Cristianetaniguti · Jan 10, 2025 · 2c5fd6c · 2c5fd6c
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -16,3 +16,5 @@ Dockerfile
 ^docs$
 ^.*\.DS_Store$
 ^tests$
+^CRAN-SUBMISSION$
+^cran-comments\.md$
diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -0,0 +1,3 @@
+Version: 3.2.0
+Date: 2025-01-10 14:49:38 UTC
+SHA: 6754ee01cdf52934627a98d931036826e23f38bb
diff --git a/README.md b/README.md
@@ -88,7 +88,7 @@ Margarido, G. R. A., Souza, A. P., &38; Garcia, A. A. F. (2007). OneMap: softwar
 
 * If you are using OneMap versions > 2.0, please cite also:
 
-Taniguti, C. H.; Taniguti, L. M.; Amadeu, R. R.; Lau, J.; de Siqueira Gesteira, G.; Oliveira, T. de P.; Ferreira, G. C.; Pereira, G. da S.;  Byrne, D.;  Mollinari, M.; Riera-Lizarazu, O.; Garcia, A. A. F. Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps. GigaScience, 12, giad092. https://doi.org/10.1093/gigascience/giad092
+Taniguti, C. H.; Taniguti, L. M.; Amadeu, R. R.; Lau, J.; de Siqueira Gesteira, G.; Oliveira, T. de P.; Ferreira, G. C.; Pereira, G. da S.;  Byrne, D.;  Mollinari, M.; Riera-Lizarazu, O.; Garcia, A. A. F. (2023) Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps. GigaScience, 12, giad092. https://doi.org/10.1093/gigascience/giad092
 
 * If you used the HMM parallelization, please cite [BatchMap](https://github.com/bschiffthaler/BatchMap) paper too:
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -0,0 +1,6 @@
+## R CMD check results
+
+0 errors | 0 warnings | 1 note
+
+* The package maintainer, Cristiane Taniguti, has updated their email address to reflect the change in affiliation from Texas A&M University to Cornell University.
+* This version includes bug fixes and introduces new functions designed to simplify data manipulation.
diff --git a/docs/Inbred_Based_Populations.html b/docs/Inbred_Based_Populations.html
diff --git a/docs/Introduction_R.html b/docs/Introduction_R.html
@@ -12,7 +12,7 @@
 
 <meta name="author" content="Statistical Genetics Lab   Department of Genetics   Luiz de Queiroz College of Agriculture   University of São Paulo" />
 
-<meta name="date" content="2025-01-09" />
+<meta name="date" content="2025-01-10" />
 
 <title>Introduction to R</title>
 
@@ -342,7 +342,7 @@ <h1 class="title toc-ignore">Introduction to R</h1>
 <h4 class="author"><a href="http://statgen.esalq.usp.br">Statistical
 Genetics Lab</a> <br /> Department of Genetics <br /> Luiz de Queiroz
 College of Agriculture <br /> University of São Paulo</h4>
-<h4 class="date">2025-01-09</h4>
+<h4 class="date">2025-01-10</h4>
 
 
 
@@ -354,8 +354,9 @@ <h4 class="date">2025-01-09</h4>
 it is assumed that the user is running Windows. Users of R under Linux
 or Mac OS should have no difficulty following this tutorial.</p>
 <p>We would like to recommend those new users, instead of using plain R,
-use it through the fantastic software <a href="https://www.rstudio.com/">RStudio</a>. With this package, there is
-no noticeable difference between operating systems.</p>
+use it through the fantastic software <a href="https://posit.co/products/open-source/rstudio/">RStudio</a>. With
+this package, there is no noticeable difference between operating
+systems.</p>
 <p>As advertised on the website, <em>RStudio is an integrated
 development environment (IDE) for R. It includes a console,
 syntax-highlighting editor that supports direct code execution, as well
@@ -460,7 +461,7 @@ <h1>Packages</h1>
 <span id="cb10-4"><a href="#cb10-4" tabindex="-1"></a><span class="co">#&gt;   rev.hclust dendextend</span></span>
 <span id="cb10-5"><a href="#cb10-5" tabindex="-1"></a><span class="co">#&gt; </span></span>
 <span id="cb10-6"><a href="#cb10-6" tabindex="-1"></a><span class="co">#&gt; </span></span>
-<span id="cb10-7"><a href="#cb10-7" tabindex="-1"></a><span class="co">#&gt; After version 3.0.0 OneMap updates has been solely for maintaining accessibility and functionality. </span></span>
+<span id="cb10-7"><a href="#cb10-7" tabindex="-1"></a><span class="co">#&gt; After version 3.2.0 OneMap updates has been solely for maintaining accessibility and functionality. </span></span>
 <span id="cb10-8"><a href="#cb10-8" tabindex="-1"></a><span class="co">#&gt;     New feature development and optimization efforts are now being directed toward the </span></span>
 <span id="cb10-9"><a href="#cb10-9" tabindex="-1"></a><span class="co">#&gt;     MAPpoly (https://github.com/mmollina/MAPpoly) and MAPpoly2 (https://github.com/mmollina/mappoly2) packages.</span></span>
 <span id="cb10-10"><a href="#cb10-10" tabindex="-1"></a><span class="co">#&gt; </span></span>

diff --git a/docs/Outcrossing_Populations.html b/docs/Outcrossing_Populations.html
diff --git a/docs/Overview.html b/docs/Overview.html
@@ -12,7 +12,7 @@
 
 <meta name="author" content="Statistical Genetics Lab   Department of Genetics   Luiz de Queiroz College of Agriculture   University of São Paulo" />
 
-<meta name="date" content="2025-01-09" />
+<meta name="date" content="2025-01-10" />
 
 <title>Overview</title>
 
@@ -241,7 +241,7 @@ <h1 class="title toc-ignore">Overview</h1>
 <h4 class="author"><a href="http://statgen.esalq.usp.br">Statistical
 Genetics Lab</a> <br /> Department of Genetics <br /> Luiz de Queiroz
 College of Agriculture <br /> University of São Paulo</h4>
-<h4 class="date">2025-01-09</h4>
+<h4 class="date">2025-01-10</h4>
 
 
 
@@ -343,8 +343,8 @@ <h4 class="date">2025-01-09</h4>
 <li>Datasets with multiallelic or dominant markers.</li>
 </ul>
 <p>For guidance on best practices in building linkage maps while
-accounting for genotyping errors, please refer to <a href="https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giad092/7330892">this
-publication</a>.</p>
+accounting for genotyping errors, please refer to Taniguti et. al
+2023.</p>
 <div id="how-to-cite" class="section level1">
 <h1>How to Cite</h1>
 <p>Margarido, G. R. A., Souza, A. P., &amp;38; Garcia, A. A. F. (2007).
@@ -357,7 +357,7 @@ <h1>How to Cite</h1>
 Gesteira, G.; Oliveira, T. de P.; Ferreira, G. C.; Pereira, G. da S.;
 Byrne, D.; Mollinari, M.; Riera-Lizarazu, O.; Garcia, A. A. F.
 Developing best practices for genotyping-by-sequencing analysis in the
-construction of linkage maps. GigaScience, 12, giad092. <a href="https://doi.org/10.1093/gigascience/giad092" class="uri">https://doi.org/10.1093/gigascience/giad092</a></p>
+construction of linkage maps. 2023. GigaScience, 12, giad092. <a href="https://doi.org/10.1093/gigascience/giad092" class="uri">https://doi.org/10.1093/gigascience/giad092</a></p>
 <ul>
 <li>If you used the HMM parallelization, please cite <a href="https://github.com/bschiffthaler/BatchMap">BatchMap</a> paper
 too:</li>

diff --git a/src/Makevars.win b/src/Makevars.win
@@ -1,2 +1 @@
-PKG_LIBS= $(BLAS_LIBS) $(FLIBS) 
-CXX_STD = CXX11
+PKG_LIBS= $(BLAS_LIBS) $(FLIBS) 
diff --git a/vignettes/Inbred_Based_Populations.Rmd b/vignettes/Inbred_Based_Populations.Rmd
@@ -36,7 +36,7 @@ mapping in outcrossing species; please read the proper vignette.
 
 If you are not familiar with `R`, we recommend first the reading of
 vignette
-[Introduction to R](https://statgen-esalq.github.io/tutorials/onemap/Introduction_R.html).
+[Introduction to R](https://cristianetaniguti.github.io/onemap/Introduction_R.html).
 You do not need to be an expert in R to build your linkage map, but
 some concepts are necessary and will help you through the process.
 
@@ -46,7 +46,7 @@ recommend all users to try [this version](https://github.com/cristianetaniguti/o
 # Best practices guidelines for using markers from sequencing data
 
 
-In [Taniguti et al., 2023](https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giad092/7330892), we introduced updates to **OneMap 3.0** and evaluated various combinations of bioinformatics tools and filters for obtaining high-quality markers and linkage maps. The paper provides practical guidelines based on these results. 
+In Taniguti et al., 2023, we introduced updates to **OneMap 3.0** and evaluated various combinations of bioinformatics tools and filters for obtaining high-quality markers and linkage maps. The paper provides practical guidelines based on these results. 
 
 The [Reads2Map](https://github.com/Cristianetaniguti/Reads2Map) workflow enables you to replicate these tests on your dataset. This comprehensive pipeline integrates tools such as BWA, GATK, FreeBayes, TASSEL, Stacks, updog, polyRAD, superMASSA, GUSMap, and OneMap to perform read alignment, SNP and genotype calling, and linkage mapping.
 
@@ -419,7 +419,7 @@ By default, `OneMap` sets a error probability of $10^{-5}$ for every genotype:
 head(simu_f2_obj$error)
 ```
 
-See [Taniguti et. al, 2023](https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giad092/7330892) Supplementary File 1 for details about the `$error` object format.
+See Taniguti et. al, 2023 Supplementary File 1 for details about the `$error` object format.
 
 For markers from sequencing technology, this value is unrealistic and generates inflated linkage maps. `OneMap` 3.0 can consider three types of genotype probabilities to consider error in the HMM chain. A single global value (global_error), a matrix with dimensions (number of individuals) x (number of markers) with genotypes errors values (genotypes_errors), and a matrix with dimensions (number of individuals)*(number of markers) x possible genotypes (genotypes_probs). See details in the function `create_probs`:
 
@@ -1870,6 +1870,8 @@ Sci._** 133, 35-41, 2008.
 Tan, Y., Fu, Y. A novel method for estimating linkage maps.
 **_Genetics_** 173, 2383-2390, 2006.
 
+Taniguti, C. H.; Taniguti, L. M.; Amadeu, R. R.; Lau, J.; de Siqueira Gesteira, G.; Oliveira, T. de P.; Ferreira, G. C.; Pereira, G. da S.;  Byrne, D.;  Mollinari, M.; Riera-Lizarazu, O.; Garcia, A. A. F. Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps. GigaScience, 12, giad092. https://doi.org/10.1093/gigascience/giad092
+
 Van Os H, Stam P, Visser R.G.F., Van Eck H.J. RECORD: a novel method
 for ordering loci on a genetic linkage map. **_Theor Appl Genet_**
 112, 30-40, 2005.