Fixing warnings and including Oscar Riera-Lizarazu as a contributor.

DESCRIPTION

@@ -22,6 +22,11 @@ Authors@R: c(person(given = "Marcelo",
                     role = "aut",
                     email = "[email protected]",
                     comment = c(ORCID="0000-0003-1114-6892")),
+            person(given = "Oscar",
+                    family = "Riera-Lizarazu",
+                    role = "ctb",
+                    email = "[email protected]",
+                    comment = c(ORCID="0000-0002-7477-4063")),
             person(given = "Guilhereme",
                     family = "Pereira",
                     role = "ctb",

R/calc_genoprob_single_parent.R

@@ -28,7 +28,7 @@
 #'
 #' @examples
 #'  ## tetraploid example
-#'  s <- make_seq_mappoly(tetra.solcap, 'seq1', info.parent = "p1")
+#'  s <- make_seq_mappoly(tetra.solcap, 'seq12', info.parent = "p1")
 #'  tpt <- est_pairwise_rf(s)
 #'  map <- est_rf_hmm_sequential(input.seq = s,
 #'                               twopt = tpt,
@@ -38,7 +38,7 @@
 #'                                extend.tail = 4,
 #'                                info.tail = TRUE, 
 #'                                sub.map.size.diff.limit = 8, 
-#'                                phase.number.limit = 20,
+#'                                phase.number.limit = 4,
 #'                                reestimate.single.ph.configuration = TRUE,
 #'                                tol = 10e-2,
 #'                                tol.final = 10e-3)

README.md

@@ -2,7 +2,7 @@
 [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/mmollina/mappoly?branch=master&svg=true)](https://ci.appveyor.com/project/mmollina/mappoly)
 ![Development](https://img.shields.io/badge/development-active-blue.svg)
 [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
-[![codecov](https://codecov.io/github/mmollina/MAPpoly/branch/master/graphs/badge.svg)](https://codecov.io/github/mmollina/MAPpoly)
+[![codecov](https://codecov.io/github/mmollina/MAPpoly/branch/master/graphs/badge.svg)](https://app.codecov.io/github/mmollina/MAPpoly)
 [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/mappoly)](https://cran.r-project.org/package=mappoly)
 [![R-universe PolyVerse Status Badge](https://polyploids.r-universe.dev/badges/mappoly)](https://polyploids.r-universe.dev)
 [![](https://cranlogs.r-pkg.org/badges/grand-total/mappoly)](https://cran.r-project.org/package=mappoly)
@@ -120,7 +120,7 @@ install.packages('mappoly')
 * Genetic mapping in polyploids
   * [MDSMap: High Density Genetic Linkage Mapping using Multidimensional Scaling](https://CRAN.R-project.org/package=MDSMap)
   * [polymapR: Linkage Analysis in Outcrossing Polyploids](https://CRAN.R-project.org/package=polymapR)
-  * [TetraploidSNPMap: Linkage maps and mapping QTLs for autotetraploid species, using SNP dosage data.](https://www.bioss.ac.uk/knowledge/tetraploidmap/)
+  * [TetraploidSNPMap: Linkage maps and mapping QTLs for autotetraploid species, using SNP dosage data.](https://www.bioss.ac.uk/knowledge-exchange/software/TetraploidSNPMap)
   
   
 * Haplotype reconstruction

inst/CITATION

@@ -1,49 +1,29 @@
 citHeader("To cite MAPpoly in publications use:")
 
-citEntry(entry = "Article",
-         title        = "Linkage Analysis and Haplotype Phasing in 
-                         Experimental Autopolyploid Populations with 
-                         High Ploidy Level Using Hidden Markov Models",
-         author       = personList(as.person("Marcelo Mollinari"),
-                                   as.person("A Augusto Franco Garcia")),
-         journal      = "G3: Genes, Genomes, Genetics",
-         year         = "2019",
-         volume       = "9",
-         number       = "10",
-         pages        = "3297--3314",
-         url          = "https://doi.org/10.1534/g3.119.400378",
-         doi          = "10.1534/g3.119.400378",
-
-         textVersion  = paste("Mollinari, M., and Garcia, A. A. F. (2019)",
-                              "Linkage analysis and haplotype phasing in ",
-                              "experimental autopolyploid populations with",
-                              "high ploidy level using hidden Markov models,",
-                              "_G3: Genes, Genomes, Genetics_, 9(10), 3297-3314",
-                              "URL https://doi.org/10.1534/g3.119.400378")
+bibentry(
+  bibtype = "Article",
+  title = "Linkage Analysis and Haplotype Phasing in Experimental Autopolyploid Populations with High Ploidy Level Using Hidden Markov Models",
+  author = c("Marcelo Mollinari", "A Augusto Franco Garcia"),
+  journal = "G3: Genes, Genomes, Genetics",
+  year = "2019",
+  volume = "9",
+  number = "10",
+  pages = "3297--3314",
+  url = "https://doi.org/10.1534/g3.119.400378",
+  doi = "10.1534/g3.119.400378",
+  textVersion = "Mollinari, M., & Garcia, A. A. F. (2019). Linkage analysis and haplotype phasing in experimental autopolyploid populations with high ploidy level using hidden Markov models. G3: Genes, Genomes, Genetics, 9(10), 3297-3314. URL: https://doi.org/10.1534/g3.119.400378"
 )
 
-citEntry(entry = "Article",
-         title        = "Unraveling the Hexaploid Sweetpotato Inheritance 
-                         Using Ultra-Dense Multilocus Mapping",
-         author       = personList(as.person("Marcelo Mollinari"),
-                                   as.person("Bode A. Olukolu"),
-                                   as.person("Guilherme da S. Pereira"),
-                                   as.person("Awais Khan"),
-                                   as.person("Dorcus Gemenet"),
-                                   as.person("G. Craig Yencho"),
-                                   as.person("Zhao-Bang Zeng")),
-         journal      = "G3: Genes, Genomes, Genetics",
-         year         = "2020",
-         volume       = "10",
-         number       = "1", 
-         pages        = "281--292",
-         url          = "https://doi.org/10.1534/g3.119.400620",
-         doi          = "10.1534/g3.119.400620",
-
-         textVersion  = paste("Mollinari M., Olukolu B. A., Pereira G.da S.,",
-                              "Khan A., Gemenet D., Yench G. C., Zeng Z-B. (2020),",
-                              " Unraveling the Hexaploid Sweetpotato Inheritance ",
-                              "Using Ultra-Dense Multilocus Mapping,",
-                              "_G3: Genes, Genomes, Genetics_. (10)1 281-292",
-                              "https://doi.org/10.1534/g3.119.400620")
+bibentry(
+  bibtype = "Article",
+  title = "Unraveling the Hexaploid Sweetpotato Inheritance Using Ultra-Dense Multilocus Mapping",
+  author = c("Marcelo Mollinari", "Bode A. Olukolu", "Guilherme da S. Pereira", "Awais Khan", "Dorcus Gemenet", "Craig Yencho", "Zhao-Bang Zeng"),
+  journal = "G3: Genes, Genomes, Genetics",
+  year = "2020",
+  volume = "10",
+  number = "1",
+  pages = "281--292",
+  url = "https://doi.org/10.1534/g3.119.400620",
+  doi = "10.1534/g3.119.400620",
+  textVersion = "Mollinari, M., Olukolu, B. A., Pereira, G. da S., Khan, A., Gemenet, D., Yencho, C., & Zeng, Z-B. (2020). Unraveling the Hexaploid Sweetpotato Inheritance Using Ultra-Dense Multilocus Mapping. G3: Genes, Genomes, Genetics, 10(1), 281-292. URL: https://doi.org/10.1534/g3.119.400620"
 )