From 4b19a30dcf59177d5c2c6dbb065e1c83ffc462d5 Mon Sep 17 00:00:00 2001
From: wangtien <r05621114@g.ntu.edu.tw>
Date: Sun, 12 Mar 2023 23:40:48 +0100
Subject: [PATCH] update for invalid links test and citation

---
 DESCRIPTION                  |  18 +++++++-------
 README.Rmd                   |   2 +-
 README.md                    |  44 +++++++++++++++++------------------
 doc/toolStability.pdf        | Bin 480754 -> 480752 bytes
 inst/CITATION                |  29 +----------------------
 man/toolStability-package.Rd |   2 +-
 6 files changed, 34 insertions(+), 61 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index d99e173..c58dde3 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -11,20 +11,20 @@ Description: Tools to calculate stability indices with parametric,
  non-parametric and probabilistic approaches. The basic data format requirement for 'toolStability' is a data frame with 3 columns including numeric trait values, genotype,and environmental labels. Output format of each function is the dataframe with chosen stability index for each genotype. 
  Function "table_stability" offers the summary table of all stability indices in this package. 
  This R package toolStability is part of the main publication: 
- Wang, Casadebaig and Chen (2023) <doi: 10.1007/s00122-023-04264-7>. 
+ Wang, Casadebaig and Chen (2023) <doi:10.1007/s00122-023-04264-7>. 
  Analysis pipeline for main publication can be found on github: <https://github.com/Illustratien/Wang_2023_TAAG/tree/V1.0.0>. 
  Sample dataset in this package is derived from another publication:  
- Casadebaig P, Zheng B, Chapman S et al. (2016) <doi: 10.1371/journal.pone.0146385>. 
- For detailed documentation of dataset, please see on Zenodo <https://doi.org/10.5281/zenodo.4729636>. 
+ Casadebaig P, Zheng B, Chapman S et al. (2016) <doi:10.1371/journal.pone.0146385>. 
+ For detailed documentation of dataset, please see on Zenodo <doi:10.5281/zenodo.4729636>. 
  Indices used in this package are from: 
- Döring TF, Reckling M (2018) <doi: 10.1016/j.eja.2018.06.007>. 
- Eberhart SA, Russell WA (1966) <doi: 10.2135/cropsci1966.0011183X000600010011x>. 
- Eskridge KM (1990) <doi: 10.2135/cropsci1990.0011183X003000020025x>. 
- Finlay KW, Wilkinson GN (1963) <doi: 10.1071/AR9630742>. 
- Hanson WD (1970) Genotypic stability. <doi: 10.1007/BF00285245>. 
+ Döring TF, Reckling M (2018) <doi:10.1016/j.eja.2018.06.007>. 
+ Eberhart SA, Russell WA (1966) <doi:10.2135/cropsci1966.0011183X000600010011x>. 
+ Eskridge KM (1990) <doi:10.2135/cropsci1990.0011183X003000020025x>. 
+ Finlay KW, Wilkinson GN (1963) <doi:10.1071/AR9630742>. 
+ Hanson WD (1970) Genotypic stability. <doi:10.1007/BF00285245>. 
  Lin CS, Binns MR (1988) <https://cdnsciencepub.com/doi/abs/10.4141/cjps88-018>. 
  Nassar R, Hühn M (1987). 
- Pinthus MJ (1973) <doi: 10.1007/BF00021563>. 
+ Pinthus MJ (1973) <doi:10.1007/BF00021563>. 
  Römer T (1917). 
  Shukla GK (1972). 
  Wricke G (1962). 
diff --git a/README.Rmd b/README.Rmd
index abb2f20..e12c728 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -43,7 +43,7 @@ text2 <- unlist(strsplit(paste0("This R",Section[[1]][2]),"\n"))
 <!-- # # cat(paste("[![develVersion](https://img.shields.io/badge/devel%20version-", dver, "-orange.svg)](https://github.com/Illustratien/toolStability)", sep = "")) -->
 <!-- # ``` -->
 [![Github Code Size](https://img.shields.io/github/languages/code-size/Illustratien/toolStability.svg)](https://github.com/Illustratien/toolStability)
-[![Codecov test coverage](https://codecov.io/gh/Illustratien/toolStability/branch/master/graph/badge.svg)](https://codecov.io/gh/Illustratien/toolStability?branch=master)
+[![Codecov test coverage](https://codecov.io/gh/Illustratien/toolStability/branch/master/graph/badge.svg)](https://app.codecov.io/gh/Illustratien/toolStability?branch=master)
 [![R-CMD-check](https://github.com/Illustratien/toolStability/workflows/R-CMD-check/badge.svg)](https://github.com/Illustratien/toolStability/actions)
 <!-- [![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-yellowgreen.svg)](https://github.com/Illustratien/toolStability/commits/master) -->
 
diff --git a/README.md b/README.md
index 249add7..0f9d98b 100644
--- a/README.md
+++ b/README.md
@@ -31,9 +31,9 @@ version](https://img.shields.io/badge/R%3E%3D-3.5.0-6666ff.svg?logo=R)](https://
 [![Github Code
 Size](https://img.shields.io/github/languages/code-size/Illustratien/toolStability.svg)](https://github.com/Illustratien/toolStability)
 [![Codecov test
-coverage](https://codecov.io/gh/Illustratien/toolStability/branch/master/graph/badge.svg)](https://codecov.io/gh/Illustratien/toolStability?branch=master)
+coverage](https://codecov.io/gh/Illustratien/toolStability/branch/master/graph/badge.svg)](https://app.codecov.io/gh/Illustratien/toolStability?branch=master)
 [![R-CMD-check](https://github.com/Illustratien/toolStability/workflows/R-CMD-check/badge.svg)](https://github.com/Illustratien/toolStability/actions)
-<!-- [![Last-changedate](https://img.shields.io/badge/last%20change-2023--03--10-yellowgreen.svg)](https://github.com/Illustratien/toolStability/commits/master) -->
+<!-- [![Last-changedate](https://img.shields.io/badge/last%20change-2023--03--12-yellowgreen.svg)](https://github.com/Illustratien/toolStability/commits/master) -->
 
 <!-- [![.](https://raw.githubusercontent.com/vitr/google-analytics-beacon/master/static/badge-flat.gif)](https://github.com/Illustratien/google-analytics-beacon) -->
 <!-- [![rstudio mirror downloads](https://cranlogs.r-pkg.org/badges/grand-total/toolStability?color=green)](https://CRAN.R-project.org/package=toolStability) -->
@@ -45,24 +45,24 @@ coverage](https://codecov.io/gh/Illustratien/toolStability/branch/master/graph/b
 non-parametric and probabilistic approaches. The basic data format requirement for 'toolStability' is a data frame with 3 columns including numeric trait values, genotype,and environmental labels. Output format of each function is the dataframe with chosen stability index for each genotype.
 Function "table_stability" offers the summary table of all stability indices in this package.
 This R package toolStability is part of the main publication:
-Wang, Casadebaig and Chen (2023) <doi: 10.1007/s00122-023-04264-7>.
+Wang, Casadebaig and Chen (2023) <doi:10.1007/s00122-023-04264-7>.
 Analysis pipeline for main publication can be found on github: <https://github.com/Illustratien/Wang_2023_TAAG/tree/V1.0.0>.
 Sample dataset in this package is derived from another publication:
-Casadebaig P, Zheng B, Chapman S et al. (2016) <doi: 10.1371/journal.pone.0146385>.
-For detailed documentation of dataset, please see on Zenodo <https://doi.org/10.5281/zenodo.4729636>.
+Casadebaig P, Zheng B, Chapman S et al. (2016) <doi:10.1371/journal.pone.0146385>.
+For detailed documentation of dataset, please see on Zenodo <doi:10.5281/zenodo.4729636>.
 Indices used in this package are from:
-Döring TF, Reckling M (2018) <doi: 10.1016/j.eja.2018.06.007>.
-Eberhart SA, Russell WA (1966) <doi: 10.2135/cropsci1966.0011183X000600010011x>.
-Eskridge KM (1990) <doi: 10.2135/cropsci1990.0011183X003000020025x>.
-Finlay KW, Wilkinson GN (1963) <doi: 10.1071/AR9630742>.
-Hanson WD (1970) Genotypic stability. <doi: 10.1007/BF00285245>.
+Döring TF, Reckling M (2018) <doi:10.1016/j.eja.2018.06.007>.
+Eberhart SA, Russell WA (1966) <doi:10.2135/cropsci1966.0011183X000600010011x>.
+Eskridge KM (1990) <doi:10.2135/cropsci1990.0011183X003000020025x>.
+Finlay KW, Wilkinson GN (1963) <doi:10.1071/AR9630742>.
+Hanson WD (1970) Genotypic stability. <doi:10.1007/BF00285245>.
 Lin CS, Binns MR (1988) <https://cdnsciencepub.com/doi/abs/10.4141/cjps88-018>.
 Nassar R, Hühn M (1987).
-Pinthus MJ (1973) <doi: 10.1007/BF00021563>.
+Pinthus MJ (1973) <doi:10.1007/BF00021563>.
 Römer T (1917).
 Shukla GK (1972).
 Wricke G (1962). -->
-<!-- Tools to calculate stability indices with parametric,  non-parametric and probabilistic approaches. The basic data format requirement for 'toolStability' is a data frame with 3 columns including numeric trait values, genotype,and environmental labels. Output format of each function is the dataframe with chosen stability index for each genotype.  Function "table_stability" offers the summary table of all stability indices in this package.  This R package toolStability is part of the main publication:  Wang, Casadebaig and Chen (2023) <doi: 10.1007/s00122-023-04264-7>.  Analysis pipeline for main publication can be found on github: <https://github.com/Illustratien/Wang_2023_TAAG/tree/V1.0.0>.  Sample dataset in this package is derived from another publication:  Casadebaig P, Zheng B, Chapman S et al. (2016) <doi: 10.1371/journal.pone.0146385>.  For detailed documentation of dataset, please see on Zenodo <https://doi.org/10.5281/zenodo.4729636>.  Indices used in this package are from:  Döring TF, Reckling M (2018) <doi: 10.1016/j.eja.2018.06.007>.  Eberhart SA, Russell WA (1966) <doi: 10.2135/cropsci1966.0011183X000600010011x>.  Eskridge KM (1990) <doi: 10.2135/cropsci1990.0011183X003000020025x>.  Finlay KW, Wilkinson GN (1963) <doi: 10.1071/AR9630742>.  Hanson WD (1970) Genotypic stability. <doi: 10.1007/BF00285245>.  Lin CS, Binns MR (1988) <https://cdnsciencepub.com/doi/abs/10.4141/cjps88-018>.  Nassar R, Hühn M (1987).  Pinthus MJ (1973) <doi: 10.1007/BF00021563>.  Römer T (1917).  Shukla GK (1972).  Wricke G (1962). -->
+<!-- Tools to calculate stability indices with parametric,  non-parametric and probabilistic approaches. The basic data format requirement for 'toolStability' is a data frame with 3 columns including numeric trait values, genotype,and environmental labels. Output format of each function is the dataframe with chosen stability index for each genotype.  Function "table_stability" offers the summary table of all stability indices in this package.  This R package toolStability is part of the main publication:  Wang, Casadebaig and Chen (2023) <doi:10.1007/s00122-023-04264-7>.  Analysis pipeline for main publication can be found on github: <https://github.com/Illustratien/Wang_2023_TAAG/tree/V1.0.0>.  Sample dataset in this package is derived from another publication:  Casadebaig P, Zheng B, Chapman S et al. (2016) <doi:10.1371/journal.pone.0146385>.  For detailed documentation of dataset, please see on Zenodo <doi:10.5281/zenodo.4729636>.  Indices used in this package are from:  Döring TF, Reckling M (2018) <doi:10.1016/j.eja.2018.06.007>.  Eberhart SA, Russell WA (1966) <doi:10.2135/cropsci1966.0011183X000600010011x>.  Eskridge KM (1990) <doi:10.2135/cropsci1990.0011183X003000020025x>.  Finlay KW, Wilkinson GN (1963) <doi:10.1071/AR9630742>.  Hanson WD (1970) Genotypic stability. <doi:10.1007/BF00285245>.  Lin CS, Binns MR (1988) <https://cdnsciencepub.com/doi/abs/10.4141/cjps88-018>.  Nassar R, Hühn M (1987).  Pinthus MJ (1973) <doi:10.1007/BF00021563>.  Römer T (1917).  Shukla GK (1972).  Wricke G (1962). -->
 
 Tools to calculate stability indices with parametric, non-parametric and
 probabilistic approaches. The basic data format requirement for
@@ -73,24 +73,24 @@ Function “table_stability” offers the summary table of all stability
 indices in this package. There are 11 stability indices in this package.
 
 This R package toolStability is part of the main publication: Wang,
-Casadebaig and Chen (2023) \<doi: 10.1007/s00122-023-04264-7\>. Analysis
+Casadebaig and Chen (2023) <doi:10.1007/s00122-023-04264-7>. Analysis
 pipeline for main publication can be found on github:
 <https://github.com/Illustratien/Wang_2023_TAAG/tree/V1.0.0>.
 
 Sample dataset in this package is derived from another publication:
-Casadebaig P, Zheng B, Chapman S et al. (2016) \<doi:
-10.1371/journal.pone.0146385\>. For detailed documentation of dataset,
-please see on Zenodo <https://doi.org/10.5281/zenodo.4729636>.
+Casadebaig P, Zheng B, Chapman S et al. (2016)
+<doi:10.1371/journal.pone.0146385>. For detailed documentation of
+dataset, please see on Zenodo <doi:10.5281/zenodo.4729636>.
 
 <!-- Indices used in this package are from: (see tutorial for detailed information) -->
-<!-- Döring TF, Reckling M (2018) <doi: 10.1016/j.eja.2018.06.007>. -->
-<!-- Eberhart SA, Russell WA (1966) <doi: 10.2135/cropsci1966.0011183X000600010011x>. -->
-<!-- Eskridge KM (1990) <doi: 10.2135/cropsci1990.0011183X003000020025x>. -->
-<!-- Finlay KW, Wilkinson GN (1963) <doi: 10.1071/AR9630742>. -->
-<!-- Hanson WD (1970) Genotypic stability. <doi: 10.1007/BF00285245>.  -->
+<!-- Döring TF, Reckling M (2018) <doi:10.1016/j.eja.2018.06.007>. -->
+<!-- Eberhart SA, Russell WA (1966) <doi:10.2135/cropsci1966.0011183X000600010011x>. -->
+<!-- Eskridge KM (1990) <doi:10.2135/cropsci1990.0011183X003000020025x>. -->
+<!-- Finlay KW, Wilkinson GN (1963) <doi:10.1071/AR9630742>. -->
+<!-- Hanson WD (1970) Genotypic stability. <doi:10.1007/BF00285245>.  -->
 <!-- Lin CS, Binns MR (1988) <https://cdnsciencepub.com/doi/abs/10.4141/cjps88-018>. -->
 <!-- Nassar R, Hühn M (1987).  https://www.jstor.org/stable/2531698 -->
-<!-- Pinthus MJ (1973) <doi: 10.1007/BF00021563>.  -->
+<!-- Pinthus MJ (1973) <doi:10.1007/BF00021563>.  -->
 <!-- Römer T (1917).  https://www.nature.com/articles/hdy197287 -->
 <!-- Shukla GK (1972). -->
 <!-- Wricke G (1962). -->
diff --git a/doc/toolStability.pdf b/doc/toolStability.pdf
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diff --git a/inst/CITATION b/inst/CITATION
index 746c6f8..8e7538a 100644
--- a/inst/CITATION
+++ b/inst/CITATION
@@ -1,30 +1,3 @@
 citHeader("To cite the R package 'toolStability' in publications use:")
 
-if(!exists("meta") || is.null(meta)) meta <- packageDescription("toolStability")
-year <- sub(".*(2[[:digit:]]{3})-.*", "\\1", meta$Date)
-if (!length(year)) {
- year <- format(packageDate("toolStability"), "%Y")
-}
-vers <- paste("R package version", meta$Version)
-
-citEntry(entry  = "Manual",
-         title  = "toolStability: Tool for Stability Indices Calculation",
-         author = personList(person(given = "T.-C.", family = "Wang",
-                                    email = "wangtien@student.hu-berlin.de",
-                                    role = c("aut", "cre"),
-				    comment = c(ORCID = "0000-0001-7952-1404")),
-				    person(given = "T.-W.", family = "Chen",
-                                    email = "tsu-wei.chen@hu-berlin.de",
-				    comment = c(ORCID = "0000-0001-7952-1404"),
-			            role = "com")),
-         year = year,
-         textVersion = paste(
-           "Wang, T-C. and Chen, T-W. (",
-           year, ").  toolStability: Tool for stability indices calculation. ",
-           vers, ", ", "https://github.com/Illustratien/toolStability/", "https://cran.r-project.org/package=toolStability",
-           ".", sep="\n"),
-         note = {c(paste(vers), "https://github.com/Illustratien/toolStability/", "https://cran.r-project.org/package=toolStability")})
-
-citFooter("This free and open-source software implements academic
-research by the authors and co-workers. If you use it, please support
-the project by citing the package.")
+citFooter("Wang, TC., Casadebaig, P. & Chen, TW. More than 1000 genotypes are required to derive robust relationships between yield, yield stability and physiological parameters: a computational study on wheat crop. Theor Appl Genet 136, 34 (2023). https://doi.org/10.1007/s00122-023-04264-7")
diff --git a/man/toolStability-package.Rd b/man/toolStability-package.Rd
index 76e09db..4f57cb3 100644
--- a/man/toolStability-package.Rd
+++ b/man/toolStability-package.Rd
@@ -6,7 +6,7 @@
 \alias{toolStability-package}
 \title{toolStability: Tool for Stability Indices Calculation}
 \description{
-Tools to calculate stability indices with parametric, non-parametric and probabilistic approaches. The basic data format requirement for 'toolStability' is a data frame with 3 columns including numeric trait values, genotype,and environmental labels. Output format of each function is the dataframe with chosen stability index for each genotype. Function "table_stability" offers the summary table of all stability indices in this package. This R package toolStability is part of the main publication: Wang, Casadebaig and Chen (2023) \doi{ 10.1007/s00122-023-04264-7}. Analysis pipeline for main publication can be found on github: \url{https://github.com/Illustratien/Wang_2023_TAAG/tree/V1.0.0}. Sample dataset in this package is derived from another publication: Casadebaig P, Zheng B, Chapman S et al. (2016) \doi{ 10.1371/journal.pone.0146385}. For detailed documentation of dataset, please see on Zenodo \url{https://doi.org/10.5281/zenodo.4729636}. Indices used in this package are from: Döring TF, Reckling M (2018) \doi{ 10.1016/j.eja.2018.06.007}. Eberhart SA, Russell WA (1966) \doi{ 10.2135/cropsci1966.0011183X000600010011x}. Eskridge KM (1990) \doi{ 10.2135/cropsci1990.0011183X003000020025x}. Finlay KW, Wilkinson GN (1963) \doi{ 10.1071/AR9630742}. Hanson WD (1970) Genotypic stability. \doi{ 10.1007/BF00285245}. Lin CS, Binns MR (1988) \url{https://cdnsciencepub.com/doi/abs/10.4141/cjps88-018}. Nassar R, Hühn M (1987). Pinthus MJ (1973) \doi{ 10.1007/BF00021563}. Römer T (1917). Shukla GK (1972). Wricke G (1962).
+Tools to calculate stability indices with parametric, non-parametric and probabilistic approaches. The basic data format requirement for 'toolStability' is a data frame with 3 columns including numeric trait values, genotype,and environmental labels. Output format of each function is the dataframe with chosen stability index for each genotype. Function "table_stability" offers the summary table of all stability indices in this package. This R package toolStability is part of the main publication: Wang, Casadebaig and Chen (2023) \doi{10.1007/s00122-023-04264-7}. Analysis pipeline for main publication can be found on github: \url{https://github.com/Illustratien/Wang_2023_TAAG/tree/V1.0.0}. Sample dataset in this package is derived from another publication: Casadebaig P, Zheng B, Chapman S et al. (2016) \doi{10.1371/journal.pone.0146385}. For detailed documentation of dataset, please see on Zenodo \doi{10.5281/zenodo.4729636}. Indices used in this package are from: Döring TF, Reckling M (2018) \doi{10.1016/j.eja.2018.06.007}. Eberhart SA, Russell WA (1966) \doi{10.2135/cropsci1966.0011183X000600010011x}. Eskridge KM (1990) \doi{10.2135/cropsci1990.0011183X003000020025x}. Finlay KW, Wilkinson GN (1963) \doi{10.1071/AR9630742}. Hanson WD (1970) Genotypic stability. \doi{10.1007/BF00285245}. Lin CS, Binns MR (1988) \url{https://cdnsciencepub.com/doi/abs/10.4141/cjps88-018}. Nassar R, Hühn M (1987). Pinthus MJ (1973) \doi{10.1007/BF00021563}. Römer T (1917). Shukla GK (1972). Wricke G (1962).
 }
 \seealso{
 Useful links: