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) . + Wang, Casadebaig and Chen (2023) . Analysis pipeline for main publication can be found on github: . Sample dataset in this package is derived from another publication: - Casadebaig P, Zheng B, Chapman S et al. (2016) . - For detailed documentation of dataset, please see on Zenodo . + Casadebaig P, Zheng B, Chapman S et al. (2016) . + For detailed documentation of dataset, please see on Zenodo . Indices used in this package are from: - Döring TF, Reckling M (2018) . - Eberhart SA, Russell WA (1966) . - Eskridge KM (1990) . - Finlay KW, Wilkinson GN (1963) . - Hanson WD (1970) Genotypic stability. . + Döring TF, Reckling M (2018) . + Eberhart SA, Russell WA (1966) . + Eskridge KM (1990) . + Finlay KW, Wilkinson GN (1963) . + Hanson WD (1970) Genotypic stability. . Lin CS, Binns MR (1988) . Nassar R, Hühn M (1987). - Pinthus MJ (1973) . + Pinthus MJ (1973) . 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")) [![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) 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) - + @@ -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) . +Wang, Casadebaig and Chen (2023) . Analysis pipeline for main publication can be found on github: . Sample dataset in this package is derived from another publication: -Casadebaig P, Zheng B, Chapman S et al. (2016) . -For detailed documentation of dataset, please see on Zenodo . +Casadebaig P, Zheng B, Chapman S et al. (2016) . +For detailed documentation of dataset, please see on Zenodo . Indices used in this package are from: -Döring TF, Reckling M (2018) . -Eberhart SA, Russell WA (1966) . -Eskridge KM (1990) . -Finlay KW, Wilkinson GN (1963) . -Hanson WD (1970) Genotypic stability. . +Döring TF, Reckling M (2018) . +Eberhart SA, Russell WA (1966) . +Eskridge KM (1990) . +Finlay KW, Wilkinson GN (1963) . +Hanson WD (1970) Genotypic stability. . Lin CS, Binns MR (1988) . Nassar R, Hühn M (1987). -Pinthus MJ (1973) . +Pinthus MJ (1973) . 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) \. Analysis +Casadebaig and Chen (2023) . Analysis pipeline for main publication can be found on github: . Sample dataset in this package is derived from another publication: -Casadebaig P, Zheng B, Chapman S et al. (2016) \. For detailed documentation of dataset, -please see on Zenodo . +Casadebaig P, Zheng B, Chapman S et al. (2016) +. For detailed documentation of +dataset, please see on Zenodo . - - - - - + + + + + - + diff --git a/doc/toolStability.pdf b/doc/toolStability.pdf index 3414cba..d51f42f 100644 Binary files a/doc/toolStability.pdf and b/doc/toolStability.pdf differ 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: