update description for links and improve visuals in ReadME

DESCRIPTION

@@ -8,13 +8,14 @@ Author: Tien-Cheng Wang [aut, cre],
 	Tsu-Wei Chen [com]
 Maintainer: Tien-Cheng Wang <[email protected]>
 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. 
+ 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. 
- Please refer to the main publication for more detail: 
+ This R package toolStability is part of the main publication: 
  Wang, Casadebaig and Chen (2023) <doi: 10.1007/s00122-023-04264-7>. 
- Sample dataset in this package is from:  
+ 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>. 

README.Rmd

@@ -16,7 +16,10 @@ knitr::opts_chunk$set(
 
 ```{r,echo = FALSE, message = FALSE}
 suppressWarnings(devtools::load_all("."))
-
+wholetext <-  packageDescription("toolStability", fields = "Description")
+Section<- strsplit(wholetext,"This R")
+text1 <- Section[[1]][1]
+text2 <- unlist(strsplit(paste0("This R",Section[[1]][2]),"\n"))
 ```
 
 ###### License: [GPL-3](https://www.r-project.org/Licenses/)
@@ -52,7 +55,40 @@ suppressWarnings(devtools::load_all("."))
 
 ## Description
 <!-- `r packageDescription("toolStability", fields = "Description")` -->
-`r gsub("\\n", "  ", packageDescription("toolStability", fields = "Description"))`
+<!-- `r gsub("\\n", "  ", packageDescription("toolStability", fields = "Description"))` -->
+`r text1` `r "There are 11 stability indices in this package."`
+
+`r text2[1]`
+`r text2[2]`
+`r text2[3]`
+
+`r text2[4]`
+`r text2[5]`
+`r text2[6]`
+
+<!-- `r text2[7]``r " (see tutorial for detailed information)"` -->
+
+<!-- `r text2[8]` -->
+
+<!-- `r text2[9]` -->
+
+<!-- `r text2[10]` -->
+
+<!-- `r text2[11]` -->
+
+<!-- `r text2[12]`  -->
+
+<!-- `r text2[13]` -->
+
+<!-- `r text2[14]` `r " https://www.jstor.org/stable/2531698"` -->
+
+<!-- `r text2[15]`  -->
+
+<!-- `r text2[16]` `r " https://www.nature.com/articles/hdy197287"` -->
+
+<!-- `r text2[17]` -->
+
+<!-- `r text2[18]` -->
 ## Installation
 The package can be installed from CRAN as follows:
 
@@ -70,8 +106,8 @@ if (!require('remotes')) install.packages('remotes')
 remotes::install_github("Illustratien/toolStability")
 ```
 
-## Detailed tutorial
-A detailed tutorial with examples and references:
+## Tutorial
+There are 11 stability indices in this package. A detailed tutorial with examples and references:
  [click here](https://illustratien.github.io/toolStability/articles/toolStability.html).
 
 ## What's new
@@ -82,12 +118,16 @@ news(package='toolStability')
 ```
 
 ## Links
-[Publication](https://link.springer.com/article/10.1007/s00122-023-04264-7)
+[Main publication](https://link.springer.com/article/10.1007/s00122-023-04264-7)
 
-[Zenodo documentation](https://doi.org/10.5281/zenodo.5804212)
+[Main publication analysis pipeline](https://github.com/Illustratien/Wang_2023_TAAG/tree/V1.0.0)
+
+[Dataset documentation](https://doi.org/10.5281/zenodo.4729636)
 
 [CRAN page](https://cran.r-project.org/package=toolStability)
 
+[Package documentation](https://doi.org/10.5281/zenodo.5804212)
+
 ## Citing `toolStability`
 To cite the methods in the package please use:
 

README.md

@@ -42,13 +42,14 @@ coverage](https://codecov.io/gh/Illustratien/toolStability/branch/master/graph/b
 ## 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.
+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.
-Please refer to the main publication for more detail:
+This R package toolStability is part of the main publication:
 Wang, Casadebaig and Chen (2023) <doi: 10.1007/s00122-023-04264-7>.
-Sample dataset in this package is from:
+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>.
@@ -61,28 +62,42 @@ 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. Please refer to the main publication for more
-detail: Wang, Casadebaig and Chen (2023) \<doi:
-10.1007/s00122-023-04264-7\>. Sample dataset in this package is from:
+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
+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\>. 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). \## Installation The package can be
-installed from CRAN as follows:
+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: (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>.  -->
+<!-- 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>.  -->
+<!-- Römer T (1917).  https://www.nature.com/articles/hdy197287 -->
+<!-- Shukla GK (1972). -->
+<!-- Wricke G (1962). -->
+
+## Installation
+
+The package can be installed from CRAN as follows:
 
 ``` r
 install.packages('toolStability', dependencies=TRUE)
@@ -98,9 +113,10 @@ if (!require('remotes')) install.packages('remotes')
 remotes::install_github("Illustratien/toolStability")
 ```
 
-## Detailed tutorial
+## Tutorial
 
-A detailed tutorial with examples and references: [click
+There are 11 stability indices in this package. A detailed tutorial with
+examples and references: [click
 here](https://illustratien.github.io/toolStability/articles/toolStability.html).
 
 ## What’s new
@@ -113,12 +129,18 @@ news(package='toolStability')
 
 ## Links
 
-[Publication](https://link.springer.com/article/10.1007/s00122-023-04264-7)
+[Main
+publication](https://link.springer.com/article/10.1007/s00122-023-04264-7)
 
-[Zenodo documentation](https://doi.org/10.5281/zenodo.5804212)
+[Main publication analysis
+pipeline](https://github.com/Illustratien/Wang_2023_TAAG/tree/V1.0.0)
+
+[Dataset documentation](https://doi.org/10.5281/zenodo.4729636)
 
 [CRAN page](https://cran.r-project.org/package=toolStability)
 
+[Package documentation](https://doi.org/10.5281/zenodo.5804212)
+
 ## Citing `toolStability`
 
 To cite the methods in the package please use: