table_stability

<code>table_stability</code> export all the stability indices in the package.

regression

dynamic

nonparametric

probablistic

static

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).

Tien-Cheng Wang

toolStability

Tool for Stability Indices Calculation

Tsu-Wei Chen

table_stability function

<dl><dt>data</dt>
<dd>a data frame containing trait, genotype and environment.</dd>
<dt>trait</dt>
<dd>colname of a column containing a numeric vector of interested trait to be analyzed.</dd>
<dt>genotype</dt>
<dd>colname of a column containing a character or factor vector labeling different genotypic varieties.</dd>
<dt>environment</dt>
<dd>colname(s) of a column containing a character or factor vector labeling different environments,
if input is a vector containing multiple column names, then it will be merged into single environment column in the function.</dd>
<dt>lambda</dt>
<dd>the minimal acceptable value of trait that the user expected from crop across environments. Lambda should between the ranges of trait vlaue.</dd>
<dt>normalize</dt>
<dd>logical, default is <code>FALSE</code>, indicating whether stability indices should be normalized to the range from 0 to 1, where 1 refer to stable and 0 is unstable.</dd>
<dt>unit.correct</dt>
<dd>logical, default is <code>FALSE</code>, returning the stability index with unit equals to squared unit of trait; when <code>TRUE</code>, returning stability index with the unit as same as unit of trait.</dd></dl>

Arguments

Author

Table of stability indices — table_stability

<dl>

<dt>data</dt>
<dd>a data frame containing trait, genotype and environment.</dd>


<dt>trait</dt>
<dd>colname of a column containing a numeric vector of interested trait to be analyzed.</dd>


<dt>genotype</dt>
<dd>colname of a column containing a character or factor vector labeling different genotypic varieties.</dd>


<dt>environment</dt>
<dd>colname(s) of a column containing a character or factor vector labeling different environments,
if input is a vector containing multiple column names, then it will be merged into single environment column in the function.</dd>


<dt>lambda</dt>
<dd>the minimal acceptable value of trait that the user expected from crop across environments. Lambda should between the ranges of trait vlaue.</dd>


<dt>normalize</dt>
<dd>logical, default is <code>FALSE</code>, indicating whether stability indices should be normalized to the range from 0 to 1, where 1 refer to stable and 0 is unstable.</dd>


<dt>unit.correct</dt>
<dd>logical, default is <code>FALSE</code>, returning the stability index with unit equals to squared unit of trait; when <code>TRUE</code>, returning stability index with the unit as same as unit of trait.</dd>

</dl>

table_stability: Table of stability indices

Description

Usage

Value

Arguments

Author

Details

References

See Also

Examples