Merge branch 'master' of https://github.com/Illustratien/toolStability

Author: Illustratien

R/table_stability.R

@@ -108,12 +108,21 @@ table_stability <- function(data, trait, genotype, environment, lambda, normaliz
     stop("Environment number must above 3")
   } else if (sample_number <= 5000 & sample_number >= 3) {
     normtest <- function(x){
-      return(shapiro.test(x)$p.value > 0.05)
+      res.ntest <- tryCatch({shapiro.test(x)},
+                            error=function(cond){
+                              return(list(p.value=0.01))
+                            })
+      return(res.ntest$p.value > 0.05)
     }
     norm.test.name <- "Shapiro"
   } else if (sample_number > 5000) {
+
     normtest <- function(x){
-      return(ad.test(x)$p.value > 0.05)
+      res.ntest <- tryCatch({ad.test(x)},
+                            error=function(cond){
+                              return(list(p.value=0.01))
+                            })
+      return(res.ntest$p.value > 0.05)
     }
     norm.test.name <- "Anderson-Darling"
   }
@@ -209,7 +218,7 @@ table_stability <- function(data, trait, genotype, environment, lambda, normaliz
                      "Variance.of.rank",
                      "Deviation.mean.squares",
                      "Genotypic.superiority.measure"
-                     )
+  )
   if (unit.correct==TRUE){
     res <- mutate_at(res,need.squared.si, sqrt)
   }

inst/CITATION

@@ -1,3 +1,2 @@
-citHeader("To cite the R package 'toolStability' in publications use:")
-
-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")
+"To cite the R package 'toolStability' in publications use:
+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"

man/toolStability-package.Rd

@@ -335,10 +335,10 @@ Ecovalence [@wricke1962] is calculated based on square and sum up the genotype
 interaction all over the environment.
 Variety with low ecovalence is considered as stable.
 Ecovalence is expressed as:
-$$W_{i} = \sum_{j}~(X_{ij} - \bar{X_{i.}} - \bar{X_{.j}} + \bar{X_{..}}^{2})$$
+$$W_{i} = \sum_{j}~(X_{ij} - \bar{X_{i.}} - \bar{X_{.j}} + \bar{X_{..}})^{2}$$
 To let $W_{i}$ comparable between experiments, we also provide the modified ecovalence ($W_{i}'$), whcih take the number of environments into account. User can get ($W_{i}'$) by setting `modify = TRUE`.
 
-$$W_{i}' = \frac{\sum_{j}~(X_{ij} - \bar{X_{i.}} - \bar{X_{.j}} + \bar{X_{..}}^{2})}{E-1}$$
+$$W_{i}' = \frac{\sum_{j}~(X_{ij} - \bar{X_{i.}} - \bar{X_{.j}} + \bar{X_{..}})^{2}}{E-1}$$
 where $X_{ij}$ is the observed phenotypic mean value of genotype $i$ (i = 1,..., G)
 in environment $j$ (j = 1,...,E), with $\bar{X_{i.}}$ denoting marginal means of genotype $i$.