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#' @exportS3Method summary S2CFA
#' @keywords methods
#' @method summary S2CFA
#' @title S3 Summary for S2CFA
#' @description S3 summary method for object of class\code{"S2CFA"}
#' @param object object of class\code{"S2CFA"}
#' @param digits integer rounds the values to the specified number of decimal places, default is \code{digits=3}.
#' @param type character with default \code{type="ex.fisher.test"}, to return wether the observed pattern are 'discriminating Types' or not significant at all based on the respective p-value. Another option for \code{type} is \code{type="pChi"}.
#' @param sorton sort results of local test by any column. By default the output is not sorted. Other options may be \code{"pat."}, \code{"disc.Type"}, etc. ... So all column names that can potentially appear in the result.
#' @param decreasing logical. Should the sort be increasing or decreasing? see \code{\link{order}}
#' @param showall logical with default \code{showall = TRUE}. To return only significant pattern (discriminating types) set it to \code{showall = FALSE}.
#' @param adjalpha character with default \code{adjalpha = "bonferroni"}. Selector for the type of alpha adjustment for multiple testing. Possible options are: \code{adjalpha = "none"}, for no adjustment; \code{adjalpha = "bonferroni"}, for bonferroni adjustment (default); \code{adjalpha = "holm"}, for alpha adjustment according to Holm (1979); other options to come ... .
#' @param ... other parameters passed trough.
#' @return a summary of the results printed on the console.
#' @references Holm, S. (1979). A simple sequentially rejective multiple test procedure. \emph{Scandinavian Journal of Statistics, 6}(2), 65–70.
#' @references Bonferroni, C. E. (1935). Il calcolo delle assicurazioni su gruppi di teste. In S.O. Carboni (Ed.), \emph{Studi in Onore del Professore Salvatore Ortu Carboni} (S. 13–60). Roma, Tipografia del Senato: Bardi.
########################### hier die summary method #class S2CFA #######################
summary.S2CFA<-function(object, digits=3, type="ex.fisher.test", sorton=NULL, decreasing=FALSE, showall=TRUE, adjalpha = "bonferroni", ...){
#object, digits=3, type="z.pChi",sorton=NULL, decreasing=FALSE, showall=TRUE, holm=FALSE, wide=FALSE, adjalpha = "bonferroni", ...
local.test <- object$local.test
global.test <- object$global.test
# object$bonferroni.alpha
# disc.Type <- ifelse(local.test[,which(names(local.test)==type)] < object$bonferroni.alpha,yes="+", no=".")
#### significant (anti)types cf. Holm ----------------------------------------
## added 29-06-2021 adapted from summary.CFA ........
if(adjalpha=="holm"){ # 30-04-2021 new type of alpha adjustment control
p_val <- local.test[,which(names(local.test)==type)]
# if(!is.null(functional)){p_val[functional] <- NA} # not implemented (yet)
ord_p <- order(p_val,decreasing = FALSE) # starting with the smallest
k <- length(p_val)
n <- length(na.omit(p_val))
alpha <- object$alpha # 30-04-2021 according to new structure of S2CFA result object
i=0
holm_res <- vector(mode = "logical", length = k)
if(i<n){ # hier nur bis n (NAs werden nicht getestet)
while(p_val[ord_p[i+1]] < alpha/(n-(i))){
holm_res[i+1] <- p_val[ord_p[i+1]] < alpha/(n-(i))
i=i+1
}
}
temp1 <- holm_res[order(ord_p)] # reorders it back
disc.Type <- ifelse(test = local.test[,which(names(local.test)==type)] < temp1,yes="+", no=".")
#subsequent added on 8-2-2020
alpha_bon_temp1 <-(alpha/1:n)[(order(rev(ord_p[1:(length(ord_p))])))]
alpha_bon_temp2 <- p_val
alpha_bon_temp2[!is.na(p_val)] <- alpha_bon_temp1
alpha_bon <- alpha_bon_temp2
templocal <- data.frame(pat.=local.test[,1], disc.Type, Holm.crit=round(alpha_bon,digits=digits), round(local.test[,2:3],digits=digits), round(local.test[,5:10],digits=digits) , check.names = FALSE)
}
### significant (anti)types cf. (classical) Bonferroni adjustment ------------
if(adjalpha=="bonferroni"){ ## condition added 21-01-2019 # 30-04-2021 new type of alpha adjustment control
disc.Type <- ifelse(test = local.test[,which(names(local.test)==type)] < object$bonferroni.alpha, yes="+",no=".")
templocal <- data.frame(pat.=local.test[,1], disc.Type, round(local.test[,2:3],digits=digits), round(local.test[,5:10],digits=digits) , check.names = FALSE)
}
### significant (anti)types without any adjustment for multiple testing ------
if(adjalpha=="none"){ ## condition 30-04-2021
disc.Type <- ifelse(test = local.test[,which(names(local.test)==type)] < object$alpha, yes="+",no=".")
templocal <- data.frame(pat.=local.test[,1], disc.Type, round(local.test[,2:3],digits=digits), round(local.test[,5:10],digits=digits) , check.names = FALSE)
}
############## END of alpha adjustment methods -------------------------------
# sort output by sorton ... --------------------------------------------------
if (length(sorton)!=0 && any(names(templocal)%in%sorton) ){ #cond. changed 8-2-2020
# sorton <- "Holm.crit"
# sorton <- "p.stir"
# any(names(templocal)%in%sorton)
sorter <- order(templocal[,which(names(templocal)==sorton)],decreasing=decreasing)
erg <- templocal[sorter,]
}
if (length(sorton)!=0 && !any(names(templocal)%in%sorton) ){ #cond. changed 8-2-2020
erg <- templocal # dann wir das sortieren ignoriert wenns der user falsch eingibt -- ohne meldung
}
if (length(sorton)==0){
erg <- templocal
# muted the subsequent code on 23-06-2021
# if (adjalpha=="holm"){
# sorton <- type
# sorter <- order(templocal[,which(names(templocal)==sorton)],decreasing=decreasing)
# erg <- templocal[sorter,]
# }#added 'rev' 8-2-2020
}
if (showall==FALSE){
erg <- erg[erg$disc.Type!=".",]
}
# cat("results of global tests:","currently not implemented !","\n")
cat("\n", "Grouping by variable:", object$grouping$var, ", with categories:", object$grouping$cats, "\n", "pattern based on variables:", object$pat,"\n", "-----------------------")
# adapted from summary.CFA #29-06-2021
if(adjalpha=="bonferroni"){
cat("\n","results of local tests:","\n", "-----------------------","\n","discriminating Type (+) / not discriminating Type (.) based on:", type,";","\n", "with Bonferroni adjusted alpha:", object$bonferroni.alpha,"\n")#changed 30-04-2021
}
if(adjalpha=="holm"){
cat("\n","results of local tests:","\n", "-----------------------","\n","discriminating Type (+) / not discriminating Type (.) based on:", type, ";","\n","with Holm adjusted alpha - see \"Holm.crit\" \n")#added 21-01-2019 #changed 30-04-2021
}
if(adjalpha=="none"){
cat("\n","results of local tests:","\n", "-----------------------","\n","discriminating Type (+) / not discriminating Type (.) based on:", type, ";","\n","with not adjusted alpha:", object$alpha,"\n")#added 30-04-2021
}
return(erg)
}
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