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Tukey_HSD {Repbio}

20 May 2024

Tukey_HSD.Rmd

Tukey_HSD

Description

This function performs multiple comparisons of treatments by means of Tukey only if the p value of the ANOVA_1 test is equal to or less than pval defined by the user. The TukeyHSD test (Tukey Honest Significant Differences) use the HSD.test() from the agricolae package.

It returns: * A TukeyHSD test table hsd_out saved as txt file as: Tukey plus the name of the model variables, acronym criteria established to classify active females to reproduction (criterio) and the txt extension. *A TukeyHSD contrast plot saved as pdf file as: Tukey plus the name of the model variables, acronym criteria established to classify active females to reproduction (criterio) and the txt extension.

The object “criterio” must be defined outside the function. For the analysis performed in Salas-Singh et al. (2022), the “criterion” object presents two options: * BP: Separate immature from mature; * AR: Separate reproductively active mature organisms from reproductively inactive mature and immature organisms.

The function requires defining:

  • Prob: A summary from ANOVA-1 function.
  • pval: The significance level (user defined).
  • HSD_main: A mine title (user defined).
  • HSD_trt: Constant( only y=model) or vector treatment applied to each experimental unit.
  • fn_hsd: This function is included in this package Repbio, it returns the phase names in descending order by the average of the response values.
  • etiquetas: A data frame containing the user-defined labels that will be used throughout the routine.
  • formula: A formula notation y~f where y is the response (independent) variable and f is a factor (categorical) variable representing group membership.
  • criterio: Criteria for separating active reproductive organisms.
  • Phases_legend: A character vector with the name or number of maturity stages, as defined by the user.
{}{Criteria for separating active reproductive organisms BP: Separate immature from mature AR: Separate reproductively active mature organisms from reproductively inactive mature and immature organisms.}

{}{}

See also: fn_hsd from agricolae (version 1.3-7).

Tukey_HSD

The function is included in the Repbio package Reproductive biology analysis.

#library(Repbio)

The function is detailed below.

Tukey_HSD <- function(Prob, pval, HSD_main, HSD_trt, fn_hsd, etiquetas,
                      formula, criterio, Phases_legend){
  #  if (summary(Prob)[[1]][1, 5]<= 0.05){
  hsd_out <- agricolae::HSD.test(Prob, HSD_trt, group=TRUE,console=TRUE,
                      main=HSD_main, unbalanced = TRUE)
  sink(paste0("04_Tablas/Tukey_", as.character(formula)[2], "_",
              as.character(formula)[1],"_", criterio, ".txt"))
  print(hsd_out)
  sink()        # End sink

  # LTPh Contrast plot  ----
  r_names <- fn_hsd(hsd_out,Phases_legend) # Phase names are added.

  pdf(paste0("03_Figuras/Tukey_", as.character(formula)[2],"_",
             as.character(formula)[1],"_", criterio, ".pdf"))
  plot(hsd_out, xlab=etiquetas[6], ylab=etiquetas[5],xaxt = "n")
  par(usr=c(0.2,6.8,0.2,7))
  axis(1, labels = r_names, cex.axis=0.75,
       tick = FALSE, at=1:length(r_names))
  dev.off()
  #   } # End if
}  # End function

Examples

Falta detallar el ejemplo

   # pval <- 0.05
   # HSD_main <- LT/nPhase
   # HSD_trt <- Phase
   # exmple <- Tukey_HSD(Prob, pval, HSD_main, HSD_trt, fn_hsd, etiquetas,
   #                      formula, criterio, Phases_legend)

References

Salas‐Singh, C., Morales‐Bojórquez, E., & Aguirre‐Villaseñor, H. (2022). Reproductive biology of the bullseye puffer Sphoeroides annulatus: Gonadosomatic index and its suitability for estimating length at maturity. Journal of Fish Biology, 101(5), 1119-1133.https://doi.org/10.1111/jfb.15174