fn_coincide {Repbio}

20 May 2024

fn_coincide

Description

The coincidence between microscopy classification and GSI is analyzed. The count is based on the number of pairs that coincide (C) and the number of pairs that are misqualified: mature by immature (MI) and immature by mature (IM).

Return a filled table with the number of coincidences and discrepancies by factor levels and the total (rows) by category (columns): Coincidence (C), mature by immature (MI) and immature by mature (IM).

The function requires defining:

• N_Phase: A numerical value indicating the number of factor levels.
• df: A data frame with the values of each individual (row) by variables (columns).
• Icut: A numerical value is the threshold value to separate into two groups.
• Coincide: A table filled with NA, with N+1 rows, one for each factor level plus 1 for the total, and four columns, the first with the name of factor levels and the rest for the categories: C, MI and IM.

fn_coincide

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

#library(Repbio)

The function is detailed below.

fn_coincide <- function(N_Phase, df, Icut, Coincide){
  df$PHIGS <- (ifelse(df$GSI >= Icut, 1, 0))
    for(i in 1:N_Phase+1){
    if(i < N_Phase+1){
      OK <- ifelse(df$Phase == i & df$MATURE == df$PHIGS, 1,0)
      MI <- ifelse(df$Phase == i & df$MATURE > df$PHIGS, 1,0)
      IM <- ifelse(df$Phase == i & df$MATURE < df$PHIGS, 1,0)
      Phase <- paste0("Phase_", as.roman(i))
    }else{
      OK <- ifelse(df$MATURE == df$PHIGS, 1,0)
      MI <- ifelse(df$MATURE > df$PHIGS, 1,0)
      IM <- ifelse(df$MATURE < df$PHIGS, 1,0)
      Phase <- "Total"
    } # End if
    Coincide [i,] <- c(Phase,sum(OK),sum(MI),sum(IM))
  } # End for
  Coincide
} # End function

Examples

Falta detallar el ejemplo.

  # N_Phase <- 6
  # df <- tmp
  # Icut <- 2
  # Coincide <- data.frame(matrix(NA, ncol = 4, nrow = as.integer(N_Phase+1)))
  # 
  # ejemplo = fn_coincide(N_Phase, df, Icut, Coincide)

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