inst/doc/mortAAR_vignette_extended.R

In mortAAR: Analysis of Archaeological Mortality Data

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# load package dependencies
library(mortAAR)
library(magrittr)

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# load dataset muensingen
muen <- mortAAR::muensingen  

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muen %>% dplyr::select(age) %>% dplyr::arrange(nchar(age), age) %>% unique()

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# correct inconsistencies
muen <- muen %>%
  dplyr::mutate(
    age = dplyr::case_when(
      .$age == ">50"    ~ "50-70",
      .$age == ">60"    ~ "60-70",
      .$age == "10+/-1" ~ "9-12",
      .$age == "10"     ~ "10-11",
      .$age == "7-8"    ~ "7-9",
      .$age == "9-10"   ~ "9-11",
      TRUE            ~  .$age
    )
  )

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# split string column
muen <- muen %>% 
  tidyr::separate(age, c("from", "to")) %>%  
  transform(from = as.numeric(from), to = as.numeric(to))  

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# apply data preparation function 
muen_prep <- muen %>% 
    prep.life.table(
    group = "sex", 
    agebeg = "from", 
    ageend = "to", 
    method = "Standard", 
    agerange = "excluded" 
  )  

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# calculate life.table
muen_result <- muen_prep %>% 
  life.table() 

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options(width = 999)

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muen_result 

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muen_result %>% 
  plot(display = c("dx","qx", "lx", "ex", "rel_popx"))  

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mag <- magdalenenberg  

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mag <- mag %>% 
  replace(mag == "60-x", "60-69")  

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mag <- mag %>% 
  tidyr::separate(a, c("from", "to")) %>%  
  transform(from = as.numeric(from), to = as.numeric(to))  

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mag_prep <- mag %>% 
  prep.life.table( 
    dec = "Dx", 
    agebeg = "from", 
    ageend = "to", 
    method = "Equal5",
    agerange = "included"
  )  

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mag_result <- mag_prep %>% 
  life.table()  

mag_result 

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mag_result %>% 
  plot(display = c("dx","qx","ex"))  

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comp <- list(mag_prep$Deceased, muen_prep$All)  

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names(comp) <- c("Magdalenenberg", "Muensingen")  

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comp_result <- comp %>% 
  life.table()  

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comp_result %>% 
  plot(display = c("dx","qx", "lx","ex"))