Author: Clemens Schmid

# Vignette >Basic usage<

#### Clemens Schmid

#### March 2017

# Load libraries

    library(mortAAR)
    library(magrittr)

# Make test data available

Data from four neolithic gallery graves in central Germany (Czarnetzki 1966).

    td <- gallery_graves

Inspect the data. Show the first ten rows of the data set:

indnr | sex | age | site
--- | --- | --- | ---
2 | m | 20-30 | Niedertiefenbach
7 | m | 20-30 | Niedertiefenbach
9 | m | 40-50 | Niedertiefenbach
9t | m | 50-60 | Niedertiefenbach
23 | m | 20-30 | Niedertiefenbach
30 | m | 20-30 | Niedertiefenbach
39 | m | 20-30 | Niedertiefenbach
45 | m | 20-30 | Niedertiefenbach
58 | m | 30-40 | Niedertiefenbach
69 | m | 20-30 | Niedertiefenbach

# Clean up data

Replace: “?” with `NA` values.

    td %>% replace(td == "?", NA) -> td

indnr | sex | age | site
--- | --- | --- | ---
2 | m | 20-30 | Niedertiefenbach
7 | m | 20-30 | Niedertiefenbach
9 | m | 40-50 | Niedertiefenbach
9t | m | 50-60 | Niedertiefenbach
23 | m | 20-30 | Niedertiefenbach
30 | m | 20-30 | Niedertiefenbach
39 | m | 20-30 | Niedertiefenbach
45 | m | 20-30 | Niedertiefenbach
58 | m | 30-40 | Niedertiefenbach
69 | m | 20-30 | Niedertiefenbach

Translate “inf_I”, “inf_I” and “juv” into numeric age ranges (Martin 1928, 580).

    td <- td %>%
      replace(td == "inf_I",  "0-6") %>%
      replace(td == "inf_II", "7-13") %>%
      replace(td == "juv",    "14-19")

indnr | sex | age | site
--- | --- | --- | ---
2 | m | 20-30 | Niedertiefenbach
7 | m | 20-30 | Niedertiefenbach
9 | m | 40-50 | Niedertiefenbach
9t | m | 50-60 | Niedertiefenbach
23 | m | 20-30 | Niedertiefenbach
30 | m | 20-30 | Niedertiefenbach
39 | m | 20-30 | Niedertiefenbach
45 | m | 20-30 | Niedertiefenbach
58 | m | 30-40 | Niedertiefenbach
69 | m | 20-30 | Niedertiefenbach

Remove rows that do not have age information.

    td <- td %>%
      dplyr::filter(!is.na(age))

indnr | sex | age | site
--- | --- | --- | ---
2 | m | 20-30 | Niedertiefenbach
7 | m | 20-30 | Niedertiefenbach
9 | m | 40-50 | Niedertiefenbach
9t | m | 50-60 | Niedertiefenbach
23 | m | 20-30 | Niedertiefenbach
30 | m | 20-30 | Niedertiefenbach
39 | m | 20-30 | Niedertiefenbach
45 | m | 20-30 | Niedertiefenbach
58 | m | 30-40 | Niedertiefenbach
69 | m | 20-30 | Niedertiefenbach

Make a decision on individual 139 from Niedertiefenbach with age less or equal 60.

    td[td$indnr == "139" & td$site == "Niedertiefenbach", ]$age <- "50-60"

indnr | sex | age | site
--- | --- | --- | ---
2 | m | 20-30 | Niedertiefenbach
7 | m | 20-30 | Niedertiefenbach
9 | m | 40-50 | Niedertiefenbach
9t | m | 50-60 | Niedertiefenbach
23 | m | 20-30 | Niedertiefenbach
30 | m | 20-30 | Niedertiefenbach
39 | m | 20-30 | Niedertiefenbach
45 | m | 20-30 | Niedertiefenbach
58 | m | 30-40 | Niedertiefenbach
69 | m | 20-30 | Niedertiefenbach

Separate the age range column.

    td <- td %>%
      tidyr::separate(age, c("from", "to"))

    ## Warning: Expected 2 pieces. Missing pieces filled with `NA` in 1 rows [35].

indnr | sex | from | to | site
--- | --- | --- | --- | ---
2 | m | 20 | 30 | Niedertiefenbach
7 | m | 20 | 30 | Niedertiefenbach
9 | m | 40 | 50 | Niedertiefenbach
9t | m | 50 | 60 | Niedertiefenbach
23 | m | 20 | 30 | Niedertiefenbach
30 | m | 20 | 30 | Niedertiefenbach
39 | m | 20 | 30 | Niedertiefenbach
45 | m | 20 | 30 | Niedertiefenbach
58 | m | 30 | 40 | Niedertiefenbach
69 | m | 20 | 30 | Niedertiefenbach

Adjust variable types.

    td <- td %>%
      transform(
        from = as.numeric(from),
        to = as.numeric(to)
      )

# Analysis preparation

Control the flow of the analysis by exemplifying what the different variables of the input data stand for.

    # tdlist <- td %>%
    #   plyr::dlply("site", identity)

    td_prepared <- prep.life.table(
      td,
      dec = NA,
      agebeg = "from",
      ageend = "to",
      group = "site",
      method = "Standard",
      agerange = "included"
    )

# Analysis

    td_result <- td_prepared %>%
      life.table()

# Plot

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

    ## Warning: Removed 1 row containing missing values (`geom_line()`).

    td_result %>% plot(display = c("ex", "rel_popx"))

    ## Warning: Removed 1 row containing missing values (`geom_line()`).

# References

Czarnetzki, A. 1966. “Die Menschlichen Skelettreste Aus Vier Neolithischen Steinkisten Hessens Und Niedersachsens.” Dissertation. Tuebingen.
Martin, Rudolf. 1928. Lehrbuch der Anthropologie in systematischer Darstellung. Mit besonderer Beruecksichtigung der anthropologischen Methoden. Band 2: Kraniologie. 2. ed. Jena: G. Fischer. https://doi.org/10.11588/diglit.37612.