Quickstart with a general workflow
Obtain a data frame of the available formulas and measurements and decide on one or more formulas later.
knitr::kable(statuAAR::getFormulaDataframe())| short | long | measures |
|---|---|---|
| bb65 | breitinger_bach_1965 | Hum2, Hum1, Rad1b, Fem1, Tib1b |
| by89 | byers_etal_1989 | MtI1 |
| fe90 | feldesman_etal_1990 | Fem1 |
| ff96 | formicola_franceschi_1996 | Fem2+Tib1, Fem1, Tib1, Hum1, Rad1 |
| mn09 | maijanen_niskanen_2009 | Fem2+Tib1, Fem1+Tib1, Fem2, Fem1, Tib1, Hum1, Rad1, Fib1, Uln1 |
| ol78 | olivier_etal_1978 | Hum1, Rad1b, Fem2, Tib1b |
| pe99 | pearson_1899 | Hum1, Rad1, Fem1, Tib1b, Tib1a |
| ra08 | raxter_etal_2008 | Fem1, Fem1+Tib1a, Fem2, Fem2+Tib1a, Fem2+Tib1b, Hum1, Hum1+Rad1, Rad1, Tib1a, Tib1b |
| sj90 | sjovold_1990 | Hum1, Rad1, Rad1b, Uln1, Fem1, Fem2, Tib1, Tib1b, Fib1 |
| te50 | telkkae_1950 | Hum1, Rad2, Uln2, Fem1, Tib1, Fib1 |
| tg01 | trotter_gleser_1952_an | Fem1, Tib1b, Fib1, Uln1, Rad1, Hum1 |
| tg02 | trotter_gleser_1952_aw | Fem1, Tib1b, Fib1, Uln1, Rad1, Hum1 |
| ve09 | vercellotti_etal_2009 | Fem2+Tib1, Fem2, Fem1, Tib1, Hum1+Rad1, Hum1, Rad1 |
| r12a | ruff_etal_2012_a | Fem1, Hum1, Rad1 |
| r12s | ruff_etal_2012_s | Fem1+Tib1, Fem1, Tib1 |
| r12n | ruff_etal_2012_n | Fem1+Tib1, Fem1, Tib1 |
| bo84 | boldsen_1984 | Fem1, Tib1 |
You may check the corresponding documentation, e.g. for breitinger_bach_1965 (Bach, 1965).
?statuAAR::breitinger_bach_1965Load some data into a data frame (e.g. from Bach, 1965) .
| sex | Hum1 | Hum2 | Rad1b | stature | Fem1 | Tib1b |
|---|---|---|---|---|---|---|
| f | 220 | 215 | 146 | 1450 | 292 | 281 |
| f | 224 | 219 | 151 | 1460 | 299 | 287 |
| f | 229 | 224 | 156 | 1470 | 307 | 293 |
| f | 233 | 229 | 162 | 1480 | 315 | 298 |
| f | 239 | 234 | 167 | 1490 | 322 | 301 |
| f | 243 | 238 | 172 | 1500 | 330 | 310 |
Prepare tabled data into a long list (statuaar_data_table) and accept the warning about the missing ID for each individual.
dl.bach1965 <- statuAAR::prep.statuaar.data(Bach1965, d.form = "wide",
measures.names = "short", sex = "sex", stats = FALSE)## Warning in statuAAR::prep.statuaar.data(Bach1965, d.form = "wide",
## measures.names = "short", : No individual identifier provided, each record
## (row) will be counted as one individual.Check the measurements using the function provided for general statistics.
statuAAR::measures.statistics(dl.bach1965)## # A tibble: 5 × 8
## measure n MinM Quart1 MedianM MeanM Quart3 MaxM
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 Fem1 64 292 382 436 434 490 557
## 2 Hum1 64 220 278 311 309 343 387
## 3 Hum2 64 215 272 304 303 337 379
## 4 Rad1b 64 146 204 238 235 270 302
## 5 Tib1b 64 281 328 371 371 414 455Get the stature estimations of the provided measurements. The function returns a list with a data frame for each formula. You can address each data frame with the short name of the corresponding formula.
knitr::kable(head(statuAAR::getStature(c('bb65'), dl.bach1965)$bb65))| sex | stature | bone | if_female | if_male | if_indet | n_measures | |
|---|---|---|---|---|---|---|---|
| 32 | m | 1540 | Hum2, Rad1b, Fem1, Tib1b | 1531 | 1540 | 1536 | 4 |
| 33 | m | 1550 | Hum2, Rad1b, Fem1, Tib1b | 1538 | 1550 | 1544 | 4 |
| 34 | m | 1560 | Hum2, Rad1b, Fem1, Tib1b | 1546 | 1560 | 1553 | 4 |
| 35 | m | 1570 | Hum2, Rad1b, Fem1, Tib1b | 1554 | 1570 | 1562 | 4 |
| 36 | m | 1580 | Hum2, Rad1b, Fem1, Tib1b | 1561 | 1580 | 1571 | 4 |
| 37 | m | 1590 | Hum2, Rad1b, Fem1, Tib1b | 1570 | 1590 | 1580 | 4 |
Basic minimal workflow
Create a data frame with measures for one individual per row. If you do not provide an individual identifier or a sex assignment, row count and indet. will be added in the subsequent data preparation. We create a minimal data frame with data for a Neanderthal Man taken from Pearson (1899, p. 205).
x <- data.frame(Fem1 = 445.2, Hum1 = 312, Rad1 = 240)
knitr::kable(x)| Fem1 | Hum1 | Rad1 |
|---|---|---|
| 445.2 | 312 | 240 |
The column names correspond to the abbreviations used for the bone measurements, so no concordance for the names is required (create.measures.concordance()). The data can be transfered the wide table into the long format with only one measure per row (prep.statuaar.data()). Furthermore, we do not opt for a general statistic to check for possible errors in the data provided.
dl.Neanderthal <- statuAAR::prep.statuaar.data(x, d.form = "wide", stat = FALSE)## Warning in statuAAR::prep.statuaar.data(x, d.form = "wide", stat = FALSE): No
## individual identifier provided, each record (row) will be counted as one
## individual.
knitr::kable(dl.Neanderthal)| Ind | Sex | variable | value |
|---|---|---|---|
| 1 | indet | Fem1 | 445.2 |
| 1 | indet | Hum1 | 312.0 |
| 1 | indet | Rad1 | 240.0 |
We now can calculate the estimated stature in various ways.
- Just use a specific function and get a data frame with the estimated stature, the bone measurements used and the alternatives:
pearson_1899(dl.Neanderthal)## sex stature bone if_female if_male if_indet n_measures
## 1 indet 1610 Hum1, Rad1, Fem1 1592 1627 1610 3- You can use the function getStature() and provide a vector of formula short names and the prepared data frame to get a list containing the corresponding data frames. You can convert the list into a single data frame with an additional column for the formula.
res.Neanderthal <- getStature(c('bo84','bb65','mn09'), dl.Neanderthal)
knitr::kable(getStatureDataframe(res.Neanderthal))| formula | id | sex | stature | bone | if_female | if_male | if_indet | n_measures |
|---|---|---|---|---|---|---|---|---|
| bo84 | 1 | indet | 1642 | Fem1 | 1633 | 1650 | 1642 | 1 |
| bb65 | 1 | indet | 1658 | Hum1, Fem1 | 1648 | 1667 | 1658 | 2 |
| mn09 | 1 | indet | 1641 | 4. Fem1 | 1638 | 1643 | 1641 | 1 |
If you want to get all possible stature estimations use “all” instead of the vector with specific abbreviations.
res.Neanderthal <- getStature('all', dl.Neanderthal)
knitr::kable(getStatureDataframe(res.Neanderthal))| formula | id | sex | stature | bone | if_female | if_male | if_indet | n_measures |
|---|---|---|---|---|---|---|---|---|
| bb65 | 1 | indet | 1658 | Hum1, Fem1 | 1648 | 1667 | 1658 | 2 |
| fe90 | 1 | indet | 1665 | Fem1 | 1665 | 1665 | 1665 | 1 |
| ff96 | 1 | indet | 1639 | 2. Fem1 | 1622 | 1656 | 1639 | 1 |
| mn09 | 1 | indet | 1641 | 4. Fem1 | 1638 | 1643 | 1641 | 1 |
| ol78 | 1 | indet | 1612 | Hum1.l, Hum1.l | 1587 | 1637 | 1612 | 2 |
| pe99 | 1 | indet | 1610 | Hum1, Rad1, Fem1 | 1592 | 1627 | 1610 | 3 |
| ra08 | 1 | indet | 1628 | Fem1, Fem1 | 1612 | 1644 | 1628 | 2 |
| sj90 | 1 | indet | 1650 | Hum1, Rad1, Fem1 | 1650 | 1650 | 1650 | 3 |
| te50 | 1 | indet | 1610 | Hum1, Fem1 | 1579 | 1640 | 1610 | 2 |
| tg01 | 1 | indet | 1628 | 4. Fem1 | 1613 | 1643 | 1628 | 1 |
| tg02 | 1 | indet | 1657 | 4. Fem1 | 1641 | 1674 | 1657 | 1 |
| ve09 | 1 | indet | 1661 | Fem1 | 1640 | 1677 | 1661 | 1 |
| r12a | 1 | indet | 1638 | Fem1 | 1633 | 1639 | 1638 | 1 |
| r12s | 1 | indet | NA | Tib1 | NA | NA | NA | NA |
| r12n | 1 | indet | NA | Tib1 | NA | NA | NA | NA |
| bo84 | 1 | indet | 1642 | Fem1 | 1633 | 1650 | 1642 | 1 |