TestDimorph examples

Table 1 Description of the main functions of the TestDimorph R package.

This is Table 2. The R script extracts summary statistics for body mass from the 1999-2000 NHANES raw data and stores it in NHANES_univariate. The “populations” are self-reported race, coded as “Black” = Non-Hispanic Black, “Mex.Am” = Mexican American, or “White” = Non-Hispanic White, and the data are restricted to ages 20-40 years (inclusive). The output are an ANOVA (type II sums of squares by default) with eta-squared values and a table of pairwise comparisons. For more information on the NHANES studies see https://www.cdc.gov/nchs/nhanes/index.htm

Table.02=function () 
{
library(TestDimorph)
options(width=100) # This option just for output from Rmarkdown
NHANES_univariate<<-extract_sum(NHANES_1999,test='uni',run=FALSE) # BMXWT (Body mass)
univariate(NHANES_univariate,es_anova = "eta2",pairwise = TRUE)
}

Table.02()

The parameter used is BMXWT

$univariate
       term   df    sumsq  meansq statistic p.value signif   eta2 lower.eta2 upper.eta2
1       Sex    1  25378.2 25378.2   63.8746  0.0000    *** 0.0429     0.0247     0.0652
2       Pop    2  20970.0 10485.0   26.3898  0.0000    *** 0.0357     0.0186     0.0558
3   Sex*Pop    2   4141.8  2070.9    5.2123  0.0056     ** 0.0073     0.0007     0.0177
4 Residuals 1424 565773.3   397.3        NA      NA   <NA>     NA         NA         NA

$pairwise
   populations   df mean.diff conf.low conf.high statistic p.value signif
1 Black-Mex.Am  764   -5.9980 -11.8657   -0.1304   -2.0067  0.0451      *
2  Black-White  965   -8.9769 -14.8397   -3.1142   -3.0048  0.0027     **
3 Mex.Am-White 1119   -2.9789  -7.4263    1.4685   -1.3142  0.1890     ns

This is Table 3. The R script extracts summary statistics for body mass, standing height, and upper arm length from the 1999-2000 NHANES raw data and stores it in NHANES_multivariate. The “populations” are self-reported race, coded as “Black” = Non-Hispanic Black, “Mex.Am” = Mexican American, or “White” = Non-Hispanic White, and the data are restricted to ages 20-40 years (inclusive). The output is a MANOVA table (type II sums of squares and cross products by default) using Wilk’s lambda (the default).

Table.03=function()
{
library(TestDimorph)
NHANES_multivariate<<-extract_sum(NHANES_1999,test='multi',run=FALSE)
multivariate(NHANES_multivariate)
}

Table.03()

The parameters used are BMXWT,BMXHT,BMXARML

        term df  Wilks approx.f num.df den.df p.value signif
1     Sex(E)  1 0.5223 433.5580      3   1422  0.0000    ***
2     Pop(E)  2 0.7637  68.4009      6   2844  0.0000    ***
3 Sex*Pop(E)  2 0.9851   3.5834      6   2844  0.0015     **

This is Table 4. The R script uses NHANES_univariate and does an ANOVA with type III sums of squares. It then applies t_greene to do Relethford and Hodges’ (1985) and Greene’s (1989) t-test for all pairs, adjusts the p-values using the false discovery rate, and finally returns a “corrplot” view (https://cran.r-project.org/package=corrplot) of the p-values.

Table.04=function()
{
library(TestDimorph)
print(univariate(NHANES_univariate, type_anova='III'))
t_greene(NHANES_univariate,plot = TRUE,padjust ="fdr")
}

Table.04()

       term   df    sumsq  meansq statistic p.value signif
1       Sex    1  17356.4 17356.4   43.6845  0.0000    ***
2       Pop    2  18902.3  9451.2   23.7877  0.0000    ***
3   Sex*Pop    2   4141.8  2070.9    5.2123  0.0056     **
4 Residuals 1424 565773.3   397.3        NA      NA   <NA>

   populations   df mean.diff conf.low conf.high statistic p.value signif
1 Black-Mex.Am  764   -5.9980 -11.8657   -0.1304   -2.0067 0.06765     ns
2  Black-White  965   -8.9769 -14.8397   -3.1142   -3.0048 0.00810     **
3 Mex.Am-White 1119   -2.9789  -7.4263    1.4685   -1.3142 0.18900     ns

This is Table 5. The R script extracts summary statistics on eight variables from four samples in the W.W. Howells’(1973, 1989, 1995, 1996) dataset. The full data set can be found in https://rdrr.io/github/geanes/bioanth/man/howell.html. The script then runs van Vark et al.’s (1989) analysis.

Table.05=function()
{
library(TestDimorph)
to_van_Vark=extract_sum(Howells,test='van',run=F)
van_vark(to_van_Vark)
}

Table.05()

The parameters used are GOL,NOL,BNL,BBH,XCB,XFB,ZYB,AUB

The maximum possible value of q is (7).

  populations statistic df p.value signif
1 NORSE-EGYPT    1.2809  2  0.5271     ns
2 NORSE-TOLAI    8.8981  2  0.0117      *
3  NORSE-PERU    0.4268  2  0.8078     ns
4 EGYPT-TOLAI    5.2097  2  0.0739     ns
5  EGYPT-PERU    0.7477  2  0.6881     ns
6  TOLAI-PERU    5.4584  2  0.0653     ns

This is Table 6. The R script writes summary statistics on femur head diameters for males and females from four samples (Curate et al. 2017; Gulhan 2017; Kranioti et al. 2009; Timonov et al. 2014) to the object df. It then uses aov_ss to do ANOVA within males and within females across the four samples with each ANOVA followed by post-hoc pairwise comparisons.

Table.06=function () 
{
# Comparisons of femur head diameter in four populations
library(TestDimorph)
df <- data.frame(
  Pop = c("Turkish", "Bulgarian", "Greek", "Portuguese"),
  m = c(150.00, 82.00, 36.00, 34.00),
  f = c(150.00, 58.00, 34.00, 24.00),
  M.mu = c(49.39, 48.33, 46.99, 45.20),
  F.mu = c(42.91, 42.89, 42.44, 40.90),
  M.sdev = c(3.01, 2.53, 2.47, 2.00),
  F.sdev = c(2.90, 2.84, 2.26, 2.90)
)
print(aov_ss(x = df, CI=0.95),digits=6)
}

Table.06()

$`Male model`
         term  df    sumsq   meansq statistic p.value signif
1 Populations   3  566.214 188.7379   25.4042       0    ***
2   Residuals 298 2213.959   7.4294        NA      NA   <NA>

$`Male posthoc`
           populations mean.diff conf.low conf.high p.value signif
1      Greek-Bulgarian     -1.34  -2.7479    0.0679  0.0686     ns
2 Portuguese-Bulgarian     -3.13  -4.5664   -1.6936  0.0000    ***
3    Turkish-Bulgarian      1.06   0.0929    2.0271  0.0254      *
4     Portuguese-Greek     -1.79  -3.4741   -0.1059  0.0323      *
5        Turkish-Greek      2.40   1.0930    3.7070  0.0000    ***
6   Turkish-Portuguese      4.19   2.8524    5.5276  0.0000    ***

$`Female model`
         term  df     sumsq  meansq statistic p.value signif
1 Populations   3   88.4265 29.4755    3.7221   0.012      *
2   Residuals 262 2074.8100  7.9191        NA      NA   <NA>

$`Female posthoc`
           populations mean.diff conf.low conf.high p.value signif
1      Greek-Bulgarian     -0.45  -2.0216    1.1216  0.8807     ns
2 Portuguese-Bulgarian     -1.99  -3.7560   -0.2240  0.0202      *
3    Turkish-Bulgarian      0.02  -1.1050    1.1450  1.0000     ns
4     Portuguese-Greek     -1.54  -3.4798    0.3998  0.1716     ns
5        Turkish-Greek      0.47  -0.9120    1.8520  0.8156     ns
6   Turkish-Portuguese      2.01   0.4104    3.6096  0.0071     **

This is Table 7. The R script uses the maximum width of the patella from Cavazzuti et al. (2019). Calculated values are the mixture index (MI) and normal intersection (NI) (Ipiña and Durand 2010), the D index (Chakraborty and Majumder 1982), and Hedges’ g (Hedges 1981). For each statistic the bias-corrected parametric bootstrap (Efron 1981; Tibshirani 1984) is run 1,000 starting from a set.seed value of 42.

Table.07=function (i.which=13) 
{
library(TestDimorph)
print(MI_index(Cremains_measurements[i.which,],B=1000,rand=F,verbose=F,plot=T))
print(MI_index(Cremains_measurements[i.which,],index_type='NI',
   B=1000,rand=F,plot=T,verbose=F))
print(D_index(Cremains_measurements[i.which,],B=1000,rand=F,verbose=F,plot=T))
print(Hedges_g(Cremains_measurements[i.which,],B=1000,rand=F,verbose=F))
}

Table.07()

   Trait lower     MI upper
1 PA-MXW 0.025 0.1108 0.231

   Trait  lower     NI upper
1 PA-MXW 0.0544 0.2496 0.521

   Trait  lower      D  upper
1 PA-MXW 0.4788 0.7504 0.9454
   Trait  lower      g  upper
1 PA-MXW 1.2094 2.2429 3.7713

References