Pairwise Mahalanobis Distance using the D2.dist function in the Biotools Package: Error Message

Kaikash777 · June 10, 2022, 1:59pm

Issue:

I'm having some trouble calculating the Mahalanobis Distance between three classes of the independent variable Country .

My aim is to calculate the Mahalanobis distance among acoustic parameters measured from a spectrogram taken from three populations in three different study regions . I want to calculate potential (dis)similarity amongst acoustic parameters between study regions.

My dependent variable has three classes "France", "Spain" and "Italy"
My data frame has multiple variables (features of acoustic parameter aspects) to be taken into account.
There are multiple observations per group (obs = 367; indicating the data frame contains more than one row per dependent variable Country ).

I want to use the D2.dist() function from the biotools package and I am following this tutorial on YouTube here. However, I got this error (see below) and I can't figure out how to fix the issue.

Error in D2.disc.default(Mean_Acoustic_Param[, -1], covar) : 
  incompatible dimensions!

As always, any help is deeply appreciated.

R-CODE:

library(biotools) #pairwise.mahalanobis function
library(cluster) #agnes function

group = matrix(Cluster_Dummy_2$Country) #what is being compared
group = t(group[,1]) #prepare for pairwise.mahalanobis function

variables = c(variables = c("Low.Freq", "High.Freq", "Peak.Freq", "Delta.Freq", "Delta.Time", "Peak.Time", 
                            "Center.Freq", "Start.Freq","End.Freq")) #variables (what is being used for comparison)

variables = as.matrix(Cluster_Dummy_2[,variables]) #prepare for pairwise.mahalanobis function
variables

#Calculate the mean for each acoustic parameter per country
Cluster_Dummy_Means<-Cluster_Dummy_2 %>% group_by(Country) %>% summarise(across(where(is.numeric), .fns =list(Mean = mean)))
Cluster_Dummy_Means   

#Produce a dataframe object as the output results are <dbl> format
Mean_Acoustic_Param<-as.data.frame(Cluster_Dummy_Means)
Mean_Acoustic_Param

#Model for MANOVA
Mahalanobis.model<-manova(variables~as.factor(group))
Mahalanobis.model

#Summarise the model
summary(Mahalanobis.model)

#Calculates a matrix of estimated variance matrix for multivariate models
store.Mahala<-SSD(Mahalanobis.model)
store.Mahala

#Estimate the covariance matrix
#Divide the variance matrix by the degrees of freedom
covar<-store.Mahala$SSD/store.Mahala$df
covar

#Percentage contribution of each dependent variable (acoustic parameters)
imp <-singh(variables, covar)
imp

#Plot the variables by their percentage importance 
plot(imp)

#Calculate the distance between groups
distance<-D2.disc(Mean_Acoustic_Param[,-1], covar)

Error in D2.disc.default(Mean_Acoustic_Param[, -1], covar) : 
  incompatible dimensions!

Data

structure(list(Low.Freq = c(435L, 94103292L, 1L, 2688L, 8471L, 
    28818L, 654755585L, 468628164L, 342491L, 2288474L, 3915L, 411L, 
    267864894L, 3312618L, 5383L, 8989443L, 1894L, 534981L, 9544861L, 
    3437614L, 475386L, 7550764L, 48744L, 2317845L, 5126197L, 2445L, 
    8L, 557450L, 450259742L, 21006647L, 9L, 7234027L, 59L, 9L, 605L, 
    9199L, 3022L, 30218156L, 46423L, 38L, 88L, 396396244L, 28934316L, 
    7723L, 95688045L, 679354L, 716352L, 76289L, 332826763L, 6L, 90975L, 
    83103577L, 9529L, 229093L, 42810L, 5L, 18175302L, 1443751L, 5831L, 
    8303661L, 86L, 778L, 23947L, 8L, 9829740L, 2075838L, 7434328L, 
    82174987L, 2L, 94037071L, 9638653L, 5L, 3L, 65972L, 0L, 936779338L, 
    4885076L, 745L, 8L, 56456L, 125140L, 73043989L, 516476L, 7L, 
    4440739L, 612L, 3966L, 8L, 9255L, 84127L, 96218L, 5690L, 56L, 
    3561L, 78738L, 1803363L, 809369L, 7131L, 0L), High.Freq = c(6071L, 
    3210L, 6L, 7306092L, 6919054L, 666399L, 78L, 523880161L, 4700783L, 
    4173830L, 30L, 811L, 341014L, 780L, 44749L, 91L, 201620707L, 
    74L, 1L, 65422L, 595L, 89093186L, 946520L, 6940919L, 655350L, 
    4L, 6L, 618L, 2006697L, 889L, 1398L, 28769L, 90519642L, 984L, 
    0L, 296209525L, 487088392L, 5L, 894L, 529L, 5L, 99106L, 2L, 926017L, 
    9078L, 1L, 21L, 88601017L, 575770L, 48L, 8431L, 194L, 62324996L, 
    5L, 81L, 40634727L, 806901520L, 6818173L, 3501L, 91780L, 36106039L, 
    5834347L, 58388837L, 34L, 3280L, 6507606L, 19L, 402L, 584L, 76L, 
    4078684L, 199L, 6881L, 92251L, 81715L, 40L, 327L, 57764L, 97668898L, 
    2676483L, 76L, 4694L, 817120L, 51L, 116712L, 666L, 3L, 42841L, 
    9724L, 21L, 4L, 359L, 2604L, 22L, 30490L, 5640L, 34L, 51923625L, 
    35544L), Peak.Freq = c(87005561L, 9102L, 994839015L, 42745869L, 
    32840L, 62737133L, 2722L, 24L, 67404881L, 999242982L, 3048L, 
    85315406L, 703037627L, 331264L, 8403609L, 3934064L, 50578953L, 
    370110665L, 3414L, 12657L, 40L, 432L, 7707L, 214L, 68588962L, 
    69467L, 75L, 500297L, 704L, 1L, 102659072L, 60896923L, 4481230L, 
    94124925L, 60164619L, 447L, 580L, 8L, 172L, 9478521L, 20L, 53L, 
    3072127L, 2160L, 27301893L, 8L, 4263L, 508L, 712409L, 50677L, 
    522433683L, 112844L, 193385L, 458269L, 93578705L, 22093131L, 
    6L, 9L, 1690461L, 0L, 4L, 652847L, 44767L, 21408L, 5384L, 304L, 
    721L, 651147L, 2426L, 586L, 498289375L, 945L, 6L, 816L, 46207L, 
    39135L, 6621028L, 66905L, 26905085L, 4098L, 0L, 14L, 88L, 530L, 
    97809006L, 90L, 6L, 260792844L, 9L, 833205723L, 99467321L, 5L, 
    8455640L, 54090L, 2L, 309L, 299161148L, 4952L, 454824L), Delta.Freq = c(5L, 
    78L, 88553L, 794L, 5L, 3859122L, 782L, 36L, 8756801L, 243169338L, 
    817789L, 8792384L, 7431L, 626921743L, 9206L, 95789L, 7916L, 8143453L, 
    6L, 4L, 6363L, 181125L, 259618L, 6751L, 33L, 37960L, 0L, 2L, 
    599582228L, 565585L, 19L, 48L, 269450424L, 70676581L, 7830566L, 
    4L, 86484313L, 21L, 90899794L, 2L, 72356L, 574280L, 869544L, 
    73418L, 6468164L, 2259L, 5938505L, 31329L, 1249L, 354L, 8817L, 
    3L, 2568L, 82809L, 29836269L, 5230L, 37L, 33752014L, 79307L, 
    1736L, 8522076L, 40L, 2289135L, 862L, 801448L, 8026L, 5L, 15L, 
    4393771L, 405914L, 71098L, 950288L, 8319L, 1396973L, 832L, 70L, 
    1746L, 61907L, 8709547L, 300750537L, 45862L, 91417085L, 79892L, 
    47765L, 5477L, 18L, 4186L, 2860L, 754038591L, 375L, 53809223L, 
    72L, 136L, 509L, 232325L, 13128104L, 1692L, 8581L, 23L), Delta.Time = c(1361082L, 
    7926L, 499L, 5004L, 3494530L, 213L, 64551179L, 70L, 797L, 5L, 
    72588L, 86976L, 5163L, 635080L, 3L, 91L, 919806257L, 81443L, 
    3135427L, 4410972L, 5810L, 8L, 46603718L, 422L, 1083626L, 48L, 
    15699890L, 7L, 90167635L, 446459879L, 2332071L, 761660L, 49218442L, 
    381L, 46L, 493197L, 46L, 798597155L, 45342274L, 6265842L, 6L, 
    3445819L, 351L, 1761227L, 214L, 959L, 908996387L, 6L, 3855L, 
    9096604L, 152664L, 7970052L, 32366926L, 31L, 5201618L, 114L, 
    7806411L, 70L, 239L, 5065L, 2L, 1L, 14472831L, 122042249L, 8L, 
    495604L, 29L, 8965478L, 2875L, 959L, 39L, 9L, 690L, 933626665L, 
    85294L, 580093L, 95934L, 982058L, 65244056L, 137508L, 29L, 7621L, 
    7527L, 72L, 2L, 315L, 6L, 2413L, 8625150L, 51298109L, 851L, 890460L, 
    160736L, 6L, 850842734L, 2L, 7L, 76969113L, 190536L), Peak.Time = c(1465265L, 
    452894L, 545076172L, 8226275L, 5040875L, 700530L, 1L, 3639L, 
    20141L, 71712131L, 686L, 923L, 770569738L, 69961L, 737458636L, 
    122403L, 199502046L, 6108L, 907L, 108078263L, 7817L, 4L, 6L, 
    69L, 721L, 786353L, 87486L, 1563L, 876L, 47599535L, 79295722L, 
    53L, 7378L, 591L, 6607935L, 954L, 6295L, 75514344L, 5742050L, 
    25647276L, 449L, 328566184L, 4L, 2L, 2703L, 21367543L, 63429043L, 
    708L, 782L, 909820L, 478L, 50L, 922L, 579882L, 7850L, 534L, 2157492L, 
    96L, 6L, 716L, 5L, 653290336L, 447854237L, 2L, 31972263L, 645L, 
    7L, 609909L, 4054695L, 455631L, 4919894L, 9L, 72713L, 9997L, 
    84090765L, 89742L, 5L, 5028L, 4126L, 23091L, 81L, 239635020L, 
    3576L, 898597785L, 6822L, 3798L, 201999L, 19624L, 20432923L, 
    18944093L, 930720236L, 1492302L, 300122L, 143633L, 5152743L, 
    417344L, 813L, 55792L, 78L), Center_Freq = c(61907L, 8709547L, 
    300750537L, 45862L, 91417085L, 79892L, 47765L, 5477L, 18L, 4186L, 
    2860L, 754038591L, 375L, 53809223L, 72L, 136L, 4700783L, 4173830L, 
    30L, 811L, 341014L, 780L, 44749L, 91L, 201620707L, 74L, 1L, 65422L, 
    595L, 89093186L, 946520L, 6940919L, 48744L, 2317845L, 5126197L, 
    2445L, 8L, 557450L, 450259742L, 21006647L, 9L, 7234027L, 59L, 
    9L, 651547554L, 45554L, 38493L, 91055218L, 38L, 1116474L, 2295482L, 
    3001L, 9L, 3270L, 141L, 53644L, 667983L, 565598L, 84L, 971L, 
    555498297L, 60431L, 6597L, 856943893L, 607815536L, 4406L, 79L, 
    4885076L, 745L, 8L, 56456L, 125140L, 73043989L, 516476L, 7L, 
    4440739L, 754038591L, 375L, 53809223L, 72L, 136L, 509L, 232325L, 
    13128104L, 1692L, 8581L, 23L, 5874213L, 4550L, 644668065L, 3712371L, 
    5928L, 8833L, 7L, 2186023L, 61627221L, 37297L, 716427989L, 21387L
    ), Start.Freq = c(426355L, 22073538L, 680374L, 41771L, 54L, 6762844L, 
    599171L, 108L, 257451851L, 438814L, 343045L, 4702L, 967787L, 
    1937L, 18L, 89301735L, 366L, 90L, 954L, 7337732L, 70891703L, 
    4139L, 10397931L, 940000382L, 7L, 38376L, 878528819L, 6287L, 
    738366L, 31L, 47L, 5L, 6L, 77848L, 2366508L, 45L, 3665842L, 7252260L, 
    6L, 61L, 3247L, 448348L, 1L, 705132L, 144L, 7423637L, 2L, 497L, 
    844927639L, 78978L, 914L, 131L, 7089563L, 927L, 9595581L, 2774463L, 
    1651L, 73509280L, 7L, 35L, 18L, 96L, 1L, 92545512L, 27354947L, 
    7556L, 65019L, 7480L, 71835L, 8249L, 64792L, 71537L, 349389666L, 
    280244484L, 82L, 6L, 40L, 353872L, 0L, 103L, 1255L, 4752L, 29L, 
    76L, 81185L, 14L, 9L, 470775630L, 818361265L, 57947209L, 44L, 
    24L, 41295L, 4L, 261449L, 9931404L, 773556640L, 930717L, 65007421L
    ), End.Freq = c(71000996L, 11613579L, 71377155L, 1942738L, 8760748L, 
    79L, 455L, 374L, 8L, 5L, 2266932L, 597833L, 155488L, 3020L, 4L, 
    554L, 4L, 16472L, 1945649L, 668181101L, 649780L, 22394365L, 93060602L, 
    172146L, 20472L, 23558847L, 190513L, 22759044L, 44L, 78450L, 
    205621181L, 218L, 69916344L, 23884L, 66L, 312148L, 7710564L, 
    4L, 422L, 744572L, 651547554L, 45554L, 38493L, 91055218L, 38L, 
    1116474L, 2295482L, 3001L, 9L, 3270L, 141L, 55595L, 38451L, 8660867L, 
    14L, 96L, 345L, 6L, 44L, 8235824L, 910517L, 1424326L, 87102566L, 
    53644L, 667983L, 565598L, 84L, 971L, 555498297L, 60431L, 6597L, 
    856943893L, 607815536L, 4406L, 79L, 7L, 28978746L, 7537295L, 
    6L, 633L, 345860066L, 802L, 1035131L, 602L, 2740L, 8065L, 61370968L, 
    429953765L, 981507L, 8105L, 343787257L, 44782L, 64184L, 12981359L, 
    123367978L, 818775L, 123745614L, 25345654L, 3L), Country = c("Holland", 
    "Holland", "Holland", "Holland", "Holland", "Holland", "Spain", 
    "Spain", "Spain", "Spain", "Spain", "Spain", "Spain", "Spain", 
    "Spain", "Spain", "Spain", "Spain", "Holland", "Holland", "Holland", 
    "Holland", "Holland", "Holland", "France", "France", "France", 
    "France", "France", "France", "France", "France", "France", "France", 
    "France", "Spain", "Spain", "Spain", "Spain", "Spain", "Spain", 
    "Spain", "Spain", "France", "France", "France", "France", "Holland", 
    "Holland", "Holland", "Holland", "Holland", "Holland", "Holland", 
    "Holland", "Holland", "Holland", "Holland", "Holland", "Holland", 
    "Spain", "Spain", "Spain", "Spain", "Spain", "Spain", "Spain", 
    "Holland", "Holland", "Holland", "Holland", "France", "France", 
    "France", "France", "France", "France", "France", "Spain", "Spain", 
    "Spain", "Spain", "Spain", "Spain", "Spain", "Spain", "Spain", 
    "Spain", "Spain", "Spain", "Spain", "Spain", "Spain", "Spain", 
    "Spain", "Spain", "France", "France", "France")), row.names = c(NA, 
    99L), class = "data.frame")

system · July 1, 2022, 2:00pm

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