Indices from a (dataset of) Multilevel Composition(s)

Compute sets of compositions and log ratio transformation for multilevel compositional data

Usage

complr(data, parts, sbp = NULL, total = 1, idvar = NULL, transform = "ilr")

Arguments

data: A data.frame or data.table containing data of all variables used in the analysis. It must include a composition and a ID variable. Required.
parts: A character vector specifying the names of compositional variables to be used. For multiple compositions, a list of character vectors can be supplied.
sbp: A signary matrix indicating sequential binary partition when transform = "ilr". If not supplied, a default sequential binary partition (sbp) will be built using function build.sbp. For multiple compositions, a list of signary sbps can be supplied.
total: A numeric value of the total amount to which the compositions should be closed. For multiple compositions, a list of numeric values can be supplied. Default is 1.
idvar: Only for multilevel data, a character string specifying the name of the variable containing IDs.
transform: A character value naming a log ratio transformation to be applied on compositional data. Can be either "ilr" (isometric logratio), "alr" (additive logratio), or "clr" (centered logratio). Default is "ilr".

Value

A complr object with at least the following elements.

comp: A vector of class acomp representing one closed composition or a matrix of class acomp representing multiple closed compositions each in one row.
between_comp: A vector of class acomp representing one closed between-person composition or a matrix of class acomp representing multiple closed between-person compositions each in one row.
within_comp: A vector of class acomp representing one closed within-person composition or a matrix of class acomp representing multiple closed within-person compositions each in one row.
logratio: Log ratio transform of composition.
between_logratio: Log ratio transform of between-person composition.
within_logratio: Log ratio transform of within-person composition.
data: The user's dataset or imputed dataset if the iiut data contains zeros.
transform: Type of transform applied on compositional data.
parts: Names of compositional variables.
idvar: Name of the variable containing IDs.
total: Total amount to which the compositions is closed.

Details

The ilr-transform maps the D-part compositional data from the simplex into non-overlapping subgroups in the (D-1)-dimension Euclidean space isometrically by using an orthonormal basis, thereby preserving the compositional properties and yielding a full-rank covariance matrix. ilr transformation should be preferred. However, the alr and clr are alternatives. The alr-transform maps a D-part composition in the Aitchison-simplex non-isometrically to a (D-1)-dimension Euclidian vectors, commonly treating the last part as the common denominator of the others. alr transformation does not rely on distance which breaks the constraint of compositional data. clr-transform maps a D-part composition in the Aitchison-simplex isometrically to a D-dimensional Euclidian vector subspace. clr transformation is not injetive, resulting in singular covariance matrices.

Examples

cilr <- complr(data = mcompd,
                parts = c("TST", "WAKE", "MVPA", "LPA", "SB"),
                idvar = "ID", total = 1440)
#>  A sequential binary partition (sbp), is required for ilr transform but is not supplied. 
#>  A default sbp, which is a pivot balance, will be applied.
str(cilr)
#> List of 5
#>  $ output   :List of 1
#>   ..$ :List of 11
#>   .. ..$ comp            : 'acomp' num [1:3540, 1:5] 542.4 458.3 270.8 525 651 99.1 49 41 76 86 297.2 117.1 488.7 259 112 460.3 653.5 624.6 398 436 41 162.1 15 182 155 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:5] "TST" "WAKE" "MVPA" "LPA" ...
#>   .. ..$ between_comp    : 'acomp' num [1:3540, 1:5] 494.2 494.2 494.2 494.2 494.2 72.3 72.3 72.3 72.3 72.3 249.3 249.3 249.3 249.3 249.3 503.9 503.9 503.9 503.9 503.| __truncated__ ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:5] "bTST" "bWAKE" "bMVPA" "bLPA" ...
#>   .. ..$ within_comp     : 'acomp' num [1:3540, 1:5] 0.2233 0.1965 0.1234 0.1948 0.2578 0.279 0.1438 0.1277 0.1928 0.233 0.2426 0.0995 0.4416 0.1905 0.0879 0.1859 0.2| __truncated__ ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:5] "wTST" "wWAKE" "wMVPA" "wLPA" ...
#>   .. ..$ logratio        : 'rmult' num [1:3540, 1:4] 1.1286 0.958 0.7506 0.889 1.2567 -0.5061 -1.344 -1.2117 -1.084 -0.7149 0.6298 -0.8348 1.3223 -0.0314 -0.6875 1.70| __truncated__ ...
#>   .. .. ..- attr(*, "orig")= 'acomp' num [1:3540, 1:5] 0.3767 0.3183 0.1881 0.3646 0.4521 0.0688 0.0341 0.0285 0.0528 0.0597 0.2064 0.0813 0.3393 0.1799 0.0778 0.3197 0| __truncated__ ...
#>   .. .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. .. ..$ : NULL
#>   .. .. .. .. ..$ : chr [1:5] "TST" "WAKE" "MVPA" "LPA" ...
#>   .. .. ..- attr(*, "V")= num [1:5, 1:4] 0.894 -0.224 -0.224 -0.224 -0.224 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:4] "z1_1" "z2_1" "z3_1" "z4_1"
#>   .. ..$ between_logratio: 'rmult' num [1:3540, 1:4] 0.89436 0.89436 0.89436 0.89436 0.89436 -1.06558 -1.06558 -1.06558 -1.06558 -1.06558 0.00968 0.00968 0.00968 0.00| __truncated__ ...
#>   .. .. ..- attr(*, "orig")= 'acomp' num [1:3540, 1:5] 0.3432 0.3432 0.3432 0.3432 0.3432 0.0502 0.0502 0.0502 0.0502 0.0502 0.1731 0.1731 0.1731 0.1731 0.1731 0.3499 0| __truncated__ ...
#>   .. .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. .. ..$ : NULL
#>   .. .. .. .. ..$ : chr [1:5] "bTST" "bWAKE" "bMVPA" "bLPA" ...
#>   .. .. ..- attr(*, "V")= num [1:5, 1:4] 0.894 -0.224 -0.224 -0.224 -0.224 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:4] "bz1_1" "bz2_1" "bz3_1" "bz4_1"
#>   .. ..$ within_logratio : 'rmult' num [1:3540, 1:4] 0.23428 0.06364 -0.14377 -0.00539 0.36234 0.55948 -0.27846 -0.14612 -0.01842 0.35066 0.62011 -0.84448 1.31261 -0.| __truncated__ ...
#>   .. .. ..- attr(*, "orig")= 'acomp' num [1:3540, 1:5] 0.2233 0.1965 0.1234 0.1948 0.2578 0.279 0.1438 0.1277 0.1928 0.233 0.2426 0.0995 0.4416 0.1905 0.0879 0.1859 0.2| __truncated__ ...
#>   .. .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. .. ..$ : NULL
#>   .. .. .. .. ..$ : chr [1:5] "wTST" "wWAKE" "wMVPA" "wLPA" ...
#>   .. .. ..- attr(*, "V")= num [1:5, 1:4] 0.894 -0.224 -0.224 -0.224 -0.224 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:4] "wz1_1" "wz2_1" "wz3_1" "wz4_1"
#>   .. ..$ dataout         : num [1:3540, 1:27] 542 458 271 525 651 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:27] "TST" "WAKE" "MVPA" "LPA" ...
#>   .. ..$ parts           : chr [1:5] "TST" "WAKE" "MVPA" "LPA" ...
#>   .. ..$ total           : num 1440
#>   .. ..$ sbp             : num [1:4, 1:5] 1 0 0 0 -1 1 0 0 -1 -1 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:5] "TST" "WAKE" "MVPA" "LPA" ...
#>   .. ..$ psi             : num [1:5, 1:4] 0.894 -0.224 -0.224 -0.224 -0.224 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : chr [1:5] "TST" "WAKE" "MVPA" "LPA" ...
#>   .. .. .. ..$ : NULL
#>  $ datain   :Classes ‘data.table’ and 'data.frame':	3540 obs. of  10 variables:
#>   ..$ ID      : num [1:3540] 185 185 185 185 185 185 185 185 185 185 ...
#>   ..$ Time    : num [1:3540] 1 2 3 4 5 6 7 8 9 10 ...
#>   ..$ Stress  : num [1:3540] 4 7 3 2 8 8 6 2 5 0 ...
#>   ..$ TST_raw : num [1:3540] 494 494 494 494 494 ...
#>   ..$ WAKE_raw: num [1:3540] 72.2 72.2 72.2 72.2 72.2 ...
#>   ..$ MVPA_raw: num [1:3540] 249 249 249 249 249 ...
#>   ..$ LPA_raw : num [1:3540] 504 504 504 504 504 ...
#>   ..$ SB_raw  : num [1:3540] 120 120 120 120 120 ...
#>   ..$ Age     : num [1:3540] 30 30 30 30 30 30 30 30 30 30 ...
#>   ..$ Female  : num [1:3540] 0 0 0 0 0 0 0 0 0 0 ...
#>   ..- attr(*, ".internal.selfref")=<externalptr> 
#>   ..- attr(*, "index")= int(0) 
#>   .. ..- attr(*, "__ID")= int [1:3540] 981 982 983 984 985 986 987 988 989 990 ...
#>  $ dataout  :Classes ‘data.table’ and 'data.frame':	3540 obs. of  37 variables:
#>   ..$ ID      : num [1:3540] 185 185 185 185 185 185 185 185 185 185 ...
#>   ..$ Time    : num [1:3540] 1 2 3 4 5 6 7 8 9 10 ...
#>   ..$ Stress  : num [1:3540] 4 7 3 2 8 8 6 2 5 0 ...
#>   ..$ TST_raw : num [1:3540] 494 494 494 494 494 ...
#>   ..$ WAKE_raw: num [1:3540] 72.2 72.2 72.2 72.2 72.2 ...
#>   ..$ MVPA_raw: num [1:3540] 249 249 249 249 249 ...
#>   ..$ LPA_raw : num [1:3540] 504 504 504 504 504 ...
#>   ..$ SB_raw  : num [1:3540] 120 120 120 120 120 ...
#>   ..$ Age     : num [1:3540] 30 30 30 30 30 30 30 30 30 30 ...
#>   ..$ Female  : num [1:3540] 0 0 0 0 0 0 0 0 0 0 ...
#>   ..$ TST     : num [1:3540] 542 458 271 525 651 ...
#>   ..$ WAKE    : num [1:3540] 99.1 49 41 76 86 ...
#>   ..$ MVPA    : num [1:3540] 297 117 489 259 112 ...
#>   ..$ LPA     : num [1:3540] 460 653 625 398 436 ...
#>   ..$ SB      : num [1:3540] 41 162 15 182 155 ...
#>   ..$ bTST    : num [1:3540] 494 494 494 494 494 ...
#>   ..$ bWAKE   : num [1:3540] 72.3 72.3 72.3 72.3 72.3 ...
#>   ..$ bMVPA   : num [1:3540] 249 249 249 249 249 ...
#>   ..$ bLPA    : num [1:3540] 504 504 504 504 504 ...
#>   ..$ bSB     : num [1:3540] 120 120 120 120 120 ...
#>   ..$ wTST    : num [1:3540] 0.223 0.197 0.123 0.195 0.258 ...
#>   ..$ wWAKE   : num [1:3540] 0.279 0.144 0.128 0.193 0.233 ...
#>   ..$ wMVPA   : num [1:3540] 0.2426 0.0995 0.4416 0.1905 0.0879 ...
#>   ..$ wLPA    : num [1:3540] 0.186 0.275 0.279 0.145 0.169 ...
#>   ..$ wSB     : num [1:3540] 0.0693 0.2853 0.028 0.2771 0.2519 ...
#>   ..$ z1_1    : num [1:3540] 1.129 0.958 0.751 0.889 1.257 ...
#>   ..$ z2_1    : num [1:3540] -0.506 -1.344 -1.212 -1.084 -0.715 ...
#>   ..$ z3_1    : num [1:3540] 0.6298 -0.8348 1.3223 -0.0314 -0.6875 ...
#>   ..$ z4_1    : num [1:3540] 1.71 0.986 2.637 0.553 0.731 ...
#>   ..$ bz1_1   : num [1:3540] 0.894 0.894 0.894 0.894 0.894 ...
#>   ..$ bz2_1   : num [1:3540] -1.07 -1.07 -1.07 -1.07 -1.07 ...
#>   ..$ bz3_1   : num [1:3540] 0.00968 0.00968 0.00968 0.00968 0.00968 ...
#>   ..$ bz4_1   : num [1:3540] 1.01 1.01 1.01 1.01 1.01 ...
#>   ..$ wz1_1   : num [1:3540] 0.23428 0.06364 -0.14377 -0.00539 0.36234 ...
#>   ..$ wz2_1   : num [1:3540] 0.5595 -0.2785 -0.1461 -0.0184 0.3507 ...
#>   ..$ wz3_1   : num [1:3540] 0.62 -0.844 1.313 -0.041 -0.697 ...
#>   ..$ wz4_1   : num [1:3540] 0.6975 -0.0264 1.6252 -0.4588 -0.2808 ...
#>   ..- attr(*, ".internal.selfref")=<externalptr> 
#>  $ transform: chr "ilr"
#>  $ idvar    : chr "ID"
#>  - attr(*, "class")= chr "complr"

calr <- complr(data = mcompd, 
                parts = list(c("TST", "WAKE"), c("MVPA", "LPA", "SB")),
                total = list(c(1440), c(1440)),
                idvar = "ID",
                transform = "ilr")
#>  A sequential binary partition (sbp), is required for ilr transform but is not supplied. 
#>  A default sbp, which is a pivot balance, will be applied.
#>  A sequential binary partition (sbp), is required for ilr transform but is not supplied. 
#>  A default sbp, which is a pivot balance, will be applied.
str(calr)
#> List of 5
#>  $ output   :List of 2
#>   ..$ :List of 11
#>   .. ..$ comp            : 'acomp' num [1:3540, 1:2] 1218 1301 1251 1258 1272 222 139 189 182 168 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:2] "TST" "WAKE"
#>   .. ..$ between_comp    : 'acomp' num [1:3540, 1:2] 1256 1256 1256 1256 1256 184 184 184 184 184 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:2] "bTST" "bWAKE"
#>   .. ..$ within_comp     : 'acomp' num [1:3540, 1:2] 0.445 0.577 0.491 0.502 0.525 0.555 0.423 0.509 0.498 0.475 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:2] "wTST" "wWAKE"
#>   .. ..$ logratio        : 'rmult' num [1:3540, 1] 1.2 1.58 1.34 1.37 1.43 ...
#>   .. .. ..- attr(*, "orig")= 'acomp' num [1:3540, 1:2] 0.8456 0.9034 0.8686 0.8735 0.8833 0.1544 0.0966 0.1314 0.1265 0.1167 ...
#>   .. .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. .. ..$ : NULL
#>   .. .. .. .. ..$ : chr [1:2] "TST" "WAKE"
#>   .. .. ..- attr(*, "V")= num [1:2, 1] 0.707 -0.707
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr "z1_1"
#>   .. ..$ between_logratio: 'rmult' num [1:3540, 1] 1.36 1.36 1.36 1.36 1.36 ...
#>   .. .. ..- attr(*, "orig")= 'acomp' num [1:3540, 1:2] 0.872 0.872 0.872 0.872 0.872 0.128 0.128 0.128 0.128 0.128 ...
#>   .. .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. .. ..$ : NULL
#>   .. .. .. .. ..$ : chr [1:2] "bTST" "bWAKE"
#>   .. .. ..- attr(*, "V")= num [1:2, 1] 0.707 -0.707
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr "bz1_1"
#>   .. ..$ within_logratio : 'rmult' num [1:3540, 1] -0.1574 0.22084 -0.02418 0.00702 0.07172 ...
#>   .. .. ..- attr(*, "orig")= 'acomp' num [1:3540, 1:2] 0.445 0.577 0.491 0.502 0.525 0.555 0.423 0.509 0.498 0.475 ...
#>   .. .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. .. ..$ : NULL
#>   .. .. .. .. ..$ : chr [1:2] "wTST" "wWAKE"
#>   .. .. ..- attr(*, "V")= num [1:2, 1] 0.707 -0.707
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr "wz1_1"
#>   .. ..$ dataout         : num [1:3540, 1:9] 1218 1301 1251 1258 1272 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:9] "TST" "WAKE" "bTST" "bWAKE" ...
#>   .. ..$ parts           : chr [1:2] "TST" "WAKE"
#>   .. ..$ total           : num 1440
#>   .. ..$ sbp             : num [1, 1:2] 1 -1
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:2] "TST" "WAKE"
#>   .. ..$ psi             : num [1:2, 1] 0.707 -0.707
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : chr [1:2] "TST" "WAKE"
#>   .. .. .. ..$ : NULL
#>   ..$ :List of 11
#>   .. ..$ comp            : 'acomp' num [1:3540, 1:3] 535.9 180.8 623.7 444.5 229.4 830.1 1008.9 797.2 683.1 893.1 74 250.3 19.1 312.4 317.5 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:3] "MVPA" "LPA" "SB"
#>   .. ..$ between_comp    : 'acomp' num [1:3540, 1:3] 411 411 411 411 411 831 831 831 831 831 199 199 199 199 199 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:3] "bMVPA" "bLPA" "bSB"
#>   .. ..$ within_comp     : 'acomp' num [1:3540, 1:3] 0.4873 0.1509 0.5897 0.3111 0.1727 0.3734 0.4166 0.3729 0.2365 0.3326 0.1393 0.4325 0.0374 0.4525 0.4947 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:3] "wMVPA" "wLPA" "wSB"
#>   .. ..$ logratio        : 'rmult' num [1:3540, 1:2] 0.6298 -0.8348 1.3223 -0.0314 -0.6875 1.7095 0.9857 2.6373 0.5533 0.7313 ...
#>   .. .. ..- attr(*, "orig")= 'acomp' num [1:3540, 1:3] 0.3722 0.1255 0.4331 0.3087 0.1593 0.5764 0.7006 0.5536 0.4744 0.6202 0.0514 0.1738 0.0133 0.2169 0.2205 ...
#>   .. .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. .. ..$ : NULL
#>   .. .. .. .. ..$ : chr [1:3] "MVPA" "LPA" "SB"
#>   .. .. ..- attr(*, "V")= num [1:3, 1:2] 8.16e-01 -4.08e-01 -4.08e-01 -2.02e-17 7.07e-01 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:2] "z1_2" "z2_2"
#>   .. ..$ between_logratio: 'rmult' num [1:3540, 1:2] 0.00968 0.00968 0.00968 0.00968 0.00968 1.01207 1.01207 1.01207 1.01207 1.01207 ...
#>   .. .. ..- attr(*, "orig")= 'acomp' num [1:3540, 1:3] 0.285 0.285 0.285 0.285 0.285 0.577 0.577 0.577 0.577 0.577 0.138 0.138 0.138 0.138 0.138 ...
#>   .. .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. .. ..$ : NULL
#>   .. .. .. .. ..$ : chr [1:3] "bMVPA" "bLPA" "bSB"
#>   .. .. ..- attr(*, "V")= num [1:3, 1:2] 8.16e-01 -4.08e-01 -4.08e-01 -2.02e-17 7.07e-01 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:2] "bz1_2" "bz2_2"
#>   .. ..$ within_logratio : 'rmult' num [1:3540, 1:2] 0.6201 -0.8445 1.3126 -0.041 -0.6972 0.6975 -0.0264 1.6252 -0.4588 -0.2808 ...
#>   .. .. ..- attr(*, "orig")= 'acomp' num [1:3540, 1:3] 0.4873 0.1509 0.5897 0.3111 0.1727 0.3734 0.4166 0.3729 0.2365 0.3326 0.1393 0.4325 0.0374 0.4525 0.4947 ...
#>   .. .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. .. ..$ : NULL
#>   .. .. .. .. ..$ : chr [1:3] "wMVPA" "wLPA" "wSB"
#>   .. .. ..- attr(*, "V")= num [1:3, 1:2] 8.16e-01 -4.08e-01 -4.08e-01 -2.02e-17 7.07e-01 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:2] "wz1_2" "wz2_2"
#>   .. ..$ dataout         : num [1:3540, 1:15] 536 181 624 445 229 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:15] "MVPA" "LPA" "SB" "bMVPA" ...
#>   .. ..$ parts           : chr [1:3] "MVPA" "LPA" "SB"
#>   .. ..$ total           : num 1440
#>   .. ..$ sbp             : num [1:2, 1:3] 1 0 -1 1 -1 -1
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:3] "MVPA" "LPA" "SB"
#>   .. ..$ psi             : num [1:3, 1:2] 0.816 -0.408 -0.408 0 0.707 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : chr [1:3] "MVPA" "LPA" "SB"
#>   .. .. .. ..$ : NULL
#>  $ datain   :Classes ‘data.table’ and 'data.frame':	3540 obs. of  10 variables:
#>   ..$ ID      : num [1:3540] 185 185 185 185 185 185 185 185 185 185 ...
#>   ..$ Time    : num [1:3540] 1 2 3 4 5 6 7 8 9 10 ...
#>   ..$ Stress  : num [1:3540] 4 7 3 2 8 8 6 2 5 0 ...
#>   ..$ TST_raw : num [1:3540] 494 494 494 494 494 ...
#>   ..$ WAKE_raw: num [1:3540] 72.2 72.2 72.2 72.2 72.2 ...
#>   ..$ MVPA_raw: num [1:3540] 249 249 249 249 249 ...
#>   ..$ LPA_raw : num [1:3540] 504 504 504 504 504 ...
#>   ..$ SB_raw  : num [1:3540] 120 120 120 120 120 ...
#>   ..$ Age     : num [1:3540] 30 30 30 30 30 30 30 30 30 30 ...
#>   ..$ Female  : num [1:3540] 0 0 0 0 0 0 0 0 0 0 ...
#>   ..- attr(*, ".internal.selfref")=<externalptr> 
#>   ..- attr(*, "index")= int(0) 
#>   .. ..- attr(*, "__ID")= int [1:3540] 981 982 983 984 985 986 987 988 989 990 ...
#>  $ dataout  :Classes ‘data.table’ and 'data.frame':	3540 obs. of  34 variables:
#>   ..$ ID      : num [1:3540] 185 185 185 185 185 185 185 185 185 185 ...
#>   ..$ Time    : num [1:3540] 1 2 3 4 5 6 7 8 9 10 ...
#>   ..$ Stress  : num [1:3540] 4 7 3 2 8 8 6 2 5 0 ...
#>   ..$ TST_raw : num [1:3540] 494 494 494 494 494 ...
#>   ..$ WAKE_raw: num [1:3540] 72.2 72.2 72.2 72.2 72.2 ...
#>   ..$ MVPA_raw: num [1:3540] 249 249 249 249 249 ...
#>   ..$ LPA_raw : num [1:3540] 504 504 504 504 504 ...
#>   ..$ SB_raw  : num [1:3540] 120 120 120 120 120 ...
#>   ..$ Age     : num [1:3540] 30 30 30 30 30 30 30 30 30 30 ...
#>   ..$ Female  : num [1:3540] 0 0 0 0 0 0 0 0 0 0 ...
#>   ..$ TST     : num [1:3540] 1218 1301 1251 1258 1272 ...
#>   ..$ WAKE    : num [1:3540] 222 139 189 182 168 ...
#>   ..$ bTST    : num [1:3540] 1256 1256 1256 1256 1256 ...
#>   ..$ bWAKE   : num [1:3540] 184 184 184 184 184 ...
#>   ..$ wTST    : num [1:3540] 0.445 0.577 0.491 0.502 0.525 ...
#>   ..$ wWAKE   : num [1:3540] 0.555 0.423 0.509 0.498 0.475 ...
#>   ..$ z1_1    : num [1:3540] 1.2 1.58 1.34 1.37 1.43 ...
#>   ..$ bz1_1   : num [1:3540] 1.36 1.36 1.36 1.36 1.36 ...
#>   ..$ wz1_1   : num [1:3540] -0.1574 0.22084 -0.02418 0.00702 0.07172 ...
#>   ..$ MVPA    : num [1:3540] 536 181 624 445 229 ...
#>   ..$ LPA     : num [1:3540] 830 1009 797 683 893 ...
#>   ..$ SB      : num [1:3540] 74 250.3 19.1 312.4 317.5 ...
#>   ..$ bMVPA   : num [1:3540] 411 411 411 411 411 ...
#>   ..$ bLPA    : num [1:3540] 831 831 831 831 831 ...
#>   ..$ bSB     : num [1:3540] 199 199 199 199 199 ...
#>   ..$ wMVPA   : num [1:3540] 0.487 0.151 0.59 0.311 0.173 ...
#>   ..$ wLPA    : num [1:3540] 0.373 0.417 0.373 0.236 0.333 ...
#>   ..$ wSB     : num [1:3540] 0.1393 0.4325 0.0374 0.4525 0.4947 ...
#>   ..$ z1_2    : num [1:3540] 0.6298 -0.8348 1.3223 -0.0314 -0.6875 ...
#>   ..$ z2_2    : num [1:3540] 1.71 0.986 2.637 0.553 0.731 ...
#>   ..$ bz1_2   : num [1:3540] 0.00968 0.00968 0.00968 0.00968 0.00968 ...
#>   ..$ bz2_2   : num [1:3540] 1.01 1.01 1.01 1.01 1.01 ...
#>   ..$ wz1_2   : num [1:3540] 0.62 -0.844 1.313 -0.041 -0.697 ...
#>   ..$ wz2_2   : num [1:3540] 0.6975 -0.0264 1.6252 -0.4588 -0.2808 ...
#>   ..- attr(*, ".internal.selfref")=<externalptr> 
#>  $ transform: chr "ilr"
#>  $ idvar    : chr "ID"
#>  - attr(*, "class")= chr "complr"

cclr <- complr(data = mcompd, sbp = sbp,
                parts = c("TST", "WAKE", "MVPA", "LPA", "SB"),
                idvar = "ID",
                 transform = "ilr")
str(cclr)
#> List of 5
#>  $ output   :List of 1
#>   ..$ :List of 11
#>   .. ..$ comp            : 'acomp' num [1:3540, 1:5] 0.3767 0.3183 0.1881 0.3646 0.4521 0.0688 0.0341 0.0285 0.0528 0.0597 0.2064 0.0813 0.3393 0.1799 0.0778 0.3197 0| __truncated__ ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:5] "TST" "WAKE" "MVPA" "LPA" ...
#>   .. ..$ between_comp    : 'acomp' num [1:3540, 1:5] 0.3432 0.3432 0.3432 0.3432 0.3432 0.0502 0.0502 0.0502 0.0502 0.0502 0.1731 0.1731 0.1731 0.1731 0.1731 0.3499 0| __truncated__ ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:5] "bTST" "bWAKE" "bMVPA" "bLPA" ...
#>   .. ..$ within_comp     : 'acomp' num [1:3540, 1:5] 0.2233 0.1965 0.1234 0.1948 0.2578 0.279 0.1438 0.1277 0.1928 0.233 0.2426 0.0995 0.4416 0.1905 0.0879 0.1859 0.2| __truncated__ ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:5] "wTST" "wWAKE" "wMVPA" "wLPA" ...
#>   .. ..$ logratio        : 'rmult' num [1:3540, 1:4] 0.291 -0.4759 -0.4983 -0.3126 0.2044 1.2022 1.5804 1.3354 1.3666 1.4313 0.6298 -0.8348 1.3223 -0.0314 -0.6875 1.7| __truncated__ ...
#>   .. .. ..- attr(*, "orig")= 'acomp' num [1:3540, 1:5] 0.3767 0.3183 0.1881 0.3646 0.4521 0.0688 0.0341 0.0285 0.0528 0.0597 0.2064 0.0813 0.3393 0.1799 0.0778 0.3197 0| __truncated__ ...
#>   .. .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. .. ..$ : NULL
#>   .. .. .. .. ..$ : chr [1:5] "TST" "WAKE" "MVPA" "LPA" ...
#>   .. .. ..- attr(*, "V")= num [1:5, 1:4] 0.548 0.548 -0.365 -0.365 -0.365 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:4] "z1_1" "z2_1" "z3_1" "z4_1"
#>   .. ..$ between_logratio: 'rmult' num [1:3540, 1:4] -0.29473 -0.29473 -0.29473 -0.29473 -0.29473 1.35958 1.35958 1.35958 1.35958 1.35958 0.00968 0.00968 0.00968 0.00| __truncated__ ...
#>   .. .. ..- attr(*, "orig")= 'acomp' num [1:3540, 1:5] 0.3432 0.3432 0.3432 0.3432 0.3432 0.0502 0.0502 0.0502 0.0502 0.0502 0.1731 0.1731 0.1731 0.1731 0.1731 0.3499 0| __truncated__ ...
#>   .. .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. .. ..$ : NULL
#>   .. .. .. .. ..$ : chr [1:5] "bTST" "bWAKE" "bMVPA" "bLPA" ...
#>   .. .. ..- attr(*, "V")= num [1:5, 1:4] 0.548 0.548 -0.365 -0.365 -0.365 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:4] "bz1_1" "bz2_1" "bz3_1" "bz4_1"
#>   .. ..$ within_logratio : 'rmult' num [1:3540, 1:4] 0.58577 -0.18117 -0.20356 -0.01787 0.49911 -0.1574 0.22084 -0.02418 0.00702 0.07172 0.62011 -0.84448 1.31261 -0.0| __truncated__ ...
#>   .. .. ..- attr(*, "orig")= 'acomp' num [1:3540, 1:5] 0.2233 0.1965 0.1234 0.1948 0.2578 0.279 0.1438 0.1277 0.1928 0.233 0.2426 0.0995 0.4416 0.1905 0.0879 0.1859 0.2| __truncated__ ...
#>   .. .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. .. ..$ : NULL
#>   .. .. .. .. ..$ : chr [1:5] "wTST" "wWAKE" "wMVPA" "wLPA" ...
#>   .. .. ..- attr(*, "V")= num [1:5, 1:4] 0.548 0.548 -0.365 -0.365 -0.365 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:4] "wz1_1" "wz2_1" "wz3_1" "wz4_1"
#>   .. ..$ dataout         : num [1:3540, 1:27] 0.377 0.318 0.188 0.365 0.452 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:27] "TST" "WAKE" "MVPA" "LPA" ...
#>   .. ..$ parts           : chr [1:5] "TST" "WAKE" "MVPA" "LPA" ...
#>   .. ..$ total           : num 1
#>   .. ..$ sbp             : num [1:4, 1:5] 1 1 0 0 1 -1 0 0 -1 0 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:5] "TST" "WAKE" "MVPA" "LPA" ...
#>   .. ..$ psi             : num [1:5, 1:4] 0.548 0.548 -0.365 -0.365 -0.365 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : chr [1:5] "TST" "WAKE" "MVPA" "LPA" ...
#>   .. .. .. ..$ : NULL
#>  $ datain   :Classes ‘data.table’ and 'data.frame':	3540 obs. of  10 variables:
#>   ..$ ID      : num [1:3540] 185 185 185 185 185 185 185 185 185 185 ...
#>   ..$ Time    : num [1:3540] 1 2 3 4 5 6 7 8 9 10 ...
#>   ..$ Stress  : num [1:3540] 4 7 3 2 8 8 6 2 5 0 ...
#>   ..$ TST_raw : num [1:3540] 494 494 494 494 494 ...
#>   ..$ WAKE_raw: num [1:3540] 72.2 72.2 72.2 72.2 72.2 ...
#>   ..$ MVPA_raw: num [1:3540] 249 249 249 249 249 ...
#>   ..$ LPA_raw : num [1:3540] 504 504 504 504 504 ...
#>   ..$ SB_raw  : num [1:3540] 120 120 120 120 120 ...
#>   ..$ Age     : num [1:3540] 30 30 30 30 30 30 30 30 30 30 ...
#>   ..$ Female  : num [1:3540] 0 0 0 0 0 0 0 0 0 0 ...
#>   ..- attr(*, ".internal.selfref")=<externalptr> 
#>   ..- attr(*, "index")= int(0) 
#>   .. ..- attr(*, "__ID")= int [1:3540] 981 982 983 984 985 986 987 988 989 990 ...
#>  $ dataout  :Classes ‘data.table’ and 'data.frame':	3540 obs. of  37 variables:
#>   ..$ ID      : num [1:3540] 185 185 185 185 185 185 185 185 185 185 ...
#>   ..$ Time    : num [1:3540] 1 2 3 4 5 6 7 8 9 10 ...
#>   ..$ Stress  : num [1:3540] 4 7 3 2 8 8 6 2 5 0 ...
#>   ..$ TST_raw : num [1:3540] 494 494 494 494 494 ...
#>   ..$ WAKE_raw: num [1:3540] 72.2 72.2 72.2 72.2 72.2 ...
#>   ..$ MVPA_raw: num [1:3540] 249 249 249 249 249 ...
#>   ..$ LPA_raw : num [1:3540] 504 504 504 504 504 ...
#>   ..$ SB_raw  : num [1:3540] 120 120 120 120 120 ...
#>   ..$ Age     : num [1:3540] 30 30 30 30 30 30 30 30 30 30 ...
#>   ..$ Female  : num [1:3540] 0 0 0 0 0 0 0 0 0 0 ...
#>   ..$ TST     : num [1:3540] 0.377 0.318 0.188 0.365 0.452 ...
#>   ..$ WAKE    : num [1:3540] 0.0688 0.0341 0.0285 0.0528 0.0597 ...
#>   ..$ MVPA    : num [1:3540] 0.2064 0.0813 0.3393 0.1799 0.0778 ...
#>   ..$ LPA     : num [1:3540] 0.32 0.454 0.434 0.276 0.303 ...
#>   ..$ SB      : num [1:3540] 0.0285 0.1126 0.0104 0.1264 0.1076 ...
#>   ..$ bTST    : num [1:3540] 0.343 0.343 0.343 0.343 0.343 ...
#>   ..$ bWAKE   : num [1:3540] 0.0502 0.0502 0.0502 0.0502 0.0502 ...
#>   ..$ bMVPA   : num [1:3540] 0.173 0.173 0.173 0.173 0.173 ...
#>   ..$ bLPA    : num [1:3540] 0.35 0.35 0.35 0.35 0.35 ...
#>   ..$ bSB     : num [1:3540] 0.0836 0.0836 0.0836 0.0836 0.0836 ...
#>   ..$ wTST    : num [1:3540] 0.223 0.197 0.123 0.195 0.258 ...
#>   ..$ wWAKE   : num [1:3540] 0.279 0.144 0.128 0.193 0.233 ...
#>   ..$ wMVPA   : num [1:3540] 0.2426 0.0995 0.4416 0.1905 0.0879 ...
#>   ..$ wLPA    : num [1:3540] 0.186 0.275 0.279 0.145 0.169 ...
#>   ..$ wSB     : num [1:3540] 0.0693 0.2853 0.028 0.2771 0.2519 ...
#>   ..$ z1_1    : num [1:3540] 0.291 -0.476 -0.498 -0.313 0.204 ...
#>   ..$ z2_1    : num [1:3540] 1.2 1.58 1.34 1.37 1.43 ...
#>   ..$ z3_1    : num [1:3540] 0.6298 -0.8348 1.3223 -0.0314 -0.6875 ...
#>   ..$ z4_1    : num [1:3540] 1.71 0.986 2.637 0.553 0.731 ...
#>   ..$ bz1_1   : num [1:3540] -0.295 -0.295 -0.295 -0.295 -0.295 ...
#>   ..$ bz2_1   : num [1:3540] 1.36 1.36 1.36 1.36 1.36 ...
#>   ..$ bz3_1   : num [1:3540] 0.00968 0.00968 0.00968 0.00968 0.00968 ...
#>   ..$ bz4_1   : num [1:3540] 1.01 1.01 1.01 1.01 1.01 ...
#>   ..$ wz1_1   : num [1:3540] 0.5858 -0.1812 -0.2036 -0.0179 0.4991 ...
#>   ..$ wz2_1   : num [1:3540] -0.1574 0.22084 -0.02418 0.00702 0.07172 ...
#>   ..$ wz3_1   : num [1:3540] 0.62 -0.844 1.313 -0.041 -0.697 ...
#>   ..$ wz4_1   : num [1:3540] 0.6975 -0.0264 1.6252 -0.4588 -0.2808 ...
#>   ..- attr(*, ".internal.selfref")=<externalptr> 
#>  $ transform: chr "ilr"
#>  $ idvar    : chr "ID"
#>  - attr(*, "class")= chr "complr"

cilr_wide <- complr(data = mcompd[!duplicated(ID)], sbp = sbp,
                parts = c("TST", "WAKE", "MVPA", "LPA", "SB"))
str(cilr_wide)
#> List of 5
#>  $ output   :List of 1
#>   ..$ :List of 11
#>   .. ..$ comp            : 'acomp' num [1:266, 1:5] 0.3767 0.3569 0.2771 0.4357 0.3678 0.0688 0.0437 0.0826 0.0368 0.05 0.2064 0.0785 0.0229 0.0716 0.0749 0.3197 0.3| __truncated__ ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:5] "TST" "WAKE" "MVPA" "LPA" ...
#>   .. ..$ between_comp    : NULL
#>   .. ..$ within_comp     : NULL
#>   .. ..$ logratio        : 'rmult' num [1:266, 1:4] 0.291 -0.339 0.211 -0.218 -0.232 1.202 1.484 0.855 1.747 1.412 0.63 -0.949 -2.076 -0.943 -0.985 1.71 0.386 0.484 0.108 0.228 ...
#>   .. .. ..- attr(*, "orig")= 'acomp' num [1:266, 1:5] 0.3767 0.3569 0.2771 0.4357 0.3678 0.0688 0.0437 0.0826 0.0368 0.05 0.2064 0.0785 0.0229 0.0716 0.0749 0.3197 0.3| __truncated__ ...
#>   .. .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. .. ..$ : NULL
#>   .. .. .. .. ..$ : chr [1:5] "TST" "WAKE" "MVPA" "LPA" ...
#>   .. .. ..- attr(*, "V")= num [1:5, 1:4] 0.548 0.548 -0.365 -0.365 -0.365 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:4] "ilr1" "ilr2" "ilr3" "ilr4"
#>   .. ..$ between_logratio: NULL
#>   .. ..$ within_logratio : NULL
#>   .. ..$ dataout         : num [1:266, 1:9] 0.377 0.357 0.277 0.436 0.368 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:9] "TST" "WAKE" "MVPA" "LPA" ...
#>   .. ..$ parts           : chr [1:5] "TST" "WAKE" "MVPA" "LPA" ...
#>   .. ..$ total           : num 1
#>   .. ..$ sbp             : num [1:4, 1:5] 1 1 0 0 1 -1 0 0 -1 0 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : NULL
#>   .. .. .. ..$ : chr [1:5] "TST" "WAKE" "MVPA" "LPA" ...
#>   .. ..$ psi             : num [1:5, 1:4] 0.548 0.548 -0.365 -0.365 -0.365 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ : chr [1:5] "TST" "WAKE" "MVPA" "LPA" ...
#>   .. .. .. ..$ : NULL
#>  $ datain   :Classes ‘data.table’ and 'data.frame':	266 obs. of  10 variables:
#>   ..$ ID      : num [1:266] 185 186 187 188 189 190 191 192 193 194 ...
#>   ..$ Time    : num [1:266] 1 1 1 1 1 1 1 1 1 1 ...
#>   ..$ Stress  : num [1:266] 4 3 4 0 0 2 4 4 0 2 ...
#>   ..$ TST_raw : num [1:266] 542 514 399 627 530 345 415 471 350 267 ...
#>   ..$ WAKE_raw: num [1:266] 99 63 119 53 72 204 37 179 56 50 ...
#>   ..$ MVPA_raw: num [1:266] 297 113 33 103 108 244 88 84 25 113 ...
#>   ..$ LPA_raw : num [1:266] 460 475 591 353 424 516 781 477 657 699 ...
#>   ..$ SB_raw  : num [1:266] 41 275 298 303 307 131 119 229 351 311 ...
#>   ..$ Age     : num [1:266] 30 20 22 27 22 25 21 20 20 32 ...
#>   ..$ Female  : num [1:266] 0 0 0 0 0 0 0 0 0 0 ...
#>   ..- attr(*, ".internal.selfref")=<externalptr> 
#>  $ dataout  :Classes ‘data.table’ and 'data.frame':	266 obs. of  19 variables:
#>   ..$ ID      : num [1:266] 185 186 187 188 189 190 191 192 193 194 ...
#>   ..$ Time    : num [1:266] 1 1 1 1 1 1 1 1 1 1 ...
#>   ..$ Stress  : num [1:266] 4 3 4 0 0 2 4 4 0 2 ...
#>   ..$ TST_raw : num [1:266] 542 514 399 627 530 345 415 471 350 267 ...
#>   ..$ WAKE_raw: num [1:266] 99 63 119 53 72 204 37 179 56 50 ...
#>   ..$ MVPA_raw: num [1:266] 297 113 33 103 108 244 88 84 25 113 ...
#>   ..$ LPA_raw : num [1:266] 460 475 591 353 424 516 781 477 657 699 ...
#>   ..$ SB_raw  : num [1:266] 41 275 298 303 307 131 119 229 351 311 ...
#>   ..$ Age     : num [1:266] 30 20 22 27 22 25 21 20 20 32 ...
#>   ..$ Female  : num [1:266] 0 0 0 0 0 0 0 0 0 0 ...
#>   ..$ TST     : num [1:266] 0.377 0.357 0.277 0.436 0.368 ...
#>   ..$ WAKE    : num [1:266] 0.0688 0.0437 0.0826 0.0368 0.05 ...
#>   ..$ MVPA    : num [1:266] 0.2064 0.0785 0.0229 0.0716 0.0749 ...
#>   ..$ LPA     : num [1:266] 0.32 0.33 0.41 0.245 0.294 ...
#>   ..$ SB      : num [1:266] 0.0285 0.191 0.2069 0.2106 0.213 ...
#>   ..$ ilr1    : num [1:266] 0.291 -0.339 0.211 -0.218 -0.232 ...
#>   ..$ ilr2    : num [1:266] 1.202 1.484 0.855 1.747 1.412 ...
#>   ..$ ilr3    : num [1:266] 0.63 -0.949 -2.076 -0.943 -0.985 ...
#>   ..$ ilr4    : num [1:266] 1.71 0.386 0.484 0.108 0.228 ...
#>   ..- attr(*, ".internal.selfref")=<externalptr> 
#>  $ transform: chr "ilr"
#>  $ idvar    : NULL
#>  - attr(*, "class")= chr "complr"