Earlier versions (pre-release and v0.1.0) of zscorer used different functions that calculated only three anthropometric indices: weight-for-age, height-for-age and weight-for-height. Also, these functions used a simplified construct of the WHO Growth Reference in which children’s ages were recorded in months compared to days in the standard WHO Growth Reference.
With the developers’ recent work on anthropometric data quality processes implemented in R (see nipnTK), a more consistent and standard set of functions were deemed necessary to calculate not just three but all anthropometric indices used in the WHO Growth Standards and to make the children’s age in the reference data consistent with the standard using days. This work has now culminated in the current zscorer function.
For the purposes of backwards compatibility and to keep a record of past codebase for previous versions of the functions, the legacy functions have been kept in zscorer. This vignette describes those functions and shows examples of how to use them.
For new users of zscorer, developers recommend to start learning and using the new functions instead of using these legacy functions. For previous zscorer users, developers recommend to review past code that use the legacy functions and if feasible adapt code to the new functions available.
The zscorer package comes with the original legacy functions included in its version 0.1.0. These functions allow for the calculation of weight-for-age, height-for-age and weight-for-height z-scores for individual children and for a cohort of children.
For this example, we will use the getWGS() function and apply it to dummy data of a 52 month old male child with a weight of 14.6 kg and a height of 98.0 cm.
# weight-for-age z-score
waz <- getWGS(sexObserved = 1, # 1 = Male / 2 = Female
firstPart = 14.6, # Weight in kilograms up to 1 decimal place
secondPart = 52, # Age in whole months
index = "wfa") # Anthropometric index (weight-for-age)
waz
#> [1] -1.187651
# height-for-age z-score
haz <- getWGS(sexObserved = 1,
firstPart = 98, # Height in centimetres
secondPart = 52,
index = "hfa") # Anthropometric index (height-for-age)
haz
#> [1] -1.741175
# weight-for-height z-score
whz <- getWGS(sexObserved = 1,
firstPart = 14.6,
secondPart = 98,
index = "wfh") # Anthropometric index (weight-for-height)
whz
#> [1] -0.1790878Applying the getWGS() function results in a calculated z-score for one child.
For this example, we will use the getCohortWGS() function and apply it to sample data anthro1 that came with zscorer.
As you will see, this dataset has the 4 variables you will need to use with getCohortWGS() to calculate the z-score for the corresponding anthropometric index. These are age, sex, weight and height.
head(anthro1)
#> psu age sex weight height muac oedema haz waz whz flag
#> 1 1 6 1 7.3 65.0 146 2 -1.23 -0.76 0.06 0
#> 2 1 42 2 12.5 89.5 156 2 -2.35 -1.39 -0.02 0
#> 3 1 23 1 10.6 78.1 149 2 -2.95 -1.06 0.57 0
#> 4 1 18 1 12.8 81.5 160 2 -0.28 1.42 2.06 0
#> 5 1 52 1 12.1 87.3 152 2 -4.21 -2.68 -0.14 0
#> 6 1 36 2 16.9 93.0 190 2 -0.54 1.49 2.49 0To calculate the three anthropometric indices for all the children in the sample, we execute the following commands in R:
# weight-for-age z-score
waz <- getCohortWGS(data = anthro1,
sexObserved = "sex",
firstPart = "weight",
secondPart = "age",
index = "wfa")
head(waz, 50)
#> [1] -0.75605549 -1.39021503 -1.05597853 1.41575096 -2.67757242
#> [6] 1.49238050 -0.12987704 -0.02348159 -1.50647344 -1.54381630
#> [11] -2.87495712 -0.43497240 -1.03899540 -1.69281855 -1.31245898
#> [16] -2.21003260 -0.01189226 -0.90917762 -0.67839855 -0.94746695
#> [21] -2.49960425 -0.95659644 -1.65442686 -1.25052760 0.67335751
#> [26] 0.30156301 0.24261346 -2.78670709 -1.15820651 -1.15477183
#> [31] -1.35540820 -0.59134959 -4.14967218 -0.45748752 -0.74331669
#> [36] -1.69725836 -1.05745067 -0.18869508 -0.42095770 -2.21030414
#> [41] -1.30536715 -3.63778143 -0.60662526 -0.54360470 -1.59171780
#> [46] -1.74745738 -0.34803338 0.69896149 -0.74467130 0.18924572
# height-for-age z-score
haz <- getCohortWGS(data = anthro1,
sexObserved = "sex",
firstPart = "height",
secondPart = "age",
index = "hfa")
head(haz, 50)
#> [1] -1.2258169 -2.3475886 -2.9518041 -0.2812852 -4.2056663 -0.5387678
#> [7] -2.4020719 -1.0317699 -2.7410884 -4.7037571 -2.5670550 -2.1144960
#> [13] -2.2323505 -2.3155458 -2.7516165 -2.7930694 0.1121349 -1.9001797
#> [19] -2.9543730 -1.9671042 -3.8716522 0.8667206 -2.8252069 -2.1412285
#> [25] -2.7994643 0.5496459 -1.4372002 -3.7979410 -2.5661752 -1.8301183
#> [31] -1.6548589 -2.7110333 -3.6399642 -1.7955069 -1.6775100 -1.0317699
#> [37] -0.4356881 -1.2660152 0.4990326 -4.6085660 -3.1662351 -1.0695930
#> [43] -1.8477936 -2.5502314 -1.8301183 -2.2755493 -3.2816532 0.4876774
#> [49] -2.4396410 -0.4794744
# weight-for-height z-score
whz <- getCohortWGS(data = anthro1,
sexObserved = "sex",
firstPart = "weight",
secondPart = "height",
index = "wfh")
head(whz, 50)
#> [1] 0.05572347 -0.01974903 0.57469112 2.06231749 -0.14080044
#> [6] 2.49047246 1.83315197 0.93614891 0.18541943 2.11599287
#> [11] -1.96943887 1.06351047 0.35315830 -0.61151003 -0.01049441
#> [16] -0.75038993 -0.08000322 0.31277573 1.56456175 0.22152087
#> [21] -0.08798757 -2.14197877 -0.30804823 0.00778227 3.21041413
#> [26] 0.07434468 1.40966986 -0.81485050 0.63816647 -0.33540392
#> [31] -0.61955533 1.35716952 -2.77364671 1.00831095 0.32842063
#> [36] -1.66705281 -1.21157702 0.89024472 -0.89865037 0.82166393
#> [41] 0.64442137 -4.39847850 0.38411140 1.48299847 -0.93068495
#> [46] -0.88558228 1.69551410 0.65143649 0.61269397 0.59813891Applying the getCohortWGS() function results in a vector of calculated z-scores for all children in the cohort or sample.
For this example, we will use the getAllWGS() function and apply it to sample data anthro1 that came with zscorer.
# weight-for-age z-score
zScores <- getAllWGS(data = anthro1,
sex = "sex",
weight = "weight",
height = "height",
age = "age",
index = "all")
head(zScores, 20)
#> waz haz whz
#> 1 -0.75605549 -1.2258169 0.05572347
#> 2 -1.39021503 -2.3475886 -0.01974903
#> 3 -1.05597853 -2.9518041 0.57469112
#> 4 1.41575096 -0.2812852 2.06231749
#> 5 -2.67757242 -4.2056663 -0.14080044
#> 6 1.49238050 -0.5387678 2.49047246
#> 7 -0.12987704 -2.4020719 1.83315197
#> 8 -0.02348159 -1.0317699 0.93614891
#> 9 -1.50647344 -2.7410884 0.18541943
#> 10 -1.54381630 -4.7037571 2.11599287
#> 11 -2.87495712 -2.5670550 -1.96943887
#> 12 -0.43497240 -2.1144960 1.06351047
#> 13 -1.03899540 -2.2323505 0.35315830
#> 14 -1.69281855 -2.3155458 -0.61151003
#> 15 -1.31245898 -2.7516165 -0.01049441
#> 16 -2.21003260 -2.7930694 -0.75038993
#> 17 -0.01189226 0.1121349 -0.08000322
#> 18 -0.90917762 -1.9001797 0.31277573
#> 19 -0.67839855 -2.9543730 1.56456175
#> 20 -0.94746695 -1.9671042 0.22152087Applying the getAllWGS() function results in a data frame of calculated z-scores for all children in the cohort or sample for all the anthropometric indices.