zscorer facilitates the calculation of a range of anthropometricz-scores (i.e.the number of standard deviations from the mean) andadds them to survey data:
Weight-for-length (wfl) z-scores for children with lengthsbetween 45 and 110 cm
Weight-for-height (wfh) z-scores for children with heightsbetween 65 and 120 cm
Length-for-age (lfa) z-scores for children aged less than 24months
Height-for-age (hfa) z-scores for children aged between 24 and228 months
Weight-for-age (wfa) z-scores for children aged between zero and120 months
Body mass index-for-age (bfa) z-scores for children aged betweenzero and 228 months
MUAC-for-age (mfa) z-scores for children aged between 3 and 228months
Triceps skinfold-for-age (tsa) z-scores for children agedbetween 3 and 60 months
Sub-scapular skinfold-for-age (ssa) z-scores for children agedbetween 3 and 60 months
Head circumference-for-age (hca) z-scores for children agedbetween zero and 60 months
The z-scores are calculated using the WHO Child Growth Standards[1],[2] for children aged between zero and 60 months or the WHOGrowth References [3] for school-aged children and adolescents.MUAC-for-age (mfa) z-scores for children aged between 60 and 228 monthsare calculated using the MUAC-for-age growth reference developed byMramba et al. (2017) [4] using data from the USA and Africa. Thisreference has been validated with African school-age children andadolescents. The zscorer comes packaged with the WHO Growth Referencesdata and the MUAC-for-age reference data.
Installation
You can install zscorer from CRAN:
install.packages("zscorer")or you can install the development version of zscorer fromGitHub with:
if(!require(remotes)) install.packages("remotes")remotes::install_github("nutriverse/zscorer")then load zscorer
# load packagelibrary(zscorer)Usage
Calculating anthropometric z-scores using the addWGSR() function
The main function in the zscorer package is addWGSR().
To demonstrate its usage, we will use the accompanying dataset inzscorer called anthro3. We inspect the dataset as follows:
head(anthro3)which returns:
#> psu age sex weight height muac oedema#> 1 1 10 1 5.7 64.2 125 2#> 2 1 10 2 5.8 64.4 121 2#> 3 1 9 2 6.5 62.2 139 2#> 4 1 11 9 6.5 64.9 129 2#> 5 1 24 2 6.5 72.9 120 2#> 6 1 12 2 6.6 69.4 126 2anthro3 contains anthropometric data from a Rapid Assessment Method(RAM) survey from Burundi.
Anthropometric indices (e.g.weight-for-height z-scores) have not beencalculated and added to the data.
We will use the addWGSR() function to add weight-for-height (wfh)z-scores to the example data:
svy <- addWGSR(data = anthro3, sex = "sex", firstPart = "weight", secondPart = "height", index = "wfh")#> ===========================================================================A new column named wfhz has been added to the dataset:
#> psu age sex weight height muac oedema wfhz#> 1 1 10 1 5.7 64.2 125 2 -2.73#> 2 1 10 2 5.8 64.4 121 2 -2.04#> 3 1 9 2 6.5 62.2 139 2 0.13#> 4 1 11 9 6.5 64.9 129 2 NA#> 5 1 24 2 6.5 72.9 120 2 -3.44#> 6 1 12 2 6.6 69.4 126 2 -2.26The wfhz column contains the weight-for-height (wfh) z-scorescalculated from the sex, weight, and height columns in theanthro3 dataset. The calculated z-scores are rounded to two decimalsplaces unless the digits option is used to specify a differentprecision (run ?addWGSR to see description of various parameters thatcan be specified in the addWGSR() function).
The addWGSR() function takes up to nine parameters to calculate eachindex separately, depending on the index required. These are describedin the Help files of the zscorer package which can be accessed asfollows:
?addWGSRThe standing parameter specifies how “stature” (i.e.length orheight) was measured. If this is not specified, and in some specialcirc*mstances, height and age rules will be applied when calculatingz-scores. These rules are described in the tablebelow.
| index | standing | age | height | Action |
|---|---|---|---|---|
| hfa or lfa | standing | < 731 days | index = lfa height = height + 0.7 cm | |
| hfa or lfa | supine | < 731 days | index = lfa | |
| hfa or lfa | unknown | < 731 days | index = lfa | |
| hfa or lfa | standing | ≥ 731 days | index = hfa | |
| hfa or lfa | supine | ≥ 731 days | index = hfa height = height - 0.7 cm | |
| hfa or lfa | unknown | ≥ 731 days | index = hfa | |
| wfh or wfl | standing | < 65 cm | index = wfl height = height + 0.7 cm | |
| wfh or wfl | standing | ≥ 65 cm | index = wfh | |
| wfh or wfl | supine | ≤ 110 cm | index = wfl | |
| wfh or wfl | supine | more than 110 cm | index = wfh height = height - 0.7 cm | |
| wfh or wfl | unknown | < 87 cm | index = wfl | |
| wfh or wfl | unknown | ≥ 87 cm | index = wfh | |
| bfa | standing | < 731 days | height = height + 0.7 cm | |
| bfa | standing | ≥ 731 days | height = height - 0.7 cm |
The addWGSR() function will not produce error messages unless there issomething very wrong with the data or the specified parameters. If anerror is encountered in a record then the value NA is returned.Error conditions are listed in the tablebelow.
| Error condition | Action |
|---|---|
Missing or nonsense value in standing parameter | Set standing to 3 (unknown) and apply appropriate height or age rules. |
Unknown index specified | Return NA for z-score. |
Missing sex | Return NA for z-score. |
Missing firstPart | Return NA for z-score. |
Missing secondPart | Return NA for z-score. |
sex is not male (1) or female (2) | Return NA for z-score. |
firstPart is not numeric | Return NA for z-score. |
secondPart is not numeric | Return NA for z-score. |
Missing thirdPart when index = "bfa" | Return NA for z-score. |
thirdPart is not numeric when index = "bfa" | Return NA for z-score. |
secondPart is out of range for specified index | Return NA for z-score. |
We can see this error behaviour using the example data:
table(is.na(svy$wfhz))#> #> FALSE TRUE #> 220 1We can display the problem record:
svy[is.na(svy$wfhz), ]#> psu age sex weight height muac oedema wfhz#> 4 1 11 9 6.5 64.9 129 2 NAThe problem is due to the value 9 in the sex column, which shouldbe coded 1 (for male) and 2 (for female). Z-scores are onlycalculated for records with sex specified as either 1 (male) or2 (female). All other values, including NA, will return NA.
The addWGSR() function requires that data are recorded using therequired units or required codes (see ?addWGSR to check units requiredby the different function parameters).
The addWGSR() function will return incorrect values if the data arenot recorded using the required units. For example, this attempt to addweight-for-age z-scores to the example data:
svy <- addWGSR(data = svy, sex = "sex", firstPart = "weight", secondPart = "age", index = "wfa")#> ===========================================================================will give incorrect results:
summary(svy$wfaz)#> Min. 1st Qu. Median Mean 3rd Qu. Max. NA's #> 3.450 7.692 9.840 9.684 11.430 15.900 1The odd range of values is due to age being recorded in months ratherthan days.
It is simple to convert all ages from months to days:
svy$age <- svy$age * (365.25 / 12)head(svy)#> psu age sex weight height muac oedema wfhz wfaz#> 1 1 304.3750 1 5.7 64.2 125 2 -2.73 3.45#> 2 1 304.3750 2 5.8 64.4 121 2 -2.04 3.95#> 3 1 273.9375 2 6.5 62.2 139 2 0.13 5.12#> 4 1 334.8125 9 6.5 64.9 129 2 NA NA#> 5 1 730.5000 2 6.5 72.9 120 2 -3.44 3.82#> 6 1 365.2500 2 6.6 69.4 126 2 -2.26 5.01before calculating and adding weight-for-age z-scores:
svy <- addWGSR(data = svy, sex = "sex", firstPart = "weight", secondPart = "age", index = "wfa")#> ===========================================================================head(svy)#> psu age sex weight height muac oedema wfhz wfaz#> 1 1 304.3750 1 5.7 64.2 125 2 -2.73 -4.13#> 2 1 304.3750 2 5.8 64.4 121 2 -2.04 -3.19#> 3 1 273.9375 2 6.5 62.2 139 2 0.13 -1.97#> 4 1 334.8125 9 6.5 64.9 129 2 NA NA#> 5 1 730.5000 2 6.5 72.9 120 2 -3.44 -4.61#> 6 1 365.2500 2 6.6 69.4 126 2 -2.26 -2.56summary(svy$wfaz)#> Min. 1st Qu. Median Mean 3rd Qu. Max. NA's #> -4.610 -1.873 -1.085 -1.154 -0.480 2.600 1The muac column in the example dataset is recorded in millimetres (mm).We need to convert this to centimetres (cm):
svy$muac <- svy$muac / 10head(svy)#> psu age sex weight height muac oedema wfhz wfaz#> 1 1 304.3750 1 5.7 64.2 12.5 2 -2.73 -4.13#> 2 1 304.3750 2 5.8 64.4 12.1 2 -2.04 -3.19#> 3 1 273.9375 2 6.5 62.2 13.9 2 0.13 -1.97#> 4 1 334.8125 9 6.5 64.9 12.9 2 NA NA#> 5 1 730.5000 2 6.5 72.9 12.0 2 -3.44 -4.61#> 6 1 365.2500 2 6.6 69.4 12.6 2 -2.26 -2.56before using the addWGS() function to calculate MUAC-for-age z-scores:
svy <- addWGSR(svy, sex = "sex", firstPart = "muac", secondPart = "age", index = "mfa")#> ===========================================================================head(svy)#> psu age sex weight height muac oedema wfhz wfaz mfaz#> 1 1 304.3750 1 5.7 64.2 12.5 2 -2.73 -4.13 -1.97#> 2 1 304.3750 2 5.8 64.4 12.1 2 -2.04 -3.19 -1.88#> 3 1 273.9375 2 6.5 62.2 13.9 2 0.13 -1.97 -0.14#> 4 1 334.8125 9 6.5 64.9 12.9 2 NA NA NA#> 5 1 730.5000 2 6.5 72.9 12.0 2 -3.44 -4.61 -2.70#> 6 1 365.2500 2 6.6 69.4 12.6 2 -2.26 -2.56 -1.46As a last example we will use the addWGSR() function to add body massindex-for-age (bfa) z-scores to the data to create a new variable calledbmiAgeZ with a precision of 4 decimal places as:
svy <- addWGSR(data = svy, sex = "sex", firstPart = "weight", secondPart = "height", thirdPart = "age", index = "bfa", output = "bmiAgeZ", digits = 4)#> ===========================================================================head(svy)#> psu age sex weight height muac oedema wfhz wfaz mfaz bmiAgeZ#> 1 1 304.3750 1 5.7 64.2 12.5 2 -2.73 -4.13 -1.97 -2.6928#> 2 1 304.3750 2 5.8 64.4 12.1 2 -2.04 -3.19 -1.88 -2.0005#> 3 1 273.9375 2 6.5 62.2 13.9 2 0.13 -1.97 -0.14 0.0405#> 4 1 334.8125 9 6.5 64.9 12.9 2 NA NA NA NA#> 5 1 730.5000 2 6.5 72.9 12.0 2 -3.44 -4.61 -2.70 -2.8958#> 6 1 365.2500 2 6.6 69.4 12.6 2 -2.26 -2.56 -1.46 -2.0796Usage - legacy functions
To maintain support for earlier versions of the package, the earlierfunctions used to calculate anthropometric z-scores forweight-for-age, height-for-age and weight-for-height have beenkept for now until future deprecation. For current users, it isrecommended to use addWGSR() and getWGSR()functions.
Calculating z-score for each of the three anthropometric indices for a single child
For this example, we will use the getWGS() function and apply it todummy data of a 52 month old male child with a weight of 14.6 kgand a height of 98.0 cm.
# weight-for-age z-scorewaz <- 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-scorehaz <- 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-scorewhz <- 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 foronechild.
Calculating z-score for each of the three anthropometric indices for a cohort or sample of children
For this example, we will use the getCohortWGS() function and apply itto sample data anthro1 that came with zscorer.
# Make a call for the anthro1 datasetanthro1As you will see, this dataset has the 4 variables you will need to usewith getCohortWGS() to calculate the z-score for the correspondinganthropometric 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 inthe sample, we execute the following commands in R:
# weight-for-age z-scorewaz <- 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-scorehaz <- 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-scorewhz <- 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 calculatedz-scores for all children in the cohort orsample.
Calculating z-scores for all of the three anthropometric indices in one function
For this example, we will use the getAllWGS() function and apply it tosample data anthro1 that came with zscorer.
# weight-for-age z-scorezScores <- 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 ofcalculated z-scores for all children in the cohort or sample for allthe anthropometric indices.
Shiny app
To use the included Shiny app, run the following command in R:
run_zscorer()This will initiate the Shiny app using the installed web browser in yourcurrent device as shown below:
References
World Health Organization. (2006). WHO child growth standards :length/height-for-age, weight-for-age, weight-for-length, weight-for-height and body mass index-for-age : methods and development.World Health Organization.https://apps.who.int/iris/handle/10665/43413
World Health Organization. (2007). WHO child growth standards : headcircumference-for-age, arm circumference-for-age, tricepsskinfold-for-age and subscapular skinfold-for-age : methods anddevelopment. World Health Organization.https://apps.who.int/iris/handle/10665/43706
de Onis M. Development of a WHO growth reference for school-agedchildren and adolescents. Bull World Health Org. 2007;85: 660–667.doi:10.2471/BLT.07.043497
Mramba L, Ngari M, Mwangome M, Muchai L, Bauni E, Walker AS, etal.A growth reference for mid upper arm circumference for ageamong school age children and adolescents, and validation formortality: growth curve construction and longitudinal cohort study.BMJ. 2017;: j3423–8.doi:10.1136/bmj.j3423
