vignettes/calculate_zscore.Rmd
calculate_zscore.RmdThe main function in the zscorer package is addWGSR().
To demonstrate its usage, we will use the accompanying dataset in zscorer called anthro3. We inspect the dataset as follows:
anthro3which 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 been calculated 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-scores calculated from the sex, weight, and height columns in the anthro3 dataset. The calculated z-scores are rounded to two decimals places unless the digits option is used to specify a different precision (run ?addWGSR to see description of various parameters that can be specified in the addWGSR() function).
The addWGSR() function takes up to nine parameters to calculate each index separately, depending on the index required. These are described in the Help files of the zscorer package which can be accessed as follows:
?addWGSRThe standing parameter specifies how “stature” (i.e. length or height) was measured. If this is not specified, and in some special circumstances, height and age rules will be applied when calculating z-scores. These rules are described in the table below.
| 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 is something very wrong with the data or the specified parameters. If an error is encountered in a record then the value NA is returned. Error conditions are listed in the table below.
| 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:
We can display the problem record:
svy[is.na(svy$wfhz), ]
#> psu age sex weight height muac oedema wfhz
#> 4 1 11 9 6.5 64.9 129 2 NAThe problem is due to the value 9 in the sex column, which should be coded 1 (for male) and 2 (for female). Z-scores are only calculated for records with sex specified as either 1 (male) or 2 (female). All other values, including NA, will return NA.
The addWGSR() function requires that data are recorded using the required units or required codes (see ?addWGSR to check units required by the different function parameters).
The addWGSR() function will return incorrect values if the data are not recorded using the required units. For example, this attempt to add weight-for-age z-scores to the example data:
svy <- addWGSR(data = svy, sex = "sex", firstPart = "weight",
secondPart = "age", index = "wfa")
#> ================================================================================will give incorrect results:
summary(svy$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 rather than 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 -2.56
summary(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 / 10
head(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 addWGSR() 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 mass index-for-age (bfa) z-scores to the data to create a new variable called bmiAgeZ 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 -2.0796