Calculate Z-scores for multiple individuals

[tamuri]

• measurement-to-sds and sds-to-measurement

• given table of input data

  • set sex or select column
  • set gestation or select column
  • specify which rows to use as input (start row and number of rows)
    • auto-determinate based on filled rows
  • select columns age
    • by date - birth and measurement column
    • age column in days, weeks, months or years
  • select measurement column and SDS columns for input/output
    • auto-selection of columns based on column names in header

• measurements determined by what's available in reference

  • height, weight, BMI, head, sitting height, leg length
  • currently maximum 6
  • calculate Z-scores for multiple measurements
    • SDS,
    • centile,
    • % predicted (of mean value [M]),
    • predicted (the mean value [M]),
    • % CV ([S] * 100),
    • skewness ([L] value),
    • LLN5 (5th centile of distribution at this age)

• units of measurements are fixed (metric)

[tamuri]

Input form for "measurement to/from sds" from LMSgrowth add-in:

[dpshelio]

How can we handle multiple sheet in the same workbook?

• Run it again for each sheet after selecting workbook?
• Two selects: sheet + column?
• enforce a single sheet upload with data on columns?

[statist7]

The first two look very similar in practice. I’d prefer not the third. The user will need to provide rectangular data.

[tamuri]

Copying Tim's comments on #25 here:

I've finally got round to finding a suitable file to test the multiple tab. It uses the ukwhopt reference. sample z scores3 csv.txt

• currently it requires CSV format, but this needs to be flexible - even including xls(x)
• there is no way to change the file once it has been selected
• it displays height and weight (which are in the file) plus BMI which isn't, then two other NA fields
• with height and weight it should calculate BMI
• it assumes age is in days - years would be a better default, or use an algorithm based on the data
• the SDS calculations are wrong, mainly NA
• use column names SDS_height, SDSweight atc, not LMS

Separately we need an option to adjust age for gestational age in preterm babies. The calculation is:

adjusted age = postnatal age + gestational age - 40 weeks

Preterm is gestational age < 37 weeks, while term is 37 to <42 weeks, with 40 weeks the expected term gestational age.

The adjustment is applied up to 2 years postnatal age but not beyond. As an example, a baby born at 27 weeks and measured at 52 postnatal weeks has an adjusted (or post-term) age of 39 weeks.

[tamuri]

Example plots from SMART Growth Chart app:

[tamuri]

From meeting on 17/1:

• [ ] Make sure sex is always specified
  • [ ] Otherwise, handle error
• [x] Display centiles curves behind the calculated centile points
  • [x] Only if dataset is for single sex (either from specifying in the drop-down or by seeing that the selected column is single sex)
• [ ] Add plotting options:
  • [x] Specify y-axis:
    • [x] Measurement (current)
    • [x] SDS
    • [x] Centile
  • [ ] Have some user-specified centile options
    • [ ] User preference
    • [x] Can be updated from the centile tab
      • [x] Automatically...?
  • [x] Join plotted points
    • [x] if identifier column is known
    • [x] otherwise, assume points are all from same individual (think about how this would work)
• [ ] Handle upload of whitespace delimited, tsv, Excel
• [x] Add a reset button that
  • [x] Goes back to the start (i.e. clear everything, display upload data form)
• [ ] Some JS to collapse the sidebar

[tamuri]

From Tim (https://github.com/UCL/LMSgrowth2/pull/43#issuecomment-602607350):

The IOTF reference is for BMI, but it doesn't work with the sample dataset as there is no BMI column. There needs to be a way to say, calculate BMI from weight and height. And ideally it would use a user-specified formula that could be extended to other constructed measures such as sitting height divided by leg length.