At the moment, the Travis build installs LMSgrowth2 with the packrat environment, which is intended for development. It's probably better now to install LMSgrowth2 as a typical R package (i.e. using devtools::install('./LMSgrowth2') (or however one should do it...I haven't looked into it yet).

Longstanding bug in Centiles: it assumes a new sheet is open to write to. If no sheet is open it fails with the error Invalid conversion number.. So if no sheet is open it needs to open one first.

Note that if a sheet is open, it writes to the first empty column.

• 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)

When using WHO06 data I see a lot of warnings in the calculator and centiles (PR #26) tab:

Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values

With @tamuri we found out that this is due to duplicate rows for years == 2 in the data, for both sexes

• one or multiple children
• either the bmi is given, or weight+height
• age in days/weeks/months/years
• cutoffs are fixed
• minimum age of 2 years

For issue #1

After starting Excel with the growth reference spreadsheets in the startup path, when you close Excel it prompts the user to save the spreadsheets despite no changes having been made.

I think this is because the growth references are saved in an older version of Excel and newer versions of Excel update the spreadsheet.

Possible solution is to update the growth reference spreadsheets that are packaged with the add-in for 64-bit versions.

• OAuth integration

It is preferred that LSMgrowth2 gracefully handles errors in input data (i.e. prefer warning rather than error)
The application should calculate measurements and statistics for as much of the input data as possible and produce warnings/errors for data that did not conform to the right format e.g. calculate Z-scores for all rows where possible and display "NA" where not.
It is believed that bad input data is self-evident given strange outputs.

Renv has now been released (https://blog.rstudio.com/2019/11/06/renv-project-environments-for-r/) which fixes some of the problems with packrat.

We should plan to switch (not urgent).

LMSgrowth for Excel writes two files, prevsds and prevrfn, to the home directory, to record default settings. They would be tidier if hidden, by adding a dot to their names.

• select the growth reference

• selection is preserved for the next run of the application by user

• currently each growth reference is a different xls file stored in a specific directory

• select six measurements to display on forms (this is limitation of excel add-in; do not replicate!)

• collaborative development

Includes guide for developers on setting up for development

We may want to use stylesheet to better control the rendering of the page.

For example, in the centile tab can be used to put some space between tables and plots, and to style the headers

Given difficulties maintaining the current Excel add-in, LMSgrowth2 seeks to implement (and expand upon) the functionality currently available in LMSgrowth in a web-based application.

LMSgrowth2 will make use of the SITAR CRAN package, which provides functions to work with LMS growth data.

This requirement issue is a container for specific sub-requirements.

• measurement-to-sds

• age for gestation

  • see vba code for exact algorithm for adjustment

• input age as

  • date of birth + date of measurement
  • age in days + weeks + months + years

• note interaction between input boxes

  • e.g. height+weight automatically calculated BMI
  • but adjusting BMI doesn't adjust height, weight (can be inconsistent)

• available measurements:

  • determined by what's available in reference
  • current LMSgrowth allow for max 6, selected by user
    • default from british1990 growth reference
      • height, weight, BMI, head, sitting height, leg length
  • calculate Z-scores for multiple measurements:
    • SDS,
    • centile,
    • % predicted (of mean value),
    • predicted (the mean value),
    • % CV ([S] * 100),
    • skewness ([L] value),
    • LLN5 (5th centile of distribution at this age

• input unit of measurement are fixed by the application (metric)

LMSgrowth2 will be a web-based application. It will be built on the R platform using Shiny.

Primary target: recent Windows, Mac, Linux browsers on the desktop
Secondary target: tablet and mobile devices (iOS, Android)

Use existing cross-platform widgets/frameworks to avoid incompatibilities and allow for responsive web design.

@statist7 - we need to setup Travis to continue to test builds of LMSgrowth2. It's simply a matter of logging into Travis using your Github credentials and adding LMSgrowth2 as a repository you want to use with Travis. Instructions are here - you only have to setup Travis+Github repo because we already have travis.yml in this repo.

Currently LMSgrowth add-in works directly on user's spreadsheets.

• allow users to upload input in xls, xlsx and csv formats
  • allow users to input data for single or multiple children
  • allow users to input data for single or multiple measurements
• allow users to directly enter data via entry forms

Allow the application to run on a user's machine
Solutions to explore:
- CRAN package
- Docker container
- All-in-one R bundle with required packages

With the release of dplyr 1.0 and R 4.0, some of the functions we're using need to be updated. I see these messages when running the app. Add any others to this issue.

Warning: `tbl_df()` is deprecated as of dplyr 1.0.0.
Please use `tibble::as_tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning: `funs()` is deprecated as of dplyr 0.8.0.
Please use a list of either functions or lambdas: 

  # Simple named list: 
  list(mean = mean, median = median)

  # Auto named with `tibble::lst()`: 
  tibble::lst(mean, median)

  # Using lambdas
  list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning: `arrange_()` is deprecated as of dplyr 0.7.0.
Please use `arrange()` instead.
See vignette('programming') for more help
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.

We don't have unit tests but we can use Travis CI for building the package at least (see here). At least that will check the dependencies & packrat config.

allow users to upload their own growth reference
requires defining standard format of growth reference data

• one column for age
• each measurement has
  • l[ambda] - power transform to deal with skewness (i.e. $y^\lambda$)
  • m[u] - median
  • s[igma] - measure of dispersion (sd/mean i.e. coefficient of variation)

Is this output of LMSchartmaker? Ensure that we handle at least that format.

Support other methods e.g. gamlss

• summary: generates table of numbers to allow user to plot growth chart
• user-defined centiles set by number or space between centiles
  • equal and unequal centile space
• for each sex
• select age unit and frequency
  • by default, use ages defined in the growth reference
• select growth measurement (height, weight etc) to output
• min and max range is determined by the growth reference

Azure, Shinyapps, Cloudlabs etc.

Docker?

Current add-in only works on 32-bit Office systems. After preliminary investigation and discussion with @statist7, it is agreed we target only latest versions of 64-bit Office on Windows. MacOS version of Excel would require significant overhaul of the current VBA codebase and forms.

• for one or multiple children
• select two ages and corresponding weight at those ages
  • calculate weight gain sds and centile

Some selected options should be preserved across runs without needing user-accounts (i.e. using cookies)

• Selected growth reference
• Previously selected options for measurements (limitated to 6 by current LMSgrowth add-in)

Requirement to discuss in light of data handling law etc:
- preserve access to previously uploaded and analysed data