thlytras / rspiro Goto Github PK

Hi! Thanks for putting this package together. Just a small note that the link to the R code in the README leads to the organizations 404 page.

Your equation for z-score is: ((obs/M)^L-1)/(LS))
However, the https://www.atsjournals.org/doi/suppl/10.1164/rccm.202205-0963OC/suppl_file/bowerman_data_supplement.pdf supplemental for 2022 paper is (obs-M)^(L-1)/(LS)

Thank you for package. I would very much appreciate the addition of z-score calculations for NHANES3 predictions.

I tried running this package today and found that the documentation for zscore_GLI didn't quite match the behavior. The documentation for the function states: "If only one spirometry argument is supplied, the function returns a numeric vector. If more are supplied, the function returns a data.frame with the same number of columns."

However, if you pass multiple spirometry measures, you instead get this confusing error.

> zscore_GLI(age=seq(25,40,5), height=c(1.8, 1.9, 1.75, 1.85),
            gender=c(2,1,2,1), FEV1=c(3.5, 4, 3.6, 3.9),  FVC=c(3.5, 4, 3.6, 3.9))
Error in zscore_GLI(age = seq(25, 40, 5), height = c(1.8, 1.9, 1.75, 1.85),  : 
  Spirometry parameter vector(s) and somatometric vectors
         (age, height, gender, ethnicity) do not have the same length.

I was able to loop through each measure to solve my problem, but I thought I'd post this issue since I ran into it. Thanks for putting this package together! I came to it from the GLI site.

In the help for pctpred_GLI help it specifies the argument:

FEV1FVC FEV1 / FVC * 100%

but it is actually just FEV1/FVC (range 0-1) that is the required argument, not *100%

presumably the same for FEV075FVC argument but not checked this

Would it be possible to implement rspiro package with the race-neutral set of GLI equations (ethnicity = 0)
Thanks

Thanks for the nice package. Might I suggest:

1. Renaming the "gender" input to "birth sex"? "Gender" might be misunderstood as gender identity. What reference value formulas have is sex assigned at birth.
2. Removing default values for sex and ethnicity. There is no reason to assume, by default, that the patient is a white male. Having a default might prevent users from noticing erroneous input and increase the chance of bias.

Thanks!

Would it be possible to support the GLI equations for TLCO and DLCO ?
Originally published in 2017 (https://pubmed.ncbi.nlm.nih.gov/28893868/) but corrected in 2020 https://www.ers-education.org/lr/show-details/?idP=240831

Hi. thanks for developing this package. I am trying to predict some PFT values and I am getting this message.

Warning message:
You have specified more than two unique values for gender. Please check your data. Returning NA.

even though I have my gender as "1" and "2"

Maher,

Hi
Is it possible to support the JRS 2014 criteria to reflect Japanese reference criteria?
I believe that the GLI 2012 and 2022 reference datasets didn't include data from Japanese participants so it may be more relevant/accurate to have an implementation of JRS 2014 within rspiro
https://www.sciencedirect.com/science/article/abs/pii/S2212534514000288 (behind a paywall)
Thanks
Nelson

Hi there,

Is it possible to add the functionality to also produce GLI z-scores?

Many thanks,

Tim

R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

I tried to install rspiro package per your instructions and got an error:
Installation failed: 'setInternet2' is defunct.

I It may be related to similar issue elsewhere.

Thanks!