R Under development (unstable) (2024-09-15 r87152 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # test that the p_bp and q_bp functions return as expected for all the different
> # source options
> library(pedbp)
> 
> # first, verify that the source input options are as expected
> x <- tryCatch(q_bp(p_sbp = 1, p_dbp = 1, male = 1, age = numeric(1), source = "Not a real source"), error = function(e) e)
> stopifnot(inherits(x, "error"))
> 
> # the message appears to print in one of two ways, using the unicode \u8220 and
> # \u8221 for the double quotes when in an interactive session, and \u22 when not
> # interactive
> stopifnot(
+           identical(x$message, "'arg' should be one of “martin2022”, “gemelli1990”, “nhlbi”, “lo2013”, “flynn2017”") |
+           identical(x$message, "'arg' should be one of \"martin2022\", \"gemelli1990\", \"nhlbi\", \"lo2013\", \"flynn2017\"")
+ )
> 
> ################################################################################
> qbp_expected <- list(sbp = rep(NA_real_, 9), dbp = rep(NA_real_, 9))
> 
> # return NA for age out of bounds
> # too young
> stopifnot(
+   isTRUE(
+     all.equal(
+       q_bp(p_sbp = 1:9/10, p_dbp = 1:9/10, male = 0, age = 0.9)
+       ,
+       qbp_expected
+       ,
+       check.attributes = FALSE
+     )
+   )
+ )
> 
> stopifnot(
+   isTRUE(
+     all.equal(
+       q_bp(p_sbp = 1:9/10, p_dbp = 1:9/10, male = 0, age = 0.9, source = "martin2022")
+       ,
+       qbp_expected
+       ,
+       check.attributes = FALSE
+     )
+   )
+ )
> 
> stopifnot(
+   isTRUE(
+     all.equal(
+       q_bp(p_sbp = 1:9/10, p_dbp = 1:9/10, male = 0, age = 0.9, source = "gemelli1990")
+       ,
+       qbp_expected
+       ,
+       check.attributes = FALSE
+     )
+   )
+ )
> 
> stopifnot(
+   isTRUE(
+     all.equal(
+       q_bp(p_sbp = 1:9/10, p_dbp = 1:9/10, male = 0, age = 35.9, source = "lo2013")
+       ,
+       qbp_expected
+       ,
+       check.attributes = FALSE
+     )
+   )
+ )
> 
> stopifnot(
+   isTRUE(
+     all.equal(
+       q_bp(p_sbp = 1:9/10, p_dbp = 1:9/10, male = 0, age = 11.9, source = "nhlbi")
+       ,
+       qbp_expected
+       ,
+       check.attributes = FALSE
+     )
+   )
+ )
> 
> stopifnot(
+   isTRUE(
+     all.equal(
+       q_bp(p_sbp = 1:9/10, p_dbp = 1:9/10, male = 0, age = 11.9, source = "flynn2017")
+       ,
+       qbp_expected
+       ,
+       check.attributes = FALSE
+     )
+   )
+ )
> 
> 
> # too old
> stopifnot(
+   isTRUE(
+     all.equal(
+       q_bp(p_sbp = 1:9/10, p_dbp = 1:9/10, male = 0, age = 19*12, source = "flynn2017")
+       ,
+       qbp_expected
+       ,
+       check.attributes = FALSE
+     )
+   )
+ )
> 
> stopifnot(
+   isTRUE(
+     all.equal(
+       q_bp(p_sbp = 1:9/10, p_dbp = 1:9/10, male = 0, age = 19*12, source = "nhlbi")
+       ,
+       qbp_expected
+       ,
+       check.attributes = FALSE
+     )
+   )
+ )
> 
> stopifnot(
+   isTRUE(
+     all.equal(
+       q_bp(p_sbp = 1:9/10, p_dbp = 1:9/10, male = 0, age = 19*12, source = "martin2022")
+       ,
+       qbp_expected
+       ,
+       check.attributes = FALSE
+     )
+   )
+ )
> 
> stopifnot(
+   isTRUE(
+     all.equal(
+       q_bp(p_sbp = 1:9/10, p_dbp = 1:9/10, male = 0, age = 19*12)
+       ,
+       qbp_expected
+       ,
+       check.attributes = FALSE
+     )
+   )
+ )
> 
> stopifnot(
+   isTRUE(
+     all.equal(
+       q_bp(p_sbp = 1:9/10, p_dbp = 1:9/10, male = 0, age = 19*12, source = "lo2013")
+       ,
+       qbp_expected
+       ,
+       check.attributes = FALSE
+     )
+   )
+ )
> 
> stopifnot(
+   isTRUE(
+     all.equal(
+       q_bp(p_sbp = 1:9/10, p_dbp = 1:9/10, male = 0, age = 13, source = "gemelli1990")
+       ,
+       qbp_expected
+       ,
+       check.attributes = FALSE
+     )
+   )
+ )
> 
> ################################################################################
> # nhlbi and flynn2017 values will be different from the publications.
> # The difference is due to having a Gaussian mean and variance estimated by the
> # three or four percentiles published.  The tests here are to verify that the
> # estimates are not too different.
> 
> # NOTE: IF THIS FAILS UPDATE THE VIGNETTE
> fq <-
+   q_bp(
+      p_sbp = flynn2017$bp_percentile/100,
+      p_dbp = flynn2017$bp_percentile/100,
+      male  = flynn2017$male,
+      age   = flynn2017$age,
+      height_percentile = flynn2017$height_percentile,
+      source = "flynn2017")
> 
> fp <-
+   p_bp(
+      q_sbp = flynn2017$sbp,
+      q_dbp = flynn2017$dbp,
+      male  = flynn2017$male,
+      age   = flynn2017$age,
+      height_percentile = flynn2017$height_percentile,
+      source = "flynn2017")
> 
> nq <-
+   q_bp(
+      p_sbp = nhlbi_bp_norms$bp_percentile/100,
+      p_dbp = nhlbi_bp_norms$bp_percentile/100,
+      male  = nhlbi_bp_norms$male,
+      age   = nhlbi_bp_norms$age,
+      height_percentile = nhlbi_bp_norms$height_percentile,
+      source = "nhlbi")
> 
> np <-
+   p_bp(
+      q_sbp = nhlbi_bp_norms$sbp,
+      q_dbp = nhlbi_bp_norms$dbp,
+      male  = nhlbi_bp_norms$male,
+      age   = nhlbi_bp_norms$age,
+      height_percentile = nhlbi_bp_norms$height_percentile,
+      source = "nhlbi")
> 
> flynn2017 <-
+   cbind(flynn2017,
+         pedbp_sbp = fq$sbp,
+         pedbp_dbp = fq$dbp,
+         pedbp_sbp_p = fp$sbp_p * 100,
+         pedbp_dbp_p = fp$dbp_p * 100
+   )
> 
> nhlbi_bp_norms <-
+   cbind(nhlbi_bp_norms,
+         pedbp_sbp = nq$sbp,
+         pedbp_dbp = nq$dbp,
+         pedbp_sbp_p = np$sbp_p * 100,
+         pedbp_dbp_p = np$dbp_p * 100
+   )
> 
> # all estimates within 2 mmHg or 2 percentage points
> stopifnot(max(abs(flynn2017$pedbp_sbp - flynn2017$sbp)) < 2)
> stopifnot(max(abs(flynn2017$pedbp_dbp - flynn2017$dbp)) < 2)
> stopifnot(max(abs(flynn2017$pedbp_sbp_p - flynn2017$bp_percentile)) < 2)
> stopifnot(max(abs(flynn2017$pedbp_dbp_p - flynn2017$bp_percentile)) < 2)
> stopifnot(max(abs(nhlbi_bp_norms$pedbp_sbp - nhlbi_bp_norms$sbp)) < 2)
> stopifnot(max(abs(nhlbi_bp_norms$pedbp_dbp - nhlbi_bp_norms$dbp)) < 2)
> 
> stopifnot(max(abs(nhlbi_bp_norms$pedbp_sbp_p - nhlbi_bp_norms$bp_percentile)) < 2)
> stopifnot(max(abs(nhlbi_bp_norms$pedbp_dbp_p - nhlbi_bp_norms$bp_percentile)) < 2)
> 
> if (interactive()) {
+   par(mfrow = c(1, 2))
+   plot(flynn2017$sbp, flynn2017$pedbp_sbp); abline(0, 1)
+   plot(flynn2017$dbp, flynn2017$pedbp_dbp); abline(0, 1)
+   summary(flynn2017$pedbp_sbp - flynn2017$sbp)
+   summary(flynn2017$pedbp_dbp - flynn2017$dbp)
+   summary(flynn2017$pedbp_sbp_p*100 - flynn2017$bp_percentile)
+   summary(flynn2017$pedbp_dbp_p*100 - flynn2017$bp_percentile)
+ 
+   qwraps2::qblandaltman(flynn2017[, c("sbp", "pedbp_sbp")])
+   qwraps2::qblandaltman(flynn2017[, c("dbp", "pedbp_dbp")])
+   qwraps2::qblandaltman(flynn2017[, c("bp_percentile", "pedbp_sbp_p")])
+   qwraps2::qblandaltman(flynn2017[, c("bp_percentile", "pedbp_dbp_p")])
+ 
+   par(mfrow = c(1, 2))
+   plot(nhlbi_bp_norms$sbp, nhlbi_bp_norms$pedbp_sbp); abline(0, 1)
+   plot(nhlbi_bp_norms$dbp, nhlbi_bp_norms$pedbp_dbp); abline(0, 1)
+   summary(nhlbi_bp_norms$pedbp_sbp - nhlbi_bp_norms$sbp)
+   summary(nhlbi_bp_norms$pedbp_dbp - nhlbi_bp_norms$dbp)
+   summary(nhlbi_bp_norms$pedbp_sbp_p*100 - nhlbi_bp_norms$bp_percentile)
+   summary(nhlbi_bp_norms$pedbp_dbp_p*100 - nhlbi_bp_norms$bp_percentile)
+ 
+   qwraps2::qblandaltman(nhlbi_bp_norms[, c("sbp", "pedbp_sbp")])
+   qwraps2::qblandaltman(nhlbi_bp_norms[, c("dbp", "pedbp_dbp")])
+   qwraps2::qblandaltman(nhlbi_bp_norms[, c("bp_percentile", "pedbp_sbp_p")])
+   qwraps2::qblandaltman(nhlbi_bp_norms[, c("bp_percentile", "pedbp_dbp_p")])
+ }
> 
> ################################################################################
> # Verify that the expected median is returned from q_bp calls for gemelli1990
> # and lo2013
> stopifnot(
+   isTRUE(
+     all.equal(
+       unname(q_bp(p_sbp = 0.5, p_dbp = 0.5, male = gemelli1990$male, age = gemelli1990$age, source = "gemelli1990"))
+       ,
+       unname(as.list(gemelli1990[c("sbp_mean", "dbp_mean")]))
+       ,
+       check.attributes = FALSE
+     )
+   )
+ )
> 
> stopifnot(
+   isTRUE(
+     all.equal(
+       unname(q_bp(p_sbp = 0.5, p_dbp = 0.5, male = lo2013$male, age = lo2013$age, source = "lo2013"))
+       ,
+       unname(as.list(lo2013[c("sbp_mean", "dbp_mean")]))
+       ,
+       check.attributes = FALSE
+     )
+   )
+ )
> 
> stopifnot(
+   isTRUE(
+     all.equal(
+       unname(p_bp(q_sbp = gemelli1990$sbp_mean, q_dbp = gemelli1990$dbp_mean, male = gemelli1990$male, age = gemelli1990$age, source = "gemelli1990"))
+       ,
+       list(rep(0.5, nrow(gemelli1990)), rep(0.5, nrow(gemelli1990)))
+       ,
+       check.attributes = FALSE
+     )
+   )
+ )
> 
> stopifnot(
+   isTRUE(
+     all.equal(
+       unname(p_bp(q_sbp = lo2013$sbp_mean, q_dbp = lo2013$dbp_mean, male = lo2013$male, age = lo2013$age, source = "lo2013"))
+       ,
+       list(rep(0.5, nrow(lo2013)), rep(0.5, nrow(lo2013)))
+       ,
+       check.attributes = FALSE
+     )
+   )
+ )
> 
> ################################################################################
> #                                 End of file                                  #
> ################################################################################
> 
> proc.time()
   user  system elapsed 
   0.20    0.06    0.26