Utility functions for adding growth standard bands to ggplot2/lattice plots

panel.who(
  x,
  x_var = "agedays",
  y_var = "htcm",
  sex = "Female",
  p = c(1, 5, 25, 50),
  color = NULL,
  alpha = 0.15,
  center = FALSE,
  labels = TRUE,
  x_trans = identity,
  y_trans = identity
)

panel.igb(
  gagebrth,
  var = "lencm",
  sex = "Female",
  p = c(1, 5, 25, 50),
  color = NULL,
  alpha = 0.15,
  center = FALSE,
  labels = TRUE,
  x_trans = identity,
  y_trans = identity
)

panel.igfet(
  gagedays,
  var = "hccm",
  p = c(1, 5, 25, 50),
  color = "green",
  alpha = 0.15,
  center = FALSE,
  labels = TRUE,
  x_trans = identity,
  y_trans = identity
)

geom_growthstandard(
  mapping = NULL,
  data = NULL,
  x_seq,
  x_var = "agedays",
  y_var,
  sex = "Female",
  p = c(1, 5, 25, 50),
  shade = NULL,
  alpha = 0.15,
  center = FALSE,
  x_trans = identity,
  y_trans = identity,
  standard = "who",
  inherit.aes = TRUE
)

geom_who(...)

geom_igb(..., var = "lencm")

geom_igfet(..., var = "hccm", color = "green")

Arguments

x, x_seq: value or vector of values that correspond to a measure defined by x_var. x_seq is used with geom_*
x_var: x variable name (typically "agedays")
y_var: y variable name (typically "htcm" or "wtkg")
sex: "Male" or "Female"
p: centiles at which to draw the growth standard band polygons (only need to specify on one side of the median)
color, shade: optional color to use for bands (will use sex to determine if not specified). shade is used with geom_*
alpha: transparency of the bands
center: should the bands be centered around the median?
labels: should the centiles be labeled? (not implemented)
x_trans: transformation function to be applied to x-axis
y_trans: transformation function to be applied to y-axis
gagebrth: gestational age at birth in days (for igb plots)
var: variable name for y axis for igb or igfet plots ("lencm", "wtkg", or "hcircm" for igb; "accm", "bpdcm", "flcm", "hccm", or "ofdcm" for igfet)
gagedays: gestational age in days (for igfet plots)
data, mapping, inherit.aes: supplied direclty to ggplot2::layer
standard: standard name to use. Either "who", "igb", or "igfet"
...: items supplied direclty to geom_growthstandard

Examples

if (FALSE) {
#### ggplot2

library(ggplot2)
p <- ggplot(data = subset(cpp, subjid == 8), aes(x = agedays, y = htcm)) +
  geom_who(x_seq = seq(0, 2600, by = 10), y_var = "htcm") +
  geom_point()

#### lattice

library(lattice)
xyplot(wtkg ~ agedays, data = subset(cpp, subjid == 8),
  panel = function(x, y, ...) {
    panel.who(x = seq(0, 2558, by = 30),
      sex = "Male", y_var = "wtkg", p = 100 * pnorm(-3:0))
    panel.xyplot(x, y, ...)
  },
  col = "black"
)

# look at Male birth lengths superposed on INTERGROWTH birth standard
# first we need just 1 record per subject with subject-level data
cppsubj <- subset(cpp, !duplicated(cpp$subjid))
xyplot(birthlen ~ jitter(gagebrth), data = subset(cppsubj, sex == "Male"),
  panel = function(x, y, ...) {
    panel.igb(gagebrth = 250:310, var = "lencm", sex = "Male")
    panel.points(x, y, ...)
  },
  col = "black", alpha = 0.75,
  xlab = "Gestational Age at Birth (days)", ylab = "Birth Length (cm)"
)
}