Computes:
log_cortisol_wake (log-transformed waking cortisol)
CAR_AUC (Cortisol Awakening Response, trapezoidal AUC over 0-60 min by default)
log_amylase (log-transformed salivary alpha-amylase)
saliva_glucose (raw salivary glucose)
Usage
saliva_markers(
data,
col_map = list(cort1 = "saliva_cort1", cort2 = "saliva_cort2", cort3 = "saliva_cort3",
amylase = "saliva_amylase", glucose = "saliva_glucose"),
verbose = FALSE,
na_action = c("keep", "omit", "error"),
na_warn_prop = 0.2,
check_extreme = FALSE,
extreme_action = c("warn", "cap", "error", "ignore"),
extreme_rules = NULL,
times = c(0, 30, 60)
)Arguments
- data
A data.frame or tibble with salivary markers.
- col_map
Named list mapping required inputs. Defaults assume same names:
cort1 -> "saliva_cort1" (nmol/L at wake)
cort2 -> "saliva_cort2" (nmol/L ~30 min)
cort3 -> "saliva_cort3" (nmol/L ~60 min)
amylase -> "saliva_amylase" (U/mL)
glucose -> "saliva_glucose" (mg/dL)
- verbose
Logical; if
TRUE, prints progress messages via hm_inform().- na_action
One of
c("keep","omit","error")for required-input NA handling. Default "keep".- na_warn_prop
Proportion \([0,1]\) to trigger high-missingness diagnostics (debug). Default 0.2.
- check_extreme
Logical; if TRUE, scan inputs for extreme values. Default FALSE.
- extreme_action
One of
c("warn","cap","error","ignore")when extremes detected. Default "warn".- extreme_rules
Optional named list of c(min,max) bounds. If NULL, broad defaults are used (keyed by mapped column names).
- times
Numeric vector of sampling times (minutes) for CAR AUC. Must align with cort1/2/3. Default c(0,30,60).
Details
Inputs are validated, missingness handled via na_action, logs made safe
(<= 0 -> NA), and optional extremes scan/cap is available.
References
Original derivations Pruessner JC, Kirschbaum C, Meinlschmid G, Hellhammer DH. Two formulas for computation of the area under the curve represent measures of total hormone concentration versus time-dependent change. Psychoneuroendocrinology. 2003;28(7):916-931. doi:10.1016/S0306-4530(02)00108-7 (AUC hormone measures) Kirschbaum C, Hellhammer DH. Salivary cortisol in psychoneuroendocrine research: recent developments and applications. Psychoneuroendocrinology. 1994;19(4):313-333. doi:10.1016/0306-4530(94)90013-2 (Salivary cortisol methods)
Validation and applications Clow A, Thorn L, Evans P, Hucklebridge F. The awakening cortisol response: methodological issues and significance. Stress. 2004;7(1):29-37. doi:10.1080/10253890410001667205 (Cortisol awakening response) Nater UM, Rohleder N. Salivary alpha-amylase as a non-invasive biomarker for the sympathetic nervous system: current state of research. Psychoneuroendocrinology. 2009;34(4):486-496. doi:10.1016/j.psyneuen.2009.01.014 (Salivary alpha-amylase marker) Scales WE, Freeman EW, McCoy NL, Klerman EB. Salivary glucose as a measure of blood glucose: correlations and applications. Diabetes Care. 1987;10(4):414-418. doi:10.2337/diacare.10.4.414 (Salivary glucose application)
Examples
df <- tibble::tibble(
saliva_cort1 = 12.5,
saliva_cort2 = 18.0,
saliva_cort3 = 16.2,
saliva_amylase = 85,
saliva_glucose = 4.2
)
saliva_markers(df) # uses default col_map
#> # A tibble: 1 × 4
#> log_cortisol_wake CAR_AUC log_amylase saliva_glucose
#> <dbl> <dbl> <dbl> <dbl>
#> 1 2.53 970. 4.44 4.2