Step1Measures | R Documentation |
Step1Measures
computes up to 19 measures for each
longitudinal trajectory. See Details for the list of measures.
Step1Measures(
Data,
Time = NULL,
ID = FALSE,
measures = c(1:18),
midpoint = NULL,
cap.outliers = FALSE
)
## S3 method for class 'trajMeasures'
print(x, ...)
## S3 method for class 'trajMeasures'
summary(object, ...)
Data |
a matrix or data frame in which each row contains the longitudinal data (trajectories). |
Time |
either |
ID |
logical. Set to |
measures |
a vector containing the numerical identifiers of the measures to compute. The default, 1:18, corresponds to measures 1-18 and thus excludes the measures which require specifying a midpoint. |
midpoint |
specifies which column of |
cap.outliers |
logical. If |
x |
object of class |
... |
further arguments passed to or from other methods. |
object |
object of class |
Each trajectory must have a minimum of 3 observations otherwise it will be omitted from the analysis.
The 19 measures and their numerical identifiers are listed below. Please refer to the vignette for the specific formulas used to compute them.
Maximum
Range (max - min)
Mean value
Standard deviation
Intercept of linear model
Slope of the linear model
R^2
: Proportion of variance explained by the linear model
Curve length (total variation)
Rate of intersection with the mean
Proportion of time spent above the mean
Minimum of the first derivative
Maximum of the first derivative
Mean of the first derivative
Standard deviation of the first derivative
Minimum of the second derivative
Maximum of the second derivative
Mean of the second derivative
Standard deviation of the second derivative
Later change/Early change
If 'cap.outliers' is set to TRUE
, or if some measures are infinite as a result of division by 0, Nishiyama's improved Chebychev bound for continuous distributions
is used to determine extreme values for each measure, corresponding to
a 0.3% probability threshold. Extreme values beyond the threshold are then capped
to the 0.3% probability threshold (see vignette for more details). If applicable, the values which
would be of the form 0/0 are set to 1.
An object of class trajMeasures
; a list containing the values
of the measures, a table of the outliers which have been capped, as well as
a curated form of the function's arguments.
Leffondre K, Abrahamowicz M, Regeasse A, Hawker GA, Badley EM, McCusker J, Belzile E. Statistical measures were proposed for identifying longitudinal patterns of change in quantitative health indicators. J Clin Epidemiol. 2004 Oct;57(10):1049-62. doi: 10.1016/j.jclinepi.2004.02.012. PMID: 15528056.
Nishiyama T, Improved Chebyshev inequality: new probability bounds with known supremum of PDF, arXiv:1808.10770v2 stat.ME https://doi.org/10.48550/arXiv.1808.10770
## Not run:
data("trajdata")
trajdata.noGrp <- trajdata[, -which(colnames(trajdata) == "Group")] #remove the Group column
m1 = Step1Measures(trajdata.noGrp, ID = TRUE, measures = 19, midpoint = NULL)
m2 = Step1Measures(trajdata.noGrp, ID = TRUE, measures = 19, midpoint = 3)
identical(m1$measures, m2$measures)
## End(Not run)
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