Help for package peRiodiCS (original) (raw)
| Type: | Package |
|---|---|
| Title: | Functions for Generating Periodic Curves |
| Version: | 0.5.0 |
| Date: | 2018-07-02 |
| Description: | Functions for generating variants of curves: restricted cubic spline, periodic restricted cubic spline, periodic cubic spline. Periodic splines can be used to model data that has periodic nature / seasonality. |
| License: | GPL-3 |
| BugReports: | https://github.com/crtahlin/peRiodiCS/issues |
| Depends: | R (≥ 2.10) |
| Imports: | graphics, Hmisc, rms |
| Suggests: | testthat |
| LazyData: | true |
| RoxygenNote: | 6.0.1 |
| NeedsCompilation: | no |
| Packaged: | 2018-07-02 15:22:31 UTC; crtah |
| Author: | Crt Ahlin [aut, cre], Lara Lusa [aut] |
| Maintainer: | Crt Ahlin crt.ahlin@gmail.com |
| Repository: | CRAN |
| Date/Publication: | 2018-07-05 09:20:07 UTC |
Basis for restricted cubic splines
Description
Function that derives the restricted cubic splines for a value/vector of values, given the knots; obtains exactly the same results as the rcs function included in the rms package.
Usage
b_rcs(x, knots, inclx = FALSE)
Arguments
| x | numerical vector |
|---|---|
| knots | vector specifying the knot locations |
| inclx | logical, if TRUE returns also the x vector |
Derive first derivatives of RCS
Description
function that derives the first derivative of the restricted cubic splines for a value/vector of values, given the knots
Usage
b_rcs_prime(x, knots)
Arguments
| x | vector of values |
|---|---|
| knots | vector of knot locations |
Generate design matrix for periodic cubic splines
Description
Generate design matrix for periodic cubic splines.
Usage
cs_per(x, knots = NULL, nk = 5, xmax = max(x, na.rm = TRUE),
xmin = min(x, na.rm = TRUE))
Arguments
| x | numerical x values to transform to new basis |
|---|---|
| knots | vector with locations of the knots of the spline |
| nk | number of knots, used only if the knots are not specified, overridden otherwise |
| xmax | value of the (theoretical) minimum of x |
| xmin | value of the (theoretical) maximum of x |
Examples
# load example data; see help("viral_east_mediteranean")
data("viral_east_mediteranean")
# calculate location of knots to use
Knots <-
Hmisc::rcspline.eval(x = viral_east_mediteranean$EpiWeek,
nk = 5, knots.only = TRUE)
# model viral infections vs weeks
model <- glm(RSV ~ cs_per(EpiWeek, knots = Knots), data = viral_east_mediteranean)
# plot model (with many points, to make it smooth)
plot_per_mod(Model = model, XvarName = "EpiWeek", Smooth = TRUE)
Plotting function for periodic curves model
Description
Plots graph of periodic curves with confidence intervals. Data should be included in the model.
Usage
plot_per_mod(Model, XvarName, Ylab = "Response", Xlab = "Covariate",
Ylim = NULL, Xlim = NULL, Xmin = NULL, Xmax = NULL, Knots = NULL,
Title = NULL, Vlines = NULL, Hlines = NULL, Cex.lab = NULL,
Cex.main = NULL, Cex.axis = NULL, Axes = TRUE, Add = FALSE,
Col = "black", PlotCI = TRUE, Smooth = FALSE, xLocation = 2)
Arguments
| Model | The built model |
|---|---|
| XvarName | Name of the x variable in the dataset (column name) |
| Ylab | Label on vertical (y) axis |
| Xlab | Label on horizontal (x) axis |
| Ylim | Limits of y axis |
| Xlim | Limits of x axis |
| Xmin | The min X of data to be predicted (if Smooth) |
| Xmax | The max X of data to be predicted (if Smooth) |
| Knots | Locations of knots of the splines |
| Title | Title of the plot |
| Vlines | Where to plot vertical lines |
| Hlines | Where to plot horizontal lines |
| Cex.lab | Character expansion (aka "size of font") for the labels |
| Cex.main | Character expansion for main text |
| Cex.axis | Character expansion for the axis text |
| Axes | Plot axes |
| Add | Add to existing plot |
| Col | Color of the plotted lines |
| PlotCI | Plot confidence intervals |
| Smooth | Make the Xaxis values equidistant (and the curve smoother) |
| xLocation | If smooth FALSE, the location of the x term in model$x[, xLocation] |
Generate design matrix for periodic restricted cubic spline
Description
Generate design matrix for periodic restricted cubic spline.
Usage
rcs_per(x, knots = NULL, nk = 5, xmin = min(x, na.rm = TRUE),
xmax = max(x, na.rm = TRUE))
Arguments
| x | numerical x values to transform to new basis |
|---|---|
| knots | vector with locations of the knots of the spline |
| nk | number of knots, used only if the knots are not specified, overridden otherwise |
| xmin | value of the (theoretical) minimum of x |
| xmax | value of the (theoretical) maximum of x #' @examples # load example data; see help("viral_east_mediteranean") data("viral_east_mediteranean") # calculate location of knots to use Knots <- Hmisc::rcspline.eval(x = viral_east_mediteranean$EpiWeek, nk = 5, knots.only = TRUE) # model viral infections vs weeks model <- glm(RSV ~ rcs_per(EpiWeek, knots = Knots), data = viral_east_mediteranean) # plot model (with many points, to make it smooth) plot_per_mod(Model = model, XvarName = "EpiWeek", Smooth = TRUE) |
Viral etiology, seasonality and severity of hospitalized patients with severe acute respiratory infections in the Eastern Mediterranean Region, 2007-2014
Description
Data about infections with different viruses across several years.
For more information see Source and References section.
Usage
viral_east_mediteranean
Format
A data frame with variables:
UniqueID
record identification number
Enrolled
Did the patient consent and enroll in the study?: 1=Yes, 0=No
Country
Country of enrollment: Egypt, Jordan, Oman, Qatar, Yemen
EpiYear
Year of enrollment: Integers (2007-2014)
EpiMonth
Month of enrollment: Integers (1-12)
EpiWeek
Week of enrollment: Integers (1-53)
Interval
Number of days between onset of symptoms and hospitalization: Integer
Stay
Number of days between hospitalization and outcome: Integer
Sex
Sex: 1=Female, 0=Male
AgeGrp
Age group: 1=<1 year, 2=1-4 years, 3=5-49 years, 4=50+ years
ChronicDis
Does the patient have any pre-existing chronic disease?: 1=Yes, 0=No
OxTherapy
Did the patient receive oxygen therapy during hospitalization?: 1=Yes, 0=No
Ventilated
Was the patient ventilated during hospitalization?: 1=Yes, 0=No
ICU
Was the patient admitted to an intensive care unit during hospitalization?: 1=Yes, 0=No
Outcome
What was the patient"'"s final hospitalization outcome?: 1=Discharge, 2=Transfer, 3=Death
RSV
Results for respiratory syncytial virus: 1=Positive, 0=Negative
AdV
Results for adenovirus: 1=Positive, 0=Negative
hMPV
Results for human metapneumovirus: 1=Positive, 0=Negative
hPIV1
Results for human parainfluenzavirus type 1: 1=Positive, 0=Negative
hPIV2
Results for human parainfluenzavirus type 2: 1=Positive, 0=Negative
hPIV3
Results for human parainfluenzavirus type 3: 1=Positive, 0=Negative
Flu
Results for influenza: 1=Positive, 0=Negative
Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0180954
References
Horton, Katherine C. AND Dueger, Erica L. AND Kandeel, Amr AND Abdallat, Mohamed AND El-Kholy, Amani AND Al-Awaidy, Salah AND Kohlani, Abdul Hakim AND Amer, Hanaa AND El-Khal, Abel Latif AND Said, Mayar AND House, Brent AND Pimentel, Guillermo AND Talaat, Maha (2017). Viral etiology, seasonality and severity of hospitalized patients with severe acute respiratory infections in the Eastern Mediterranean Region, 2007-2014. PLOS ONE, 12, 1-17.