From 0f6883134a60fb5b2e854b91a786e16ac6053b2e Mon Sep 17 00:00:00 2001
From: Maia Kapur <39382798+mkapur-noaa@users.noreply.github.com>
Date: Wed, 11 Dec 2024 10:24:34 -0800
Subject: [PATCH] doc gam based functions

---
 NAMESPACE            |  4 ++++
 man/Deriv.Rd         | 27 +++++++++++++++++++++++++++
 man/check_Deriv.Rd   | 25 +++++++++++++++++++++++++
 man/check_data.Rd    | 26 ++++++++++++++++++++++++++
 man/confint_Deriv.Rd | 23 +++++++++++++++++++++++
 5 files changed, 105 insertions(+)
 create mode 100644 man/Deriv.Rd
 create mode 100644 man/check_Deriv.Rd
 create mode 100644 man/check_data.Rd
 create mode 100644 man/confint_Deriv.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 6ae9268..5c6b8c9 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,2 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(Deriv)
+export(check_Deriv)
+export(check_data)
+export(confint_Deriv)
diff --git a/man/Deriv.Rd b/man/Deriv.Rd
new file mode 100644
index 0000000..cab63c5
--- /dev/null
+++ b/man/Deriv.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/Deriv.R
+\name{Deriv}
+\alias{Deriv}
+\title{Evaluate first derivative of GAM smooth(s), adapted from
+\href{https://gist.githubusercontent.com/gavinsimpson/e73f011fdaaab4bb5a30/raw/82118ee30c9ef1254795d2ec6d356a664cc138ab/Deriv.R}{Gavin Simpson}.}
+\usage{
+Deriv(mod, n = 200, eps = 1e-04, newdata, term)
+}
+\arguments{
+\item{mod}{the output of {mgcv::gam()}}
+
+\item{n}{number of intervals over which to evaluate each smooth. default 200.}
+
+\item{eps}{tolerance threshold. default 1e-4.}
+
+\item{newdata}{optional; data.frame of new smooth parameters to evaluate}
+
+\item{term}{string smooth name, i.e. "year". must match values in mod and newdata}
+}
+\value{
+a vector of derivative values of length n
+}
+\description{
+Evaluate first derivative of GAM smooth(s), adapted from
+\href{https://gist.githubusercontent.com/gavinsimpson/e73f011fdaaab4bb5a30/raw/82118ee30c9ef1254795d2ec6d356a664cc138ab/Deriv.R}{Gavin Simpson}.
+}
diff --git a/man/check_Deriv.Rd b/man/check_Deriv.Rd
new file mode 100644
index 0000000..88e225e
--- /dev/null
+++ b/man/check_Deriv.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/check_Deriv.R
+\name{check_Deriv}
+\alias{check_Deriv}
+\title{Check whether the CI of the derivative includes zero or not}
+\usage{
+check_Deriv(x, d, upper, lower, eval = 0, crit.eval)
+}
+\arguments{
+\item{x}{vector of values over which derivatives were evaluated}
+
+\item{d}{vector output of {Deriv()}}
+
+\item{upper}{upper confidence interval; output of {confint_Deriv()}}
+
+\item{lower}{lower confidence interval; output of {confint_Deriv()}}
+
+\item{eval}{the value that you would like to examine. default 0}
+}
+\value{
+vector of confidence intervals of same length as object.
+}
+\description{
+Check whether the CI of the derivative includes zero or not
+}
diff --git a/man/check_data.Rd b/man/check_data.Rd
new file mode 100644
index 0000000..1b645ee
--- /dev/null
+++ b/man/check_data.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/check_data.R
+\name{check_data}
+\alias{check_data}
+\title{load, check and plot input data for use in breakpoint detection}
+\usage{
+check_data(dat, sex = FALSE, showPlot = TRUE)
+}
+\arguments{
+\item{dat}{data.frame with columns year, age, length, sex (optional)}
+
+\item{sex}{logical. does your data frame include a sex column?}
+
+\item{showPlot}{logical. do you want to visualize your input data?}
+}
+\value{
+plots
+}
+\description{
+load, check and plot input data for use in breakpoint detection
+}
+\examples{
+\dontrun{
+read_rep(fn = 'inst/example_data/goasr.rep')
+}
+}
diff --git a/man/confint_Deriv.Rd b/man/confint_Deriv.Rd
new file mode 100644
index 0000000..8b22dff
--- /dev/null
+++ b/man/confint_Deriv.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/confint_Deriv.R
+\name{confint_Deriv}
+\alias{confint_Deriv}
+\title{Calculate confidence interval of derivative, adapted from
+\href{https://gist.githubusercontent.com/gavinsimpson/e73f011fdaaab4bb5a30/raw/82118ee30c9ef1254795d2ec6d356a664cc138ab/Deriv.R}{Gavin Simpson}.}
+\usage{
+confint_Deriv(object, term, alpha = 0.05, ...)
+}
+\arguments{
+\item{object}{vector output of {Deriv()}}
+
+\item{term}{string smooth name, i.e. "year". must match values in mod and newdata}
+
+\item{alpha}{confidence threshold. default 0.05 (for 95% CI)}
+}
+\value{
+vector of confidence intervals of same length as object.
+}
+\description{
+Calculate confidence interval of derivative, adapted from
+\href{https://gist.githubusercontent.com/gavinsimpson/e73f011fdaaab4bb5a30/raw/82118ee30c9ef1254795d2ec6d356a664cc138ab/Deriv.R}{Gavin Simpson}.
+}