From 6f71243e65701a38ec26c615ad07ecdd541e2e86 Mon Sep 17 00:00:00 2001
From: jimianelli <jimianelli@users.noreply.github.com>
Date: Tue, 6 Aug 2024 19:52:53 +0000
Subject: [PATCH] Docs: run devtools::document()

---
 man/dat2list.Rd           | 12 ++++++------
 man/plotSPM.Rd            | 26 ++++++++++++++++----------
 man/plotSPMx.Rd           | 24 ++++++++++++++++++++++++
 man/print_Tier3_tables.Rd | 25 -------------------------
 4 files changed, 46 insertions(+), 41 deletions(-)
 create mode 100644 man/plotSPMx.Rd
 delete mode 100644 man/print_Tier3_tables.Rd

diff --git a/man/dat2list.Rd b/man/dat2list.Rd
index c89d655..10a77b1 100644
--- a/man/dat2list.Rd
+++ b/man/dat2list.Rd
@@ -2,21 +2,21 @@
 % Please edit documentation in R/readData.R
 \name{dat2list}
 \alias{dat2list}
-\title{Read Data File into List Object}
+\title{Convert Data to List}
 \usage{
 dat2list(fn)
 }
 \arguments{
-\item{fn}{Filename of the data file to be read.}
+\item{fn}{A character string representing the file name to be read.}
 }
 \value{
-A list object containing the data from the file.
+A list with numeric data or character strings based on the content of the file.
 }
 \description{
-Reads a data file formatted for a projection model and converts it into a list object.
-The function handles numeric and NA values appropriately.
+This function reads data from a file and converts it into a list.
+If the data are numeric, it maintains the numeric list. If the data are strings, it returns a character string.
 }
 \examples{
 # Example usage:
-# myDataList <- dat2list("datafile.dat")
+# result <- dat2list("datafile.txt")
 }
diff --git a/man/plotSPM.Rd b/man/plotSPM.Rd
index 1754c13..148f776 100644
--- a/man/plotSPM.Rd
+++ b/man/plotSPM.Rd
@@ -2,23 +2,29 @@
 % Please edit documentation in R/plot-res.R
 \name{plotSPM}
 \alias{plotSPM}
-\title{Plot Results from SPM Analysis from a Tibble}
+\title{Plot SPM Data}
 \usage{
-plotSPM(df, alt = 2, thisyr = 2022, mytitle = NULL)
+plotSPM(df, alt = c(1, 3, 5, 7), mytitle = NULL)
 }
 \arguments{
-\item{df}{A tibble containing the results from `spm_detail.csv`.}
+\item{df}{A dataframe containing the SPM data with columns `Year`, `Alt`, `variable`, and `value`.}
 
-\item{alt}{The alternative to be plotted.}
+\item{alt}{A vector of alternatives to include in the plot. Default is `c(1, 4, 5, 7)`.}
 
-\item{thisyr}{The current year for the projection model.}
-
-\item{mytitle}{Title for the plot}
+\item{mytitle}{An optional title for the plot. Default is `NULL`.}
 }
 \value{
-A combined plot of the results from the SPM analysis.
+A ggplot object.
 }
 \description{
-This function creates plots from the results of a Stock Production Model (SPM) analysis contained in a tibble.
-It generates three separate plots for different metrics and combines them using the `patchwork` package.
+This function filters and processes a dataframe, then creates a plot
+of the SPM data with error bands and faceting by type and alternative.
+}
+\examples{
+# Example usage:
+df <- data.frame(Year = rep(2000:2020, 4),
+                 Alt = rep(1:4, each = 21),
+                 variable = rep(c("mean_ub", "mean_lb", "mean_mean"), times = 28),
+                 value = runif(84, 0, 1))
+plotSPM(df)
 }
diff --git a/man/plotSPMx.Rd b/man/plotSPMx.Rd
new file mode 100644
index 0000000..9ac0224
--- /dev/null
+++ b/man/plotSPMx.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plot-res.R
+\name{plotSPMx}
+\alias{plotSPMx}
+\title{Plot Results from SPM Analysis from a Tibble}
+\usage{
+plotSPMx(df, alt = 2, thisyr = 2022, mytitle = NULL)
+}
+\arguments{
+\item{df}{A tibble containing the results from `spm_detail.csv`.}
+
+\item{alt}{The alternative to be plotted.}
+
+\item{thisyr}{The current year for the projection model.}
+
+\item{mytitle}{Title for the plot}
+}
+\value{
+A combined plot of the results from the SPM analysis.
+}
+\description{
+This function creates plots from the results of a Stock Production Model (SPM) analysis contained in a tibble.
+It generates three separate plots for different metrics and combines them using the `patchwork` package.
+}
diff --git a/man/print_Tier3_tables.Rd b/man/print_Tier3_tables.Rd
deleted file mode 100644
index 510aa55..0000000
--- a/man/print_Tier3_tables.Rd
+++ /dev/null
@@ -1,25 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/readData.R
-\name{print_Tier3_tables}
-\alias{print_Tier3_tables}
-\title{Print Tier 3 Tables}
-\usage{
-print_Tier3_tables(df, modname = "base", stock = "BSAI Atka mackerel")
-}
-\arguments{
-\item{df}{Data frame containing Tier 3 data.}
-
-\item{modname}{Name of the model used, defaults to "base".}
-
-\item{stock}{Name of the stock, defaults to "BSAI Atka mackerel".}
-}
-\value{
-HTML tables for the specified Tier 3 data.
-}
-\description{
-Generates and prints HTML tables for Tier 3 projections including catch, ABC, fishing mortality, and spawning biomass for various scenarios.
-}
-\examples{
-# Example usage:
-# print_Tier3_tables(myDataFrame, "model1", "Some Fish Stock")
-}