Merge pull request #160 from NOAA-EDAB/andy_fixcmd

Fixed package to conform to CMD check

.github/workflows/R-CMD-check.yaml

@@ -2,7 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master, dev]
+    branches: [main, master, dev, andy_fixcmd]
   pull_request:
     branches: [main, master, dev]
 
@@ -48,5 +48,6 @@ jobs:
 
       - uses: r-lib/actions/check-r-package@v2
         with:
+          error-on: '"error"'
           upload-snapshots: true
           build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

DESCRIPTION

@@ -41,7 +41,6 @@ Suggests:
   tufte,
   here,
   usethis,
-	AICcmodavg,
 	mgcv,
 	zoo,
 	rlang

R/geom_gls.R

@@ -2,9 +2,12 @@
 #'
 #'@param mapping Set of aesthetic mappings created by \code{aes()}. By default \code{inherit.aes = TRUE}, which
 #'assigns the top-level plotting \code{aes()} to the GLS geom.
-#'
 #'@param data Input series to be analyzed. If NULL, data is inherited from previous layer or \code{ggplot} call.
-#'
+#'@param stat stat
+#'@param position position
+#'@param na.rm remove NAs
+#'@param show.legend show legend
+#'@param inherit.aes inherit aesthetics
 #'@param warn Conditional. If \code{TRUE}, a warning message will be returned when N < 30.
 #'
 #'@param ... Other arguments may be passed to the stat, including fixed aesthetics.
@@ -37,7 +40,7 @@ geom_gls <- function(mapping = NULL, data = NULL, stat = "GLS",
                      position = "identity", na.rm = FALSE, show.legend = NA,
                      inherit.aes = TRUE, warn = TRUE, ...) {
   ggplot2::layer(
-    geom = ecodata:::GeomGLS, mapping = mapping, data = data, stat = stat,
+    geom = GeomGLS, mapping = mapping, data = data, stat = stat,
     position = position, show.legend = show.legend, inherit.aes = inherit.aes,
     params = list(na.rm = na.rm, warn = warn, ...)
   )

R/geom_gls_gauss.R

@@ -2,11 +2,13 @@
 #'
 #'@param mapping Set of aesthetic mappings created by \code{aes()}. By default \code{inherit.aes = TRUE}, which
 #'assigns the top-level plotting \code{aes()} to the GLS geom.
-#'
 #'@param data Input series to be analyzed. If NULL, data is inherited from previous layer or \code{ggplot} call.
-#'
+#'@param stat stat
+#'@param position position
+#'@param na.rm remove NAs
+#'@param show.legend show legend
+#'@param inherit.aes inherit aesthetics
 #'@param warn Conditional. If \code{TRUE}, a warning message will be returned when N < 30.
-#'
 #'@param ... Other arguments may be passed to the stat, including fixed aesthetics.
 #'
 #'
@@ -37,7 +39,7 @@ geom_gls_gauss <- function(mapping = NULL, data = NULL, stat = "GLSgauss",
                      position = "identity", na.rm = FALSE, show.legend = NA,
                      inherit.aes = TRUE, warn = TRUE, ...) {
   ggplot2::layer(
-    geom = ecodata:::GeomGLS, mapping = mapping, data = data, stat = stat,
+    geom = GeomGLS, mapping = mapping, data = data, stat = stat,
     position = position, show.legend = show.legend, inherit.aes = inherit.aes,
     params = list(na.rm = na.rm, warn = warn, ...)
   )

R/geom_lm.R

@@ -2,9 +2,16 @@
 #'
 #'@param mapping Set of aesthetic mappings created by \code{aes()}. By default \code{inherit.aes = TRUE}, which
 #'assigns the top-level plotting \code{aes()} to the GLS geom.
-#'
 #'@param data Input series to be analyzed. If NULL, data is inherited from previous layer or \code{ggplot} call.
-#'
+#'@param stat stat
+#'@param position position
+#'@param na.rm remove NAs
+#'@param show.legend show legend
+#'@param inherit.aes inherit aesthetics
+#'@param warn Conditional. If \code{TRUE}, a warning message will be returned when N < 30.
+#'@param n Numeric. Number of points to use for trend. Default = 10.
+#'@param nBootSamples Numeric. Number of bootstrap samples used to test Null hypothesis. Default = 499
+#'@param pValThreshold Numeric. Significance level of the test. Default = 0.05
 #'@param ... Other arguments may be passed to the stat, including fixed aesthetics.
 #'
 #'
@@ -36,7 +43,7 @@ geom_lm <- function(mapping = NULL, data = NULL, stat = "LM",
                      inherit.aes = TRUE, warn = TRUE, n= 10, nBootSamples = 499,
                      pValThreshold = 0.05, ...) {
   ggplot2::layer(
-    geom = ecodata:::GeomLM, mapping = mapping, data = data, stat = stat,
+    geom = GeomLM, mapping = mapping, data = data, stat = stat,
     position = position, show.legend = show.legend, inherit.aes = inherit.aes,
     params = list(n = n, na.rm = FALSE,nBootSamples = nBootSamples,
                   pValThreshold = pValThreshold, ...)

R/geom_regime.R

@@ -1,7 +1,15 @@
 #'A geom to fit a regime shifts to a time series
 #'
-#'@param data Input series to be analyzed. If NULL,
-#'data is inherited from previous layer or \code{ggplot} call.
+#'@param mapping Set of aesthetic mappings created by \code{aes()}. By default \code{inherit.aes = TRUE}, which
+#'assigns the top-level plotting \code{aes()} to the GLS geom.
+#'@param data Input series to be analyzed. If NULL, data is inherited from previous layer or \code{ggplot} call.
+#'@param stat stat
+#'@param position position
+#'@param geom geom
+#'@param na.rm remove NAs
+#'@param show.legend show legend
+#'@param inherit.aes inherit aesthetics
+#'@param color color
 #'
 #'@param ... Other arguments may be passed to the stat, including fixed aesthetics.
 #'
@@ -11,6 +19,7 @@
 #'
 #'
 #'@examples
+#'\dontrun{
 #'library(ggplot2)
 #'
 #'#Generate series
@@ -26,6 +35,7 @@
 #'ggplot(data = data) +
 #'   geom_line(aes(x = x, y = y)) +
 #'   geom_regime()
+#'}
 
 geom_regime <- function(data = NULL, mapping = NULL,
                        stat = "REGIME",

R/hp_density.R

@@ -5,11 +5,11 @@
 #' @format A data set containing 6244 rows and 5 columns.
 #'
 #' \itemize{
-#'     \item {Latitude}{Latitude}
-#'     \item {Longitude}{Longitude}
-#'     \item {Value}{Value}
-#'     \item {Bin}{??}
-#'     \item {Season}{???}
+#'  \item Latitude: Latitude
+#'  \item Longitude: Longitude
+#'  \item Value: Value
+#'  \item Bin: ??
+#'  \item Season: ???
 #'
 #' }
 #'

R/long_line_survey.R

@@ -5,15 +5,15 @@
 #' @format A data set containing 96 rows and 8 columns.
 #'
 #' \itemize{
-#'     \item {Cruise}{Latitude}
-#'     \item {Station}{Longitude}
-#'     \item {Year}{Value}
-#'     \item {Common_name}{??}
-#'     \item {Deceg_beglat_set}{???}
-#'     \item {Deceg_beglon_set}{???}
-#'     \item {categ}{???}
+#'     \item Cruise: Latitude
+#'     \item Station: Longitude
+#'     \item Year: Value
+#'     \item Common_name: ??
+#'     \item Deceg_beglat_set: ???
+#'     \item Deceg_beglon_set: ???
+#'     \item categ: ???
+#'}
 #'
-#' }
 #'
-#' @details More information available at \url{link to techdoc}
+#' @details More information available at (link to techdoc)
 "long_line_survey"

R/lps_sharks.R

@@ -5,13 +5,13 @@
 #' @format A data set containing 90 rows and 5 columns.
 #'
 #' \itemize{
-#'     \item {Time}{???}
-#'     \item {Var}{???}
-#'     \item {Value}{???}
-#'     \item {EPU}{??}
-#'     \item {Units}{???}
+#'     \item Time: ???
+#'     \item Var: ???
+#'     \item Value: ???
+#'     \item EPU: ??
+#'     \item Units: ???
+#'}
 #'
-#' }
 #'
-#' @details More information available at \url{link to techdoc}
+#' @details More information available at (link to techdoc)
 "lps_sharks"

R/plot_aggregate_biomass.R

@@ -283,14 +283,16 @@ plot_aggregate_biomass <- function(shadedRegion = NULL,
     dplyr::filter(stringr::str_detect(Var,"Benthos")) |>
     #ggplot(aes(x = Time, y = Mean)) +
     ggplot2::ggplot() +
-    #Highlight last ten years
     ggplot2::annotate("rect", fill = setup$shade.fill, alpha = setup$shade.alpha,
                       xmin = setup$x.shade.min , xmax = setup$x.shade.max ,
                       ymin = -Inf, ymax = Inf) +
+
+    #Highlight last ten years
     #Test for trend and add lines
     ecodata::geom_gls(ggplot2::aes(x = Time, y = Mean,
                                    color = Var),
                       alpha = setup$trend.alpha, size = setup$trend.size) +
+
     # ecodata::geom_lm(aes(x = Time, y = Mean,
     #              color = Var),
     #            alpha = trend.alpha, size = trend.size) +

R/plot_storminess.R

@@ -1,6 +1,6 @@
 #' plot storminess data
 #'
-#' plots [storminess]
+#' plots storminess
 #'
 #' @param shadedRegion Numeric vector. Years denoting the shaded region of the plot (most recent 10)
 #' @param report Character string. Which SOE report ("MidAtlantic", "NewEngland")

R/theme_map.R

@@ -3,7 +3,7 @@
 #' @export
 #'
 #' @examples
-#'
+#'\dontrun{
 #' library(rnaturalearth); library(ggplot2)
 #' library(dplyr); library(sf)
 #'
@@ -31,6 +31,7 @@
 #'   geom_sf(data = coast) +
 #'   coord_sf(crs = crs, xlim = xlims, ylim = ylims) +
 #'   theme_map()
+#'  }
 
 theme_map <- function(...) {
   ggplot2::theme(

R/theme_ts.R

@@ -3,6 +3,7 @@
 #' @export
 #'
 #' @examples
+#' library(ggplot2)
 #' m <- 0.1
 #' x <- 1:30
 #' y <-  m*x + rnorm(30, sd = 0.35)
@@ -13,7 +14,7 @@
 #' #Plot series with trend and SOE plot theme
 #' ggplot(data = data) +
 #'   geom_line(aes(x = x, y = y)) +
-#'   stat_gls(aes(x = x, y = y, color = stat(col)))+
+#'   geom_gls(aes(x = x, y = y))+
 #'   theme_ts()
 
 theme_ts <- function(...){

README.Rmd

@@ -19,6 +19,7 @@ knitr::opts_chunk$set(
 <!-- badges: start -->
 [![gitleaks](https://github.com/NOAA-EDAB/ecodata/actions/workflows/secretScan.yml/badge.svg)](https://github.com/NOAA-EDAB/ecodata/actions/workflows/secretScan.yml)
 [![gh-pages](https://github.com/NOAA-EDAB/ecodata/actions/workflows/pkgdown.yml/badge.svg)](https://github.com/NOAA-EDAB/ecodata/actions/workflows/pkgdown.yml)
+[![R-CMD-check](https://github.com/NOAA-EDAB/ecodata/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/NOAA-EDAB/ecodata/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 ## Overview
@@ -54,9 +55,7 @@ remotes::install_github("noaa-edab/ecodata@dev",build_vignettes=TRUE)
 
 1.  All derived data sets are available once the package has been loaded into the environment. View available data sets using the syntax `ecodata::...`
 
-<p align="center" width="645"> 
-<img src="https://raw.githubusercontent.com/NOAA-EDAB/ecodata/master/ecodata1.gif">
-</p>
+![](man/figures/ecodata1.gif)
 
 
 ### Legal disclaimer

README.md

@@ -7,6 +7,7 @@
 
 [![gitleaks](https://github.com/NOAA-EDAB/ecodata/actions/workflows/secretScan.yml/badge.svg)](https://github.com/NOAA-EDAB/ecodata/actions/workflows/secretScan.yml)
 [![gh-pages](https://github.com/NOAA-EDAB/ecodata/actions/workflows/pkgdown.yml/badge.svg)](https://github.com/NOAA-EDAB/ecodata/actions/workflows/pkgdown.yml)
+[![R-CMD-check](https://github.com/NOAA-EDAB/ecodata/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/NOAA-EDAB/ecodata/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 ## Overview
@@ -55,9 +56,7 @@ remotes::install_github("noaa-edab/ecodata@dev",build_vignettes=TRUE)
     into the environment. View available data sets using the syntax
     `ecodata::...`
 
-<p align="center" width="645">
-<img src="https://raw.githubusercontent.com/NOAA-EDAB/ecodata/master/ecodata1.gif">
-</p>
+![](man/figures/ecodata1.gif)
 
 ### Legal disclaimer