version update to 2.3.1 to fix concept tags, added CITATATION, NEWS u…

…pdates

NEWS.md

@@ -1,3 +1,11 @@
+#### SWMPr 2.3.1
+
+* Added `collMethd` argument to `import_local` function to specify diel or standard monthly sampling for nutrient samples
+
+* Minor fix to `swmpr` function if trailing white spaces found at end of each qaqc column
+
+* Minor fix to help files if searching by concept, e.g., `help.search('analyze', package = "SWMPr")`
+
 #### SWMPr 2.3.0
 
 * Added informative error message if IP address not registered for using CDMO web services

R/swmpr_analyze.R

@@ -530,8 +530,6 @@ decomp <- function(dat_in, ...) UseMethod('decomp')
 #' @param frequency chr string or numeric vector indicating the periodic component of the input parameter.  Only \code{'daily'} or \code{'annual'} are accepted as chr strings.  Otherwise a numeric vector specifies the number of observations required for a full cycle of the input parameter.  Defaults to \code{'daily'} for a diurnal parameter.
 #' @param start numeric vector indicating the starting value for the time series given the frequency.  Only required if \code{frequency} is numeric. See \code{\link[stats]{ts}}.
 #' 
-#' @concept analyze
-#' 
 #' @export
 #' 
 #' @method decomp swmpr
@@ -556,8 +554,6 @@ decomp.swmpr <- function(dat_in, param, type = 'additive', frequency = 'daily',
 #' 
 #' @param date_col chr string of the name of the date column
 #' 
-#' @concept analyze
-#' 
 #' @export
 #' 
 #' @method decomp default
@@ -672,8 +668,6 @@ decomp_cj <- function(dat_in, ...) UseMethod('decomp_cj')
 #' 
 #' @export
 #' 
-#' @concept analyze
-#' 
 #' @method decomp_cj swmpr
 decomp_cj.swmpr <- function(dat_in, param, vals_out = FALSE, event = TRUE, type = c('add', 'mult'), center = c('mean', 'median'), ...){
 
@@ -694,8 +688,6 @@ decomp_cj.swmpr <- function(dat_in, param, vals_out = FALSE, event = TRUE, type
 #' 
 #' @export
 #' 
-#' @concept analyze
-#' 
 #' @method decomp_cj default
 decomp_cj.default <- function(dat_in, param, date_col, vals_out = FALSE, event = TRUE, type = c('add', 'mult'), center = c('mean', 'median'), ...){
 
@@ -816,8 +808,6 @@ plot.swmpr <- function(x, type = 'l', ...) {
 #' @importFrom stats formula
 #' @importFrom graphics lines
 #' 
-#' @concept analyze
-#' 
 #' @method lines swmpr
 lines.swmpr <- function(x, ...) {
 
@@ -937,8 +927,6 @@ plot_summary <- function(swmpr_in, ...) UseMethod('plot_summary')
 #' 
 #' @export
 #' 
-#' @concept analyze
-#' 
 #' @method plot_summary swmpr
 plot_summary.swmpr <- function(swmpr_in, param, years = NULL, plt_sep = FALSE, sum_out = FALSE, ...){
 
@@ -1255,8 +1243,6 @@ overplot <- function(dat_in, ...) UseMethod('overplot')
 #' 
 #' @export
 #' 
-#' @concept analyze
-#' 
 #' @method overplot swmpr
 overplot.swmpr <- function(dat_in, select = NULL, subset = NULL, operator = NULL, ylabs = NULL, xlab = NULL, cols = NULL, lty = NULL, lwd = NULL, pch = NULL, type = NULL, ...){
 
@@ -1281,8 +1267,6 @@ overplot.swmpr <- function(dat_in, select = NULL, subset = NULL, operator = NULL
 #' @importFrom grDevices colorRampPalette
 #' @importFrom graphics axis axis.POSIXct legend mtext par
 #' 
-#' @concept analyze
-#' 
 #' @method overplot default
 overplot.default <- function(dat_in, date_var, select = NULL, ylabs = NULL, xlab = NULL, cols = NULL, lty = NULL, lwd = NULL, inset = -0.15, cex = 1, xloc = 'top', yloc = NULL, pch = NULL, type = NULL, ...){
 
@@ -1475,8 +1459,6 @@ ecometab <- function(dat_in, ...) UseMethod('ecometab')
 #' 
 #' @export
 #' 
-#' @concept analyze
-#' 
 #' @method ecometab swmpr
 ecometab.swmpr <- function(dat_in, depth_val = NULL, metab_units = 'mmol', trace = FALSE, ...){
 
@@ -1524,8 +1506,6 @@ ecometab.swmpr <- function(dat_in, depth_val = NULL, metab_units = 'mmol', trace
 #' @rdname ecometab
 #'
 #' @export
-#'
-#' @concept analyze
 #' 
 #' @method ecometab default
 ecometab.default <- function(dat_in, tz, lat, long, depth_val = NULL, metab_units = 'mmol', trace = FALSE, ...){
@@ -1776,8 +1756,6 @@ plot_metab <- function(swmpr_in, ...) UseMethod('plot_metab')
 #'
 #' @export
 #'
-#' @concept analyze
-#'
 #' @method plot_metab swmpr
 plot_metab.swmpr <- function(swmpr_in, by = 'months', alpha = 0.05, width = 10, pretty = TRUE, ...){
 

R/swmpr_organize.R

@@ -38,8 +38,6 @@ qaqc <- function(swmpr_in, ...) UseMethod('qaqc')
 #' @param qaqc_keep character string of qaqc flags to keep, default \code{'0'}, any number of flag codes can be supplied including three character error codes (see examples)
 #' @param trace logical for progress output on console, default \code{FALSE}
 #' 
-#' @concept organize
-#' 
 #' @export
 #' 
 #' @method qaqc swmpr
@@ -210,8 +208,6 @@ qaqcchk <- function(swmpr_in) UseMethod('qaqcchk')
 #' 
 #' @export
 #' 
-#' @concept organize
-#' 
 #' @method qaqcchk swmpr
 qaqcchk.swmpr <- function(swmpr_in){
 
@@ -283,8 +279,6 @@ cens_id <- function(swmpr_in, ...) UseMethod('cens_id')
 #' 
 #' @export
 #' 
-#' @concept organize
-#' 
 #' @method cens_id swmpr
 cens_id.swmpr <- function(swmpr_in, flag_type = 'both', select = NULL, ...){ 
 
@@ -404,8 +398,6 @@ rem_reps <- function(swmpr_in, ...) UseMethod('rem_reps')
 #' 
 #' @export
 #' 
-#' @concept organize
-#' 
 #' @method rem_reps swmpr
 rem_reps.swmpr <- function(swmpr_in, FUN = function(x) mean(x, na.rm = TRUE), ...){
 
@@ -656,8 +648,6 @@ setstep <- function(dat_in, ...) UseMethod('setstep')
 #' 
 #' @export
 #' 
-#' @concept organize
-#' 
 #' @method setstep swmpr
 setstep.swmpr <- function(dat_in, timestep = 15, differ= NULL, ...){ 
 
@@ -678,8 +668,6 @@ setstep.swmpr <- function(dat_in, timestep = 15, differ= NULL, ...){
 #' 
 #' @export
 #' 
-#' @concept organize
-#' 
 #' @method setstep default
 setstep.default <- function(dat_in, date_col, timestep = 15, differ= NULL, ...){ 
 
@@ -795,8 +783,6 @@ comb <- function(...) UseMethod('comb')
 #' 
 #' @export
 #' 
-#' @concept organize
-#' 
 #' @method comb swmpr
 comb.swmpr <- function(..., timestep = 15, differ= NULL, method = 'union'){
 
@@ -847,8 +833,6 @@ comb.swmpr <- function(..., timestep = 15, differ= NULL, method = 'union'){
 #' 
 #' @export
 #' 
-#' @concept organize
-#' 
 #' @method comb default
 comb.default <- function(..., date_col, timestep = 15, differ= NULL, method = 'union'){
 

cran-comments.md

@@ -1,26 +1,16 @@
 ## Resubmission 
 
-This is a resubmission for a version update to 2.3.0.  All contributing authors were added to the DESCRIPTION file.
+This is a version update to 2.3.1.  Fixes to documentation include removal of multi-line multi-par \concept entries.
 
 ## Test environments
-* ubuntu 14.04.5 LTS (on travis-ci), R 3.4.2
-* OS X (on travis-ci), R 3.4.3
-* Windows install (on AppVeyor), R 3.4.3 Patched (2018-02-03 r74202)
+* ubuntu 14.04.5 LTS (on travis-ci), R 3.6.0
+* OS X (on travis-ci), R 3.6.0
+* Windows install (on AppVeyor), R 3.6.0 Patched (2019-05-24 r76605)
 * win-builder [http://win-builder.r-project.org/](http://win-builder.r-project.org/) (devel and release)
-* local Windows 7 install, R 3.4.1
+* local Windows 7 install, R 3.6.0
 
 ## R CMD check results
-There were no ERRORs or WARNINGs. 
-
-There was 1 NOTE, related to a change in my contact email: 
-
-* checking CRAN incoming feasibility ... NOTE
-Maintainer: 'Marcus W. Beck <[email protected]>'
-
-New maintainer:
-  Marcus W. Beck <[email protected]>
-Old maintainer(s):
-  Marcus W. Beck <[email protected]>
+There were no NOTEs, ERRORs, or WARNINGs. 
 
 ## Downstream dependencies
-None.
+I have also run R CMD check on the SWMPrExtension downstream dependency for SWMPr. There were no ERRORs, WARNINGs, or NOTEs.

inst/CITATION

@@ -0,0 +1,18 @@
+bibentry(bibtype = "Article",
+  title        = "{SWMPr: An R Package for Retrieving, Organizing, and Analyzing Environmental Data for Estuaries}",
+  author       = c(
+                  person(
+                    given = c("Marcus", "W."),
+                    family = "Beck",
+                    email = "[email protected]"
+                    )
+                  ),
+  journal      = "{The R Journal}",
+  year         = "2016",
+  volume       = "8",
+  number       = "1",
+  pages        = "219-232",
+  doi          = "10.32614/RJ-2016-015",
+
+  header       = "To cite SWMPr in publications use:"
+)