Merge pull request #12 from CSHS-CWRA/ch_prefix

added prefix ch_ to all functions

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: CSHShydRology
 Title: Canadian hydrological analyses
-Version: 1.0.1
-Date: 2019-05-07
+Version: 1.1.0
+Date: 2019-09-03
 Authors@R: c(person("Kevin", "Shook", email = "Kevin.Shook@usask.ca", role = c("cre")),
              person("Paul", "Whitfield", email = "paul.h.whitfield@gmail.com", role = c("aut")),
              person("Robert", "Chlumsky", email = "rchlumsk@gmail.com", role = c("aut")),

NAMESPACE

@@ -1,28 +1,28 @@
 # Generated by roxygen2: do not edit by hand
 
-export(binned_MannWhitney)
-export(booth_plot)
+export(ch_binned_MannWhitney)
+export(ch_booth_plot)
+export(ch_fdcurve)
+export(ch_flow_raster)
+export(ch_flow_raster_qa)
+export(ch_flow_raster_trend)
+export(ch_get_AHCCD_monthly)
+export(ch_get_peaks)
+export(ch_get_wscstation)
+export(ch_hydrograph_plot)
+export(ch_polar_plot)
+export(ch_polar_plot_prep)
+export(ch_read_AHCCD_daily)
+export(ch_read_AHCCD_monthly)
+export(ch_read_ECDE_flows)
+export(ch_regime_plot)
+export(ch_wtr_yr)
 export(cut_block)
 export(date_subset)
 export(doys)
-export(fdcurve)
-export(flow_raster)
-export(flow_raster_qa)
-export(flow_raster_trend)
-export(get_AHCCD_monthly)
-export(get_peaks)
-export(get_wscstation)
-export(hydrograph_plot)
-export(polar_plot)
-export(polar_plot_prep)
-export(read_AHCCD_daily)
-export(read_AHCCD_monthly)
-export(read_ECDE_flows)
-export(regime_plot)
 export(slice)
 export(stack_EC)
 export(sub_set_Years)
-export(wtr_yr)
 import(curl)
 import(fields)
 import(grDevices)

NEWS.md

@@ -1,3 +1,6 @@
+# CSHShydRology 1.1.0
+* Renamed all functions to have the prefix "ch"
+
 # CSHShydRology 1.0.0
 * First official version
 * Contains functions by Paul Whitfield and Rob Chlumsky

R/Basic_data-manipulations-functions.R

@@ -2,10 +2,10 @@
 #' @name Basic_data_manipulation-functions
 #' @description These functions read in or convert values among formats
 #' \describe{
-#'  \item{read_ECDE_flows}{Reads a file of WSC daily flows from ECDataExplorer}
-#'  \item{get_wscstation}{Reads station information from a data file produced by ECDE}
-#'  \item{get_AHCCD_monthly}{Downloads monthly Adjusted and Homogenized Canadian Climate Data (AHCCD) values}
-#'  \item{read_AHCCD_daily}{Reads file of daily AHCCD values}
-#'  \item{read_AHCCD_monthly}{Reads file of monthly AHCCD values}
+#'  \item{ch_read_ECDE_flows}{Reads a file of WSC daily flows from ECDataExplorer}
+#'  \item{ch_get_wscstation}{Reads station information from a data file produced by ECDE}
+#'  \item{ch_get_AHCCD_monthly}{Downloads monthly Adjusted and Homogenized Canadian Climate Data (AHCCD) values}
+#'  \item{ch_read_AHCCD_daily}{Reads file of daily AHCCD values}
+#'  \item{ch_read_AHCCD_monthly}{Reads file of monthly AHCCD values}
 #' }
 NULL

R/StatisticalHydrology-functions.R

@@ -2,8 +2,8 @@
 #' @name StatisticalHydrology-functions
 #' @description These functions perform statistical analyses
 #' \describe{
-#'  \item{binned_MannWhitney}{ Compares two time periods of data using Mann-Whitney test}
-#'  \item{fdcurve}{Finds flow exceedence probabilities}
-#'  \item{get_peaks}{Finds peak flows over a specified threshold}
+#'  \item{ch_binned_MannWhitney}{ Compares two time periods of data using Mann-Whitney test}
+#'  \item{ch_fdcurve}{Finds flow exceedence probabilities}
+#'  \item{ch_get_peaks}{Finds peak flows over a specified threshold}
 #' }
 NULL

R/Visualization-functions.R

@@ -3,12 +3,12 @@
 #' @description These functions are primarily intended for graphing, although
 #' some analyses may also be done.
 #' \describe{
-#'  \item{booth_plot}{Plot of peaks over a threshold}
-#'  \item{flow_raster}{Raster plot of streamflows}
-#'  \item{flow_raster_qa}{Raster plot of streamflows with WSC quality flags}
-#'  \item{flow_raster_trend}{Raster plot and simple trends of observed streamflows}
-#'  \item{hydrograph_plot}{Plots hydrographs and/or precipitation}
-#'  \item{polar_plot}{Polar plot of daily streamflows}
-#'  \item{regime_plot}{Plots the regime of daily streamflows}
+#'  \item{ch_booth_plot}{Plot of peaks over a threshold}
+#'  \item{ch_flow_raster}{Raster plot of streamflows}
+#'  \item{ch_flow_raster_qa}{Raster plot of streamflows with WSC quality flags}
+#'  \item{ch_flow_raster_trend}{Raster plot and simple trends of observed streamflows}
+#'  \item{ch_hydrograph_plot}{Plots hydrographs and/or precipitation}
+#'  \item{ch_polar_plot}{Polar plot of daily streamflows}
+#'  \item{ch_regime_plot}{Plots the regime of daily streamflows}
 #' }
 NULL

R/binned_MannWhitney.R → R/ch_binned_MannWhitney.R

@@ -1,8 +1,8 @@
 #' Compares two time periods of data using Mann-Whitney test
 #'
-#' It bins data based upon a bin size, extracting data for two time periods
+#' It bins data based upon a specified size, extracting data for two time periods
 #' and tests for change between two such periods. Result can be passed to 
-#' \code{polar_plot} for visualization
+#' \code{ch_polar_plot} for visualization
 #'
 #' @author Paul Whitfield <paul.h.whitfield@gmail.com>
 #' @references
@@ -40,21 +40,21 @@
 #' 	}
 #' @import stats
 #' @export
-#' @seealso \code{\link{polar_plot}} \code{\link{polar_plot_prep}}
+#' @seealso \code{\link{ch_polar_plot}} \code{\link{ch_polar_plot_prep}}
 #' @examples
 #' \dontrun{
 #' # fails due to missing data in both periods
 #' range1 <- c(1960,1969)
 #' range2 <- c(1990,1999)
-#' b_MW <- binned_MannWhitney(W05AA008, step=5, range1, range2, ptest=0.05)}
+#' b_MW <- ch_binned_MannWhitney(W05AA008, step=5, range1, range2, ptest=0.05)}
 #'
 #' range1 <- c(1970,1979)
 #' range2 <- c(1990,1999)
-#' b_MW <- binned_MannWhitney(W05AA008, step = 5, range1, range2, 
+#' b_MW <- ch_binned_MannWhitney(W05AA008, step = 5, range1, range2, 
 #' ptest = 0.05, station_ID = "05AA008", station_name= "Crowsnest River at Frank")
 #'
 
-binned_MannWhitney <- function(mdata, step, range1, range2, ptest = 0.05, 
+ch_binned_MannWhitney <- function(mdata, step, range1, range2, ptest = 0.05, 
                                station_ID = "", station_name = "", 
                                variable = "discharge") {
   fail <- FALSE

R/booth_plot.R → R/ch_booth_plot.R

@@ -3,8 +3,8 @@
 #' A Booth plot is a plot of peaks over threshold flood events with duration on the horizontal and
 #' either magnitude (default) or volume on the vertical axis
 #'
-#' @param events A data frame of POT events from the function \code{get_peaks}
-#' @param threshold The threshold used by \code{get_peaks}
+#' @param events A data frame of POT events from the function \code{ch_get_peaks}
+#' @param threshold The threshold used by \code{ch_get_peaks}
 #' @param title Plot title
 #' @param type The plot type, either \option{mag} (magnitude, the default) or \option{vol} (volume)
 #' @param colour1 A vector of length 12 with line colours of rings or symbols. Defaults to those used by Booth.
@@ -21,15 +21,15 @@
 #' @export
 #' @return No value is returned; a standard \R graphic is created.
 #' @keywords plot
-#' @seealso \code{\link{get_peaks}}
+#' @seealso \code{\link{ch_get_peaks}}
 #' @examples
 #' threshold <- 0.1 * max(W05AA008$Flow)  # arbitrary threshold
-#' peaks <- get_peaks(W05AA008, threshold)
+#' peaks <- ch_get_peaks(W05AA008, threshold)
 #' events <- peaks$POTevents
-#' booth_plot(events, threshold, title = "05AA008", type='mag')
-#' booth_plot(events, threshold, title = "05AA008", type='vol')
+#' ch_booth_plot(events, threshold, title = "05AA008", type='mag')
+#' ch_booth_plot(events, threshold, title = "05AA008", type='vol')
 
-booth_plot <- function(events, threshold, title, type = "mag", colour1 = 1, colour2 = 1) {
+ch_booth_plot <- function(events, threshold, title, type = "mag", colour1 = 1, colour2 = 1) {
 
   # set common items
   mname <- c("Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec")

R/fdcurve.R → R/ch_fdcurve.R

@@ -29,13 +29,13 @@
 #' @examples
 #' flow <- W05AA008$Flow
 #' # plot with Gustard 1992 curves
-#' test <- fdcurve(flow, title="Station", normal=FALSE, gust=TRUE)
+#' test <- ch_fdcurve(flow, title = "Station", normal = FALSE, gust = TRUE)
 #'
 #' # plot with normalized exceedance probability
-#' test <- fdcurve(flow, title="Station", normal=TRUE, gust=FALSE)
+#' test <- ch_fdcurve(flow, title = "Station", normal = TRUE, gust = FALSE)
 #
 
-fdcurve <- function(flow, title = "", normal = FALSE, gust = TRUE) {
+ch_fdcurve <- function(flow, title = "", normal = FALSE, gust = TRUE) {
 
   ## load the values for the Gustard curves for %mean flow for Type Curves Gustard et al 1992.
   g <- array(NA, dim = c(19, 7))

R/flow_raster.R → R/ch_flow_raster.R

@@ -10,13 +10,13 @@
 #' @importFrom graphics axis legend par plot points polygon image
 #' @importFrom fields image.plot
 #' @export
-#' @seealso \code{\link{flow_raster_trend}} \code{\link{flow_raster_qa}}
+#' @seealso \code{\link{ch_flow_raster_trend}} \code{\link{ch_flow_raster_qa}}
 #'
 #' @examples
-#' flow_raster(W05AA008)
+#' ch_flow_raster(W05AA008)
 #'
 
-flow_raster <- function(dframe, title="", rastercolours = c("lightblue", "cyan", "blue", "slateblue", "orange", "red")) {
+ch_flow_raster <- function(dframe, title="", rastercolours = c("lightblue", "cyan", "blue", "slateblue", "orange", "red")) {
 
   ##### Fixed labels and text strings
   DOY <- "Day of Year"

R/flow_raster_qa.R → R/ch_flow_raster_qa.R

@@ -19,13 +19,13 @@
 #' @importFrom timeDate dayOfYear as.timeDate
 #' @importFrom fields image.plot
 #' @export
-#' @seealso \code{\link{flow_raster_trend}} \code{\link{flow_raster}}
+#' @seealso \code{\link{ch_flow_raster_trend}} \code{\link{ch_flow_raster}}
 #'
 
 #' @examples
-#' flow_raster_qa(W05AA008, "Station W05AA008")
+#' ch_flow_raster_qa(W05AA008, "Station W05AA008")
 
-flow_raster_qa <- function(dframe, title = "") {
+ch_flow_raster_qa <- function(dframe, title = "") {
   ##### Fixed labels and text strings
   DOY <- "Day of Year"
   ylabelq <- expression(paste("Discharge m"^{3}, "/sec"))

R/flow_raster_trend.R → R/ch_flow_raster_trend.R

@@ -51,13 +51,13 @@
 #' @importFrom fields image.plot
 #' @importFrom graphics axis legend par plot points polygon
 #' @export 
-#' @seealso \code{\link{flow_raster}}
+#' @seealso \code{\link{ch_flow_raster}}
 #' @examples
 #'  mdoy <- doys(W05AA008$Date)
-#'  mplot <- flow_raster_trend(W05AA008$Date, W05AA008$Flow, step=5, station="05AA008")
+#'  mplot <- ch_flow_raster_trend(W05AA008$Date, W05AA008$Flow, step = 5, station = "05AA008")
 #'
 
-flow_raster_trend <- function(date, flow, step = 5, stationID = "", title = "", missing = FALSE,
+ch_flow_raster_trend <- function(date, flow, step = 5, stationID = "", title = "", missing = FALSE,
                          colours = c("lightblue", "cyan", "blue", "slateblue", "darkblue", "red")) {
   l_disch <- expression(paste("m"^{3}, "/sec"))
 
@@ -116,7 +116,6 @@ flow_raster_trend <- function(date, flow, step = 5, stationID = "", title = "",
   arrow <- array(1, length(period))
 
   for (i in 1:length(period)) { ### loop over getting values for periods of year
-
     med_n[i] <- median(qsliced[i, ], na.rm = TRUE)
     max_n[i] <- max(qsliced[i, ], na.rm = TRUE)
     min_n[i] <- min(qsliced[i, ], na.rm = TRUE)
@@ -167,7 +166,7 @@ flow_raster_trend <- function(date, flow, step = 5, stationID = "", title = "",
   par(oma = c(0, 0, 3, 0))
   qcols <- colorRampPalette(colours)
 
-  nf <- layout(matrix(c(2, 4, 1, 3), 2, 2, byrow = TRUE), c(3, 1), c(1, 3), TRUE)
+  # nf <- layout(matrix(c(2, 4, 1, 3), 2, 2, byrow = TRUE), c(3, 1), c(1, 3), TRUE)
 
 
   #####################################################  panel one raster image

R/get_AHCCD_monthly.R → R/ch_get_AHCCD_monthly.R

@@ -20,7 +20,7 @@
 
 #' @return Returns a data frame with the monthly values and associated variables.
 #' @author Kevin Shook
-#' @seealso  \code{\link{read_AHCCD_daily}} \code{\link{read_AHCCD_monthly}}
+#' @seealso  \code{\link{ch_read_AHCCD_daily}} \code{\link{ch_read_AHCCD_monthly}}
 #' @references Use of the data must cite \cite{Mekis, E and L.A. Vincent, 2011: An overview of 
 #' the second generation adjusted daily temperature and precipitation dataset for trend analysis in Canada. 
 #' Atmosphere-Ocean, 49 (2), 163-177.}
@@ -30,26 +30,26 @@
 #' @export
 #'
 #' @examples
-#' stoon_monthly_precip <- get_AHCCD_monthly("4057120", "SK", "PCP")
-get_AHCCD_monthly <- function(station, province, variable, url = "http://dd.weather.gc.ca/climate/ahccd/geojson/historical/monthly/") {
+#' stoon_monthly_precip <- ch_get_AHCCD_monthly("4057120", "SK", "PCP")
+ch_get_AHCCD_monthly <- function(station, province, variable, url = "http://dd.weather.gc.ca/climate/ahccd/geojson/historical/monthly/") {
 
   provinces <- c("AB", "BC", "MB", "NB", "NL","NS", "NT", "NU", "ON", "PE", "QC", "SK", "YT")
   variables <- c("PCP", "RA", "SN", "TMAX", "TMIN", "TMEAN", "PSFC", "SFCWND", "SLP")
 
   # check that parameters are passed
-  if (station == "" | is.null(station) ){
+  if (station == "" | is.null(station) ) {
     stop("station not specified")
   }
 
-  if (province == "" | is.null(province)){
+  if (province == "" | is.null(province)) {
     stop("province not specified")
   }
 
-  if (variable == "" | is.null(variable) ){
+  if (variable == "" | is.null(variable) ) {
     stop("variable not specified")
   }
 
-  if (url == "" | is.null(url) ){
+  if (url == "" | is.null(url) ) {
     stop("url not specified")
   }
 
@@ -68,7 +68,7 @@ get_AHCCD_monthly <- function(station, province, variable, url = "http://dd.weat
 
   # make sure station name is valid, i.e. that the variable exists
 
-    all <- fromJSON(station_file, flatten=FALSE)
+    all <- fromJSON(station_file, flatten = FALSE)
     vals <- all$features$properties
     return(vals)
 }

R/get_peaks.R → R/ch_get_peaks.R

@@ -35,13 +35,13 @@
 #' for analysis of the 2013 flood in the Upper Bow River, Canada. Hydrological Processes 30:4657-73. doi:
 #' 10.1002/hyp.10957.
 #' @export
-#' @seealso \code{\link{booth_plot}}
+#' @seealso \code{\link{ch_booth_plot}}
 #' @examples
 #' threshold <- 0.9*max(W05AA008$Flow)  # arbitrary threshold
-#' my_peaks <- get_peaks(W05AA008, threshold)
+#' my_peaks <- ch_get_peaks(W05AA008, threshold)
 #' str(my_peaks)
 
-get_peaks <- function(dataframe, threshold) {
+ch_get_peaks <- function(dataframe, threshold) {
   data <- dataframe$Flow
   Date <- dataframe$Date
   event <- array(0, dim = length(data))

R/get_wscstation.R → R/ch_get_wscstation.R

@@ -37,12 +37,12 @@
 #'
 #' @examples
 #' df <- HYDAT_list
-#' s_info <- get_wscstation("05BB001", df)
+#' s_info <- ch_get_wscstation("05BB001", df)
 #' title <- s_info[21]
 #' print(title)
 #'
 
-get_wscstation <- function(stnID, stn) {
+ch_get_wscstation <- function(stnID, stn) {
 
   rhbn <- NULL
   stninfo <- stn[stn$Station == stnID, ]

R/hydrograph_plot.R → R/ch_hydrograph_plot.R

@@ -58,19 +58,19 @@
 #' precip <- data.frame("Date" = dd," precip" = abs(rnorm(length(dd))) * 10)
 #'
 #' # basic hydrograph plot
-#' hydrograph_plot(flows = df, winter_shading = FALSE)
+#' ch_hydrograph_plot(flows = df, winter_shading = FALSE)
 #'
 #' # with different labels
-#' hydrograph_plot(flows = df, winter_shading = FALSE, flow_labels = c("simulated", "observed"))
+#' ch_hydrograph_plot(flows = df, winter_shading = FALSE, flow_labels = c("simulated", "observed"))
 #'
 #' # with a few more options turned on
-#' hydrograph_plot(flows = df, precip = precip)
+#' ch_hydrograph_plot(flows = df, precip = precip)
 #'
 #' # increase the plot ranges to separate flows and precip; add a legend box
-#' hydrograph_plot(flows = df, precip = precip, range_mult_flow = 1.7, 
+#' ch_hydrograph_plot(flows = df, precip = precip, range_mult_flow = 1.7, 
 #' range_mult_precip = 2, leg_box = TRUE)
 
-hydrograph_plot <- function(flows = NULL, 
+ch_hydrograph_plot <- function(flows = NULL, 
                             precip = NULL, 
                             prd = NULL, 
                             winter_shading = FALSE,