v2.0.1.9043

Issue #25 , Issues #37
Polishing rough edges.

DESCRIPTION

@@ -1,26 +1,24 @@
 Package: ContDataQC
 Title: Quality Control (QC) of Continous Monitoring Data
-Version: 2.0.1.9041
+Version: 2.0.1.9043
 Authors@R: c(
 	person("Erik W.", "Leppo", email="[email protected]",role=c("aut","cre")),
 	person("Ann","Roseberry Lincoln", role="ctb"),
 	person("Jen", "Stamp", role="ctb"),
 	person("John", "van Sickles", role="ctb"))
 Description: Quality control checks on continuous data files from Hobo data loggers.  Also aggregates and subsets files by a given date range.  And runs basic statistics. Outputs reports to Word (requires knitr and Pandoc).  
 Depends:
-    R (>= 3.3.3),
-    dataRetrieval,
-    zoo,
-    knitr,
-    survival,
-    doBy,
-    rmarkdown
+    R (>= 3.3.3)
 License: CC0
 Encoding: UTF-8
 LazyData: true
 URL: https://github.com/leppott/ContDataQC
 BugReports: https://github.com/leppott/ContDataQC/issues
 RoxygenNote: 6.0.1
 Suggests: knitr,
-    rmarkdown
+    rmarkdown,
+    dataRetrieval,
+    zoo,
+    survival,
+    doBy,
 VignetteBuilder: knitr

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(CompSiteCDF)
 export(ContDataQC)
 export(Export.IHA)
 export(Export.StreamThermal)

NEWS.md

@@ -2,22 +2,20 @@ NEWS-ContDataQC
 ================
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
-    #> Last Update: 2017-09-20 13:49:24
+    #> Last Update: 2017-09-27 09:50:48
 
 Version history.
 
 Planned Updates
 ===============
 
--   Spell out "AW"" and other abbreviations (e.g., AirWater). 20170308. On hold.
+-   ~~Spell out "AW"" and other abbreviations (e.g., AirWater). 20170308. On hold.~~
 
--   Gaps in data not always evident in the plots. 20170308.
+-   ~~Gaps in data not always evident in the plots. 20170308.~~
 
--   Use futile.logger to better log output for user. Issue \#29. 20170606.
+-   ~~Use futile.logger to better log output for user. Issue \#29. 20170606.~~
 
--   Add option for Report output for PDF or DOCX or HTML. Defaults to DOCSX. Will need to change documentation for report functions. 20170823.
-
--   ~~Flesh out export for StreamThermal. 20170919.~~
+-   ~~Add option for Report output for PDF or DOCX or HTML. Defaults to DOCSX. Will need to change documentation for report functions. 20170823.~~
 
 -   Debug Aggregate operation. 20170919.
 
@@ -27,12 +25,33 @@ Planned Updates
 
 -   Update Vignette when done. 20170919.
 
+-   Run devtools::check(). 20170926.
+
+v2.0.1.9043
+===========
+
+2017-09-27
+
+-   DESCRIPTION. As suggested by check(), move packages from Depends to Suggests. 20170927.
+
+-   Update ReadMe. 20170927.
+
+v2.0.1.9042
+===========
+
+2017-09-21
+
+-   CompSiteCDF() to compare multiple sites on a site CDF. 20170921.
+
 v2.0.1.9041
 ===========
 
 2017-09-20
 
--   Export.StreamThermal. Rename from Export.ST() to Export.StreamThermal(). And update Vignette. 20170920.
+-   Export.StreamThermal.
+-   Rename from Export.ST() to Export.StreamThermal() .20170920.
+-   Complete function and documentation. 20170920.
+-   Update Vignette. 20170920.
 
 -   Export.IHA. Tweak opening text. 20170920.
 

NEWS.rmd

@@ -39,6 +39,20 @@ Version history.
 
 * Update Vignette when done.  20170919.
 
+* Run devtools::check().  20170926.
+
+# v2.0.1.9043
+2017-09-27
+
+* DESCRIPTION.  As suggested by check(), move packages from Depends to Suggests.  20170927.
+
+* Update ReadMe.  20170927.
+
+# v2.0.1.9042
+2017-09-21
+
+* CompSiteCDF() to compare multiple sites on a site CDF.  20170921.
+
 # v2.0.1.9041
 2017-09-20
 

R/CompSiteCDF.R

@@ -0,0 +1,176 @@
+#' CompSiteCDF, compare CDFs of sites
+#'
+#' Takes as an input a data frame with date and up to 5 columns of parameter data.
+#' Column names are SiteIDs and values are daily means for some measurement.
+#'
+#' CDFs are generate for year, season, and year/season and saved to a PDF
+#'
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+# [email protected] (EWL)
+# 20170921
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+#' @param df.input Input data as CSV.  Needs 6 columns (SampleID and up to 5 SiteIDs).
+#' @param dir.input Directory where data file is located.
+#' @param dir.output Directory where PDF file is to be saved.
+#' @param ParamName.xlab Parameter name for x-axis on plots
+#' @return Returns a PDF of CDFs.
+#' @keywords continuous data, CDF, site comparison
+#' @examples
+#' # load bio data
+#' df.data <- data_CompSiteCDF
+#' dim(df.data)
+#' View(df.data)
+#'
+#' # subsample
+#' mySize <- 200
+#' Seed.MS <- 18171210
+#' bugs.mysize <- rarify(inbug=DF.biodata, sample.ID="SampRep",abund="Count",subsiz=mySize, mySeed=Seed.MS)
+#' dim(bugs.mysize)
+#' View(bugs.mysize)
+#' # save the data
+#' write.table(bugs.mysize,paste("bugs",mySize,"txt",sep="."),sep="\t")
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+#' @export
+CompSiteCDF <- function(df.input, dir.input, dir.output, ParamName.xlab){##FUNCTION.rarify.START
+
+  # add year, month, season
+  # assume Date is POSIXct
+
+
+
+  #for testing load ContData.env
+  source(file.path(getwd(),"R","config.R"))
+
+  ParamName.xlab <- ContData.env$myLab.WaterTemp
+
+
+  #df.data <- data_CompSiteCDF
+  wd <- getwd()
+  myFile <- "CDF_WaterTemp_2014_MA.csv"
+  data.import <- read.csv(file.path(wd,"data-raw",myFile))
+
+
+  # Site Names (Columns)
+  Col.Sites <- names(data.import)[!(names(data.import) %in% ContData.env$myName.Date)]
+
+
+  # # Add columns
+  # myName.Yr       <- "Year"
+  # myName.Mo       <- "Month"
+  # myName.Season   <- "Season"
+  # myName.YrSeason <- "YearSeason"
+
+
+
+  # add time period fields
+  data.import[,ContData.env$myName.Yr]   <- format(as.Date(data.import[,ContData.env$myName.Date]),format="%Y")
+  data.import[,ContData.env$myName.Mo]   <- format(as.Date(data.import[,ContData.env$myName.Date]),format="%m")
+  data.import[,ContData.env$myName.YrMo] <- format(as.Date(data.import[,ContData.env$myName.Date]),format="%Y%m")
+  data.import[,ContData.env$myName.MoDa] <- format(as.Date(data.import[,ContData.env$myName.Date]),format="%m%d")
+  # data.import[,ContData.env$myName.JuDa] <- as.POSIXlt(data.import[,ContData.env$myName.Date], format=ContData.env$myFormat.Date)$yday +1
+  # ## add Season fields
+  data.import[,ContData.env$myName.Season] <- NA
+  data.import[,ContData.env$myName.Season][as.numeric(data.import[,ContData.env$myName.MoDa])>=as.numeric("0101") & as.numeric(data.import[,ContData.env$myName.MoDa])<as.numeric(ContData.env$myTimeFrame.Season.Spring.Start)] <- "Winter"
+  data.import[,ContData.env$myName.Season][as.numeric(data.import[,ContData.env$myName.MoDa])>=as.numeric(ContData.env$myTimeFrame.Season.Spring.Start) & as.numeric(data.import[,ContData.env$myName.MoDa])<as.numeric(ContData.env$myTimeFrame.Season.Summer.Start)] <- "Spring"
+  data.import[,ContData.env$myName.Season][as.numeric(data.import[,ContData.env$myName.MoDa])>=as.numeric(ContData.env$myTimeFrame.Season.Summer.Start) & as.numeric(data.import[,ContData.env$myName.MoDa])<as.numeric(ContData.env$myTimeFrame.Season.Fall.Start)] <- "Summer"
+  data.import[,ContData.env$myName.Season][as.numeric(data.import[,ContData.env$myName.MoDa])>=as.numeric(ContData.env$myTimeFrame.Season.Fall.Start) & as.numeric(data.import[,ContData.env$myName.MoDa])<as.numeric(ContData.env$myTimeFrame.Season.Winter.Start)] <- "Fall"
+  data.import[,ContData.env$myName.Season][as.numeric(data.import[,ContData.env$myName.MoDa])>=as.numeric(ContData.env$myTimeFrame.Season.Winter.Start) & as.numeric(data.import[,ContData.env$myName.MoDa])<=as.numeric("1231")] <- "Winter"
+  data.import[,ContData.env$myName.YrSeason] <- paste(data.import[,ContData.env$myName.Yr],data.import[,ContData.env$myName.Season],sep="")
+  #
+  View(data.import)
+
+
+  # calc CDF
+  x <- ecdf(data.import[,Col.Sites[1]])
+  plot(x, col="blue")
+
+  # plot
+  i=1
+
+  myDate <- format(Sys.Date(),"%Y%m%d")
+  myTime <- format(Sys.time(),"%H%M%S")
+  strFile <- "CompSiteCDF_"
+  strFile.Out <- paste(paste("CompSiteCDF",myDate,myTime,sep=ContData.env$myDelim),"pdf",sep=".")
+
+  # Color Blind Palatte
+ # http://www.cookbook-r.com/Graphs/Colors_(ggplot2)/
+  # The palette with grey:
+  cbPalette <- c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7")
+
+  # The palette with black:
+  cbbPalette <- c("#000000", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7")
+
+
+  #~~~~~~~~~~~~~~~~~~~
+  {
+  myDate <- format(Sys.Date(),"%Y%m%d")
+  myTime <- format(Sys.time(),"%H%M%S")
+  strFile <- "CompSiteCDF_"
+  strFile.Out <- paste(paste("CompSiteCDF",myDate,myTime,sep=ContData.env$myDelim),"pdf",sep=".")
+  #
+  pdf(file=strFile.Out, width=7, height=10)##PDF.START
+    par(mfrow=c(2,1))
+
+    myColors <- cbPalette #rainbow(length(Col.Sites))
+
+    # PLOT 1
+    for (j in 1:length(Col.Sites)){##FOR.j.START
+      # subset out NA
+      data.j <- data.import[,Col.Sites[j]]
+      # different first iteration
+      if (j==1) {##IF.j==1,START
+        hist(data.import[,Col.Sites[j]], prob=TRUE, border="white"
+             ,main="All Data", xlab=ParamName.xlab, ylab="Proportion = value")
+        box()
+      }##IF.j==1.END
+      # plot lines
+      lines(density(data.j, na.rm=TRUE), col=myColors[j], lwd=2)
+    }##FOR.j.END
+    legend("topright",Col.Sites,fill=myColors)
+
+
+    # Plot 2
+    myLWD <- 1.5
+    for (i in 1:length(Col.Sites)){##FOR.i.START
+      #myColors <- cbPalette #rainbow(length(Col.Sites))
+      if(i==1){##IF.i==1.START
+        plot(ecdf(data.import[,Col.Sites[i]]), col=myColors[i], verticals=TRUE, lwd=myLWD, do.p=FALSE #pch=19, cex=.75 #do.p=FALSE
+             #, col.01line="white"
+             , main="All Data", xlab=ParamName.xlab, ylab="Proportion <= value" )
+      } else {
+        plot(ecdf(data.import[,Col.Sites[i]]), col=myColors[i], verticals=TRUE, lwd=myLWD, do.p=FALSE, add=T)
+      }##IF.i==1.END
+    }##FOR.i.END
+    legend("bottomright",Col.Sites,fill=myColors)
+
+
+  dev.off() ##PDF.END
+  }
+  #~~~~~~~~~~~~~~~~~~~
+
+
+  #Plot Proportion equal to each value.
+  # Round to single digit first
+  x <- round(data.import$Browns,1)
+  y <- as.data.frame(table(x))
+
+  z <- sum(y$Freq)
+  y$Freq <- y$Freq/z
+  y$x <- as.numeric(y$x)  # works for plot but converts to rowID
+
+
+  plot(y, type="l")
+
+
+  AA <- data.import$Browns[!is.na(data.import$Browns)]
+
+  hist(AA, prob=TRUE)
+  lines(density(AA), col="blue", lwd=2)
+  box()
+
+
+  cat(paste0("PDF created; ",strFile.Out))
+  flush.console()
+
+
+} #end of function; ##FUNCTION.rarify.END

R/data.r

@@ -52,3 +52,12 @@
 #'
 "data_bio2rarify"
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+#' data_CompSiteCDF
+#'
+#' Test data for CompSiteCDF().  Includes daily mean water temp (C) data for 5.
+#'
+#' @format a data frame with 349 observations and 6 variables:
+#'
+#'
+"data_CompSiteCDF"
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~