Merge pull request #13 from jfisher-usgs/master

Merge with upstream

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: wrv
 Title: Wood River Valley Groundwater-Flow Model
-Version: 1.1.2
+Version: 1.1.3
 Authors@R: person(given=c("Jason", "C."), family="Fisher", role=c("aut", "cre"), email="jfisher@usgs.gov")
 Description: A processing program for the groundwater-flow model of the Wood
     River Valley aquifer system, south-central Idaho. Included in the package is
@@ -9,21 +9,20 @@ Depends:
     R (>= 3.2.0)
 Imports:
     dplyr,
-    grDevices,
-    graphics,
     inlmisc,
     methods,
     sp,
     stats,
-    raster,
-    rgdal,
-    rgeos
+    raster
 Suggests:
     animation,
     dataRetrieval,
     git2r,
+    grDevices,
     knitr,
     leaflet,
+    rgdal,
+    rgeos,
     sfsmisc,
     viridis,
     xtable

Makefile

@@ -21,7 +21,7 @@ install: build
 
 check:
 	cd ..;\
-	R CMD check --no-build-vignettes --as-cran $(PKGNAME)_$(PKGVERS).tar.gz;\
+	R CMD check --no-build-vignettes $(PKGNAME)_$(PKGVERS).tar.gz;\
 
 rd2tex:
 	cd ..;\

NEWS.md

@@ -1,10 +1,16 @@
+# wrv 1.1.3
+
+- Specify `seq.date.by` argument in calls to `inlmisc::PlotGraph` function.
+  The latest version of **inlmisc** determines a default value for `seq.date.by`,
+  its previous default was `seq.date.by =  "year"`.
+
 # wrv 1.1.2
 
 - In `RunWaterBalance` function, sum groundwater diversions for `div.gw` dataset records having an identical site location and stress period.
 
 - Remove hard codding of irrigation years in appendix C, see `irr.lands` dataset creation.
 
-- In `GetWellConfig` function, fixed error that occurred when a well was located outside the model grid.
+- In `GetWellConfig` function, fix error that occurred when a well was located outside the model grid.
 
 - Specify `desc` argument in `inlmisc::SummariseBudget` function call, required for new version of **inlmisc** package.
 

R/data.R

@@ -571,7 +571,7 @@
 #' col <- c("red", "blue", "green")
 #' ylab <- paste("Discharge in cubic", c("meters per day", "acre-foot per year"))
 #' inlmisc::PlotGraph(gage.disch, ylab = ylab, col = col, lty = 1:3,
-#'                    conversion.factor = 0.29611)
+#'                    conversion.factor = 0.29611, seq.date.by = "year")
 #' leg <- sprintf("USGS \%s", names(gage.disch)[-1])
 #' legend("topright", leg, col = col, lty = 1:3, inset = 0.02, cex = 0.7,
 #'        box.lty = 1, bg = "#FFFFFFE7")
@@ -620,7 +620,7 @@
 #' col <- c("red", "blue", "green")
 #' ylab <- paste("Gage height in", c("meters", "feet"))
 #' inlmisc::PlotGraph(gage.height, ylab = ylab, col = col, lty = 1:3,
-#'                    conversion.factor = 3.28084)
+#'                    conversion.factor = 3.28084, seq.date.by = "year")
 #' leg <- sprintf("USGS \%s", names(gage.height)[-1])
 #' legend("topright", leg, col = col, lty = 1:3, inset = 0.02, cex = 0.7,
 #'        box.lty = 1, bg = "#FFFFFFE7")
@@ -1196,7 +1196,8 @@
 #'
 #' col <- c("red", "blue", "green")
 #' ylab <- paste("Precipitation in", c("meters", "feet"))
-#' inlmisc::PlotGraph(d, ylab = ylab, col = col, lty = 1:3, conversion.factor = 3.28084)
+#' inlmisc::PlotGraph(d, ylab = ylab, col = col, lty = 1:3,
+#'                    conversion.factor = 3.28084, seq.date.by = "year")
 #' legend("topright", zones, col = col, lty = 1:3, inset = 0.02, cex = 0.7,
 #'        box.lty = 1, bg = "#FFFFFFE7")
 #'

R/zzz.R

@@ -2,7 +2,7 @@
   if (interactive()) {
     ver <- read.dcf(file.path(lib, pkg, "DESCRIPTION"), "Version")
     packageStartupMessage(pkg, ": version: ", ver)
-    if (ver < 1 || grepl("\\.9000$", ver)) {
+    if (ver < 1 || grepl("\\.9[0-9]{3}$", ver)) {
       s <- paste("This information is preliminary or provisional and is subject to revision.",
                  "It is being provided to meet the need for timely best science.",
                  "The information has not received final approval by the U.S. Geological Survey (USGS) and",

README.md

@@ -2,6 +2,7 @@
 
 [![Travis-CI Build Status](https://travis-ci.org/USGS-R/wrv.svg?branch=master)](https://travis-ci.org/USGS-R/wrv)
 [![CC0](https://img.shields.io/badge/license-CC0--1.0-brightgreen.svg)](https://creativecommons.org/publicdomain/zero/1.0/)
+[![USGS Category](https://img.shields.io/badge/USGS-Research-blue.svg)](https://owi.usgs.gov/R/packages.html#research)
 
 ## Overview
 

inst/doc/sir20165080_AppendixC.R

@@ -202,7 +202,7 @@ cols <- "#327CCB"
 ylab <- paste("Monthly precipitation, in", c("meters", "feet"))
 ltys <- c(1, 2)
 inlmisc::PlotGraph(d, xlim=tr.interval, ylab=ylab, col=cols, lty=0,
-                   conversion.factor=1 / ft.to.m, center.date.labels=TRUE)
+                   conversion.factor=1 / ft.to.m, center.date.labels=TRUE, seq.date.by="year")
 lines(d1, lty=ltys[1], col=cols, type="s")
 lines(d2, lty=ltys[2], col=cols, type="s")
 legend("topright", c("Measured", "Estimated"), col=cols, lty=ltys, inset=0.02,
@@ -390,7 +390,7 @@ cols <- rep(c("#1B9E77", "#D95F02", "#7570B3"), 2)
 ltys <- c(rep(1, 3), rep(3, 3))
 ylab <- paste("Gage height, in", c("meters", "feet"))
 inlmisc::PlotGraph(x, ylab=ylab, col=cols, lty=ltys, conversion.factor=1 / ft.to.m,
-                   center.date.labels=TRUE)
+                   center.date.labels=TRUE, seq.date.by="year")
 leg <- c(sprintf("%s measured",  names(d)[-1]),
          sprintf("%s estimated", names(d)[-1]))
 legend("topright", leg, col=cols, lty=ltys, inset=0.02, cex=0.7, box.lty=1,

inst/doc/sir20165080_AppendixC.Rnw

@@ -405,7 +405,7 @@ cols <- "#327CCB"
 ylab <- paste("Monthly precipitation, in", c("meters", "feet"))
 ltys <- c(1, 2)
 inlmisc::PlotGraph(d, xlim=tr.interval, ylab=ylab, col=cols, lty=0,
-                   conversion.factor=1 / ft.to.m, center.date.labels=TRUE)
+                   conversion.factor=1 / ft.to.m, center.date.labels=TRUE, seq.date.by="year")
 lines(d1, lty=ltys[1], col=cols, type="s")
 lines(d2, lty=ltys[2], col=cols, type="s")
 legend("topright", c("Measured", "Estimated"), col=cols, lty=ltys, inset=0.02,
@@ -681,7 +681,7 @@ cols <- rep(c("#1B9E77", "#D95F02", "#7570B3"), 2)
 ltys <- c(rep(1, 3), rep(3, 3))
 ylab <- paste("Gage height, in", c("meters", "feet"))
 inlmisc::PlotGraph(x, ylab=ylab, col=cols, lty=ltys, conversion.factor=1 / ft.to.m,
-                   center.date.labels=TRUE)
+                   center.date.labels=TRUE, seq.date.by="year")
 leg <- c(sprintf("%s measured",  names(d)[-1]),
          sprintf("%s estimated", names(d)[-1]))
 legend("topright", leg, col=cols, lty=ltys, inset=0.02, cex=0.7, box.lty=1,

inst/doc/sir20165080_AppendixD.R

@@ -472,7 +472,7 @@ d[nrow(d), 1] <- d[nrow(d), 1] + ndays
 ylab <- paste("Tributary basin underflow, in", c("cubic meters per day", "acre-feet per year"))
 cols  <- rainbow(ncol(d), start=0.0, end=0.8)
 PlotGraph(d, ylab=ylab, conversion.factor=m3.per.d.to.af.per.yr, col=cols,
-          center.date.labels=TRUE, scientific=FALSE)
+          center.date.labels=TRUE, scientific=FALSE, seq.date.by="year")
 leg <- format(match(colnames(d)[-1], make.names(tributaries@data$Name)))
 legend("topright", leg, lwd=1, col=cols, ncol=2,
        pt.cex=1, inset=0.02, cex=0.7, box.lty=1, box.lwd=0.5,
@@ -732,7 +732,8 @@ x <- tr.stress.periods
 y <- rbind(norm.gage.height[, -1], norm.gage.height[nrow(norm.gage.height), -1])
 ylab <- paste("Normalized mean gage-height, in", c("meters", "feet"))
 cols <- c("#1B9E77", "#D95F02", "#7570B3")
-PlotGraph(x, y, ylab=ylab, col=cols, conversion.factor=m.to.ft, center.date.labels=TRUE)
+PlotGraph(x, y, ylab=ylab, col=cols, conversion.factor=m.to.ft,
+          center.date.labels=TRUE, seq.date.by="year")
 legend("topright", colnames(y), lwd=c(1, 1, 1), col=cols, inset=0.02, cex=0.7,
        box.lty=1, box.lwd=0.5, bg="#FFFFFFCD", title=expression(bold("Streamgages")))
 
@@ -828,7 +829,8 @@ d[d[, 3] > 0, 3] <- 0
 ylab <- paste("Total flow across water table, in", c("cubic meters per day", "acre-feet per year"))
 col <- c("#67A9CF", "#C80C0B")
 PlotGraph(d, ylab=ylab, col=col, fill=paste0(col, "66"),
-          conversion.factor=m3.per.d.to.af.per.yr, scientific=TRUE, center.date.labels=TRUE)
+          conversion.factor=m3.per.d.to.af.per.yr, scientific=TRUE,
+          center.date.labels=TRUE, seq.date.by="year")
 legend("topright", c("Recharge", "Discharge"), col=col, lty=1,
        inset=0.02, cex=0.7, box.lty=1, box.lwd=0.5, bg="#FFFFFFCD")
 
@@ -843,7 +845,8 @@ x <- tr.stress.periods
 ylab <- paste("Total withdrawals from wells, in", c("cubic meters per day", "acre-feet per year"))
 col <- "#C80C0B"
 PlotGraph(x, y, ylab=ylab, col=col, fill=paste0(col, "66"),
-          conversion.factor=m3.per.d.to.af.per.yr, scientific=TRUE, center.date.labels=TRUE)
+          conversion.factor=m3.per.d.to.af.per.yr, scientific=TRUE,
+          center.date.labels=TRUE, seq.date.by="year")
 
 ## ----include=FALSE-------------------------------------------------------
 v <- "Steady-state areal recharge. Values are preliminary and were modified by adjustments to irrigation efficiency during the model-calibration process."
@@ -905,7 +908,8 @@ y <- rbind(m, m[nrow(m), , drop=FALSE])
 ylab <- paste("Seepage rate, in", c("cubic meters per day", "acre-feet per year"))
 col <- "#67A9CF"
 PlotGraph(x, y, ylab=ylab, col=col, fill=paste0(col, "66"),
-          conversion.factor=m3.per.d.to.af.per.yr, scientific=c(FALSE, TRUE, FALSE), center.date.labels=TRUE)
+          conversion.factor=m3.per.d.to.af.per.yr, scientific=c(FALSE, TRUE, FALSE),
+          center.date.labels=TRUE, seq.date.by="year")
 
 ## ----include=FALSE-------------------------------------------------------
 v <- "Seepage beneath the Bellevue Waste Water Treatment Plant Ponds."
@@ -919,7 +923,8 @@ y <- rbind(m, m[nrow(m), , drop=FALSE])
 ylab <- paste("Seepage rate, in", c("cubic meters per day", "acre-feet per year"))
 col <- "#67A9CF"
 PlotGraph(x, y, ylab=ylab, col=col, fill=paste0(col, "66"),
-          conversion.factor=m3.per.d.to.af.per.yr, scientific=FALSE, center.date.labels=TRUE)
+          conversion.factor=m3.per.d.to.af.per.yr, scientific=FALSE,
+          center.date.labels=TRUE, seq.date.by="year")
 
 ## ------------------------------------------------------------------------
 misc <- cbind(misc, ss = apply(misc[, ss.yr.mo], 1, mean))
@@ -1310,7 +1315,8 @@ FUN <- function(desc) {
   xlab <- "Simulated hydraulic head, in meters above the NAVD88"
   ylab <- paste("Hydraulic head residual, in", c("meters (m)", "feet"))
   PlotGraph(dd, xlab=xlab, ylab=ylab, type="n", xlim=xlim, ylim=ylim,
-            conversion.factor=m.to.ft, bg.polygon=bg.polygon)
+            conversion.factor=m.to.ft, bg.polygon=bg.polygon,
+            seq.date.by="year")
   abline(h=0, col="#333333", lwd=1)
   for (i in seq_along(desc))
     points(d[d$desc %in% desc[i], c("head.sim", "head.res")], pch=20, col=col[i])
@@ -1432,7 +1438,8 @@ FUN <- function(idx, add.legend=FALSE) {
   bg.polygon <- list(x=xy.coords(c(xbuf, rev(xbuf)), c(rep(ylim[1], 2), rep(ylim[2], 2))), col=cols[3])
   ylab <- paste("Hydraulic head in", c("meters", "feet"), "above the NAVD88")
   PlotGraph(dd.sim, xlim=xlim, ylim=ylim, ylab=ylab, col=cols[2],
-            conversion.factor=m.to.ft, bg.polygon=bg.polygon, center.date.labels=TRUE)
+            conversion.factor=m.to.ft, bg.polygon=bg.polygon,
+            center.date.labels=TRUE, seq.date.by="year")
   lines(x=as.Date(dd.obs$DateTime), y=dd.obs$head.obs, type="b", pch=20, lwd=0.5, col=cols[1])
   if (add.legend) {
     labs <- c("Measured groundwater level", "Simulated groundwater level", "Warm-up period in simulation")
@@ -1484,7 +1491,8 @@ d[d[, 2] < 0, 2] <- 0
 d[d[, 3] > 0, 3] <- 0
 col <- c("#67A9CF", "#C80C0B")
 PlotGraph(d, ylab=ylab, col=col, fill=paste0(col, "66"),
-          conversion.factor=m3.per.d.to.af.per.yr, scientific=TRUE, center.date.labels=TRUE)
+          conversion.factor=m3.per.d.to.af.per.yr, scientific=TRUE,
+          center.date.labels=TRUE, seq.date.by="year")
 legend("bottomright", c("Recharge", "Discharge"), col=col, lty=1,
        inset=0.02, cex=0.7, box.lty=1, box.lwd=0.5, bg="#FFFFFFCD")
 
@@ -1539,7 +1547,8 @@ FUN <- function(d, add.legend=FALSE) {
   ylab <- paste("Stream-aquifer flow exchange, in", c("cubic meters per day", "cubic feet per second"))
   PlotGraph(d[, 1:3], xlim=xlim, ylab=ylab, col=cols[1:2],
             conversion.factor=1 / cfs.to.m3.per.d, bg.polygon=bg.polygon,
-            scientific=c(FALSE, TRUE, FALSE), center.date.labels=TRUE)
+            scientific=c(FALSE, TRUE, FALSE), center.date.labels=TRUE,
+            seq.date.by="year")
   if (add.legend) {
     labs <- c("Measured", "Simulated", "Warm-up period")
     legend("topright", labs, pch=c(NA, NA, 22), lwd=c(1, 1, NA),
@@ -1730,7 +1739,8 @@ v <- c(paste("Graph showing", paste0(tolower(substr(v, 1, 1)), substr(v, 2, ncha
 ylab <- paste("Groundwater discharge, in", c("cubic meters per day", "acre-feet per year"))
 col <- "#C80C0B"
 PlotGraph(d.drain.1, ylab=ylab, col=col, fill=paste0(col, "66"),
-          conversion.factor=m3.per.d.to.af.per.yr, scientific=FALSE, center.date.labels=TRUE)
+          conversion.factor=m3.per.d.to.af.per.yr, scientific=FALSE,
+          center.date.labels=TRUE, seq.date.by="year")
 
 ## ----include=FALSE-------------------------------------------------------
 v <- "Groundwater discharge across the Silver Creek outlet boundary---based on uncalibrated model results."

inst/doc/sir20165080_AppendixD.Rnw

@@ -870,7 +870,7 @@ d[nrow(d), 1] <- d[nrow(d), 1] + ndays
 ylab <- paste("Tributary basin underflow, in", c("cubic meters per day", "acre-feet per year"))
 cols  <- rainbow(ncol(d), start=0.0, end=0.8)
 PlotGraph(d, ylab=ylab, conversion.factor=m3.per.d.to.af.per.yr, col=cols,
-          center.date.labels=TRUE, scientific=FALSE)
+          center.date.labels=TRUE, scientific=FALSE, seq.date.by="year")
 leg <- format(match(colnames(d)[-1], make.names(tributaries@data$Name)))
 legend("topright", leg, lwd=1, col=cols, ncol=2,
        pt.cex=1, inset=0.02, cex=0.7, box.lty=1, box.lwd=0.5,
@@ -1306,7 +1306,8 @@ x <- tr.stress.periods
 y <- rbind(norm.gage.height[, -1], norm.gage.height[nrow(norm.gage.height), -1])
 ylab <- paste("Normalized mean gage-height, in", c("meters", "feet"))
 cols <- c("#1B9E77", "#D95F02", "#7570B3")
-PlotGraph(x, y, ylab=ylab, col=cols, conversion.factor=m.to.ft, center.date.labels=TRUE)
+PlotGraph(x, y, ylab=ylab, col=cols, conversion.factor=m.to.ft,
+          center.date.labels=TRUE, seq.date.by="year")
 legend("topright", colnames(y), lwd=c(1, 1, 1), col=cols, inset=0.02, cex=0.7,
        box.lty=1, box.lwd=0.5, bg="#FFFFFFCD", title=expression(bold("Streamgages")))
 @
@@ -1463,7 +1464,8 @@ d[d[, 3] > 0, 3] <- 0
 ylab <- paste("Total flow across water table, in", c("cubic meters per day", "acre-feet per year"))
 col <- c("#67A9CF", "#C80C0B")
 PlotGraph(d, ylab=ylab, col=col, fill=paste0(col, "66"),
-          conversion.factor=m3.per.d.to.af.per.yr, scientific=TRUE, center.date.labels=TRUE)
+          conversion.factor=m3.per.d.to.af.per.yr, scientific=TRUE,
+          center.date.labels=TRUE, seq.date.by="year")
 legend("topright", c("Recharge", "Discharge"), col=col, lty=1,
        inset=0.02, cex=0.7, box.lty=1, box.lwd=0.5, bg="#FFFFFFCD")
 @
@@ -1480,7 +1482,8 @@ x <- tr.stress.periods
 ylab <- paste("Total withdrawals from wells, in", c("cubic meters per day", "acre-feet per year"))
 col <- "#C80C0B"
 PlotGraph(x, y, ylab=ylab, col=col, fill=paste0(col, "66"),
-          conversion.factor=m3.per.d.to.af.per.yr, scientific=TRUE, center.date.labels=TRUE)
+          conversion.factor=m3.per.d.to.af.per.yr, scientific=TRUE,
+          center.date.labels=TRUE, seq.date.by="year")
 @
 
 <<include=FALSE>>=
@@ -1554,7 +1557,8 @@ y <- rbind(m, m[nrow(m), , drop=FALSE])
 ylab <- paste("Seepage rate, in", c("cubic meters per day", "acre-feet per year"))
 col <- "#67A9CF"
 PlotGraph(x, y, ylab=ylab, col=col, fill=paste0(col, "66"),
-          conversion.factor=m3.per.d.to.af.per.yr, scientific=c(FALSE, TRUE, FALSE), center.date.labels=TRUE)
+          conversion.factor=m3.per.d.to.af.per.yr, scientific=c(FALSE, TRUE, FALSE),
+          center.date.labels=TRUE, seq.date.by="year")
 @
 
 <<include=FALSE>>=
@@ -1570,7 +1574,8 @@ y <- rbind(m, m[nrow(m), , drop=FALSE])
 ylab <- paste("Seepage rate, in", c("cubic meters per day", "acre-feet per year"))
 col <- "#67A9CF"
 PlotGraph(x, y, ylab=ylab, col=col, fill=paste0(col, "66"),
-          conversion.factor=m3.per.d.to.af.per.yr, scientific=FALSE, center.date.labels=TRUE)
+          conversion.factor=m3.per.d.to.af.per.yr, scientific=FALSE,
+          center.date.labels=TRUE, seq.date.by="year")
 @
 
 \noindent Steady-state volumetric flow rates are calculated by averaging flows over time.
@@ -2140,7 +2145,8 @@ FUN <- function(desc) {
   xlab <- "Simulated hydraulic head, in meters above the NAVD88"
   ylab <- paste("Hydraulic head residual, in", c("meters (m)", "feet"))
   PlotGraph(dd, xlab=xlab, ylab=ylab, type="n", xlim=xlim, ylim=ylim,
-            conversion.factor=m.to.ft, bg.polygon=bg.polygon)
+            conversion.factor=m.to.ft, bg.polygon=bg.polygon,
+            seq.date.by="year")
   abline(h=0, col="#333333", lwd=1)
   for (i in seq_along(desc))
     points(d[d$desc %in% desc[i], c("head.sim", "head.res")], pch=20, col=col[i])
@@ -2300,7 +2306,8 @@ FUN <- function(idx, add.legend=FALSE) {
   bg.polygon <- list(x=xy.coords(c(xbuf, rev(xbuf)), c(rep(ylim[1], 2), rep(ylim[2], 2))), col=cols[3])
   ylab <- paste("Hydraulic head in", c("meters", "feet"), "above the NAVD88")
   PlotGraph(dd.sim, xlim=xlim, ylim=ylim, ylab=ylab, col=cols[2],
-            conversion.factor=m.to.ft, bg.polygon=bg.polygon, center.date.labels=TRUE)
+            conversion.factor=m.to.ft, bg.polygon=bg.polygon,
+            center.date.labels=TRUE, seq.date.by="year")
   lines(x=as.Date(dd.obs$DateTime), y=dd.obs$head.obs, type="b", pch=20, lwd=0.5, col=cols[1])
   if (add.legend) {
     labs <- c("Measured groundwater level", "Simulated groundwater level", "Warm-up period in simulation")
@@ -2409,7 +2416,8 @@ d[d[, 2] < 0, 2] <- 0
 d[d[, 3] > 0, 3] <- 0
 col <- c("#67A9CF", "#C80C0B")
 PlotGraph(d, ylab=ylab, col=col, fill=paste0(col, "66"),
-          conversion.factor=m3.per.d.to.af.per.yr, scientific=TRUE, center.date.labels=TRUE)
+          conversion.factor=m3.per.d.to.af.per.yr, scientific=TRUE,
+          center.date.labels=TRUE, seq.date.by="year")
 legend("bottomright", c("Recharge", "Discharge"), col=col, lty=1,
        inset=0.02, cex=0.7, box.lty=1, box.lwd=0.5, bg="#FFFFFFCD")
 @
@@ -2477,7 +2485,8 @@ FUN <- function(d, add.legend=FALSE) {
   ylab <- paste("Stream-aquifer flow exchange, in", c("cubic meters per day", "cubic feet per second"))
   PlotGraph(d[, 1:3], xlim=xlim, ylab=ylab, col=cols[1:2],
             conversion.factor=1 / cfs.to.m3.per.d, bg.polygon=bg.polygon,
-            scientific=c(FALSE, TRUE, FALSE), center.date.labels=TRUE)
+            scientific=c(FALSE, TRUE, FALSE), center.date.labels=TRUE,
+            seq.date.by="year")
   if (add.legend) {
     labs <- c("Measured", "Simulated", "Warm-up period")
     legend("topright", labs, pch=c(NA, NA, 22), lwd=c(1, 1, NA),
@@ -2777,7 +2786,8 @@ v <- c(paste("Graph showing", paste0(tolower(substr(v, 1, 1)), substr(v, 2, ncha
 ylab <- paste("Groundwater discharge, in", c("cubic meters per day", "acre-feet per year"))
 col <- "#C80C0B"
 PlotGraph(d.drain.1, ylab=ylab, col=col, fill=paste0(col, "66"),
-          conversion.factor=m3.per.d.to.af.per.yr, scientific=FALSE, center.date.labels=TRUE)
+          conversion.factor=m3.per.d.to.af.per.yr, scientific=FALSE,
+          center.date.labels=TRUE, seq.date.by="year")
 @
 
 <<include=FALSE>>=