- Fork and rebrand wq to wql
- Added roxygen documentation

- eof: Shift id to row name in output.
- eofPlot: Fix for non-numeric row names in original data.
- mannKen: Use different definition of relative sen slope.
- pett: Add change.size. Get actual change.time for zoo objects.
- phenoAmp: Change to more versatile output statistics. Change argument name.
- phenoPhase: Change argument name.
- seaKen: Use different definition of relative sen slope.
- trendHomog: Ignore seasons with insufficient data.

- Add back html vignette.
- Fix global variable notes.
- eof: Calculation method changed.
- eofNum: Remove ruleN-based colouring.
- eofPlot: Remove Monte Carlo lines.
- plotTsTile: Default to median instead of mean.
- ruleN: Remove.

- decompTs: Remove startyr and endyr. Add median as default centering method.
- mannKen: Remove “tau” argument. Use median instead of mean for relative. Add exact p-values. Allow matrix and data.frame. Change plot.
- pett.R: Add new function with plot for Pettitt test.
- plotTs: Remove plot.order argument. Improve legend.
- plotTsAnom: Remove plot.order argument.
- seaKen: Allow matrix and data.frame. Add plot.
- seaRoll: Change arguments and plot.
- seasonTrend: Change arguments. Remove ls trend method. Improve legend.

- eofPlot.R: Fix argument to geom_hline.

- wq-internal.R: Removed.
- plot WqData-class: Added global variable definitions.

- ammFrac: Remove.
- layOut: Remove.

- mannKen: Preserve station order in data matrix.
- mannKen: Modify examples to be more useful.
- NAMESPACE: Add importFrom(“methods”).
- NAMESPACE: Remove all require(zoo) from functions.
- plotSeason: Enable plotting by arbitrary eras.
- plotSeason: Fixed error when num.era=1.
- vignette: Remove unnecessary commands from preamble.
- wqData: Require locus to be length 3.
- WqData-class: Change tz=“UTC” default in as.Date for summary.

`[`

: method now exists for WqData objects.- plotTsTile: has additional options and a corrected help file.
- subset, transform: no longer used within code.
- wqData: handles collision between locus and wq variables with same name.
- minor bug fixes.

- Vignette (re-)included.
- Minor changes in plotting functions.

- Updated for ggplot2 0.9.2.

- Minor changes to manual.

- Minor changes to code, with no changes in behaviour.

- Addresses issues introduced with version 0.9 of ggplot2.
- Uses reshape2 instead of reshape.
- plotTsAnom and seasonTrend: minor plotting changes.

- date2decyear: Converts dates to numeric years.
- interpTs: More options for replacing NAs.
- plotTs: Time series line plot plus isolated points
- plotTsAnom: Now works for matrix time series.
- theme_wq: Simplified version of theme_grey in package “ggplot2”.
- tsMake: No longer excruciatingly slow when layer = “max.depths”

- plotTsAnom: time series anomaly plot.
- tsMake: Now aggregates depths (and days) by quantiles as well as means.
- plotSeason: Fixed problem with missing data treatment.
- tsSub: Fixed problem with incorrect starting month.

- plot method for class “WqData”: Boxplots instead of stripcharts. Also fixed behaviour when less than 10 unique variables.
- plotSeason: Changed “by.month” option to standardized anomalies.
- tsMake: Added option to create series for “bottom” of water column.
- Version requirement is R 10.0.
- Vignette file size fixed so it can be downloaded from HTML help.

- All plot functions now produce objects of class “ggplot”.
- layOut: Lays out graphs of class ggplot.
- mannKen: Added mts and plot options.
- meanSub: Utility function to average subsets.
- mts2ts: Prepare spatial time series for further analysis.
- plotSeason: Added another way of plotting.
- seaRoll: Plotting is an additional option.
- trendHomog: Test for homogeneity of seasonal trends.
- tsSub: Utility function to drop seasons in a ts.
- plotEof: Changed to eofPlot.

- phenoPhase: Integration defaults can now be changed, if necessary.
- plotSeason: Added smoother when type=‘by.month’.
- seasonTrend: Changed appearance and some options.
- plotSeason: Fixed problem when type=‘by.month’.
- plotTsTile: Now plots correct colours when four=FALSE.
- tsMake: Fixed problem when layer of class “numeric”.

- wqData: Changed “narrow” to “long”.
- plotSeas: Changed to plotSeason.
- ammFrac: New function for un-ionized ammonium.
- plotSeason: Added option to plot individual months for entire record.
- seasonTrend: New function for time series trends by season.
- tsMake: Now allows for more ways of specifying depths.
- mannKen, seaKen: Now gives correct sign when trend given as %.
- phenoAmp: Fixed problem when subsetting months leaves no data for year.
- phenoPhase: Fixed problem when subsetting months and x is a “zoo” object.
- plotSeason: Now handles num = 1.
- tsMake: Fixed problem when focus consisted of a single variable or site.

- interpTs: Option to fill with long-term mean or median.
- plotSeas: Option to choose number of intervals.
- WqData plot method: Option to choose variables.
- phenoPhase: Fixed problem where max.time month number given relative to subset rather than whole year
- plotTsTile: More useful error message when not enough data.
- seaRoll: Fixed problem with frequencies other than 12.
- tsMake: Remove need to specify layer if no depth info.
- WqData subset method: Removed because of strategy that WqData objects should not be changed.
- wqData: Argument value “narrow” changed to more conventional “long”.
- wqData: Now requires time.format to be specified.
- wqData: Now ensures variable is a factor when type = “long”.