NEWS.md
In dplR: Dendrochronology Program Library in R

dplR 1.8.0

A large release. This file lists what users need to know; the ChangeLog has the full record, with the reasons for each change.

read.tucson() is new, and no longer fills gaps inside a series with zeros. A gap is now NA, so detrend() and other functions that reject NA inside a series stop on such data until the gap is filled on purpose. fill.internal.NA = 0 reproduces the old values. The old reader is kept as read.tucson.legacy().
detrend() and detrend.series() now default to method = "Spline". The old default ran every method and returned a list, not indices. Code that relied on it must now name the methods.
detrend() with one method, rcs(), cms() and i.detrend() now return class "rwi" (ring-width indices). This used to be a plain data.frame, or class "rwl" for rcs(), cms() and i.detrend(). The values are unchanged.
bai.in() and bai.out() now return class "bai" (basal area increment). They used to return class "rwl". The areas are unchanged.
Functions now warn when given the wrong kind of series. Those that want ring widths (detrend(), rcs(), bai.in(), rwl.report(), ...) warn on class "rwi". Those that want indices (chron(), rwi.stats(), sss(), ...) warn on class "rwl". Indices read from a file come back as "rwl"; label them with as.rwi().
detrend(), rcs(), cms(), i.detrend(), interseries.cor(), corr.rwl.seg() and subset() drop series with no values, with a message naming them. Before, they stopped or kept a column of NA.
Data that can be negative, such as indices from detrend(difference = TRUE), are no longer sign-flipped when normalized. That flipping gave wrong rbar, EPS and interseries correlations (GitHub issue 22). Results for ring widths and ratio indices are unchanged.
detrend.series(difference = TRUE) now uses fitted curves that go below zero as they are, instead of swapping them for a simpler fit.
caps() stops on a series containing NA. Before, it returned all NA.
Some first arguments were renamed: chron(x) and chron.ars(x) are now rwi, and sgc(x) is now rwl. Calls that named the argument x = must change.
nyrs and ar.order.max were added to the crossdating and statistics functions, next to n and prewhiten. Arguments after them passed by position now shift. An old call that shifts stops with an error; none silently changes meaning.
csv2rwl() is deprecated in favour of read.sheet(), and may refuse files it used to accept wrongly.

rwl.check() looks for defects in a collection (duplicate or empty series, gaps, zeros, units errors, dating errors) and returns them as rows with stable IDs, for one file or a whole archive.
xdate.report() and write.xdate.report() produce a COFECHA-style crossdating report, with A and B flags and the lag and correlation gain for each flagged segment.
corr.rwl.seg() gains lag.max. It tests each segment at shifted dates and returns the best lag. Negative lags mean missing rings, as in COFECHA.
read.sheet() and write.sheet() read and write spreadsheet-shaped files (years down, series across, or long format). read.rwl() uses them for csv.
The readers handle files that are not valid UTF-8, and read.tucson() records what it saw in a provenance record that travels with the data.
The "rwi" class has summary(), which gives collection statistics and flags series that don't fit, and plot(x, plot.type = "image"), which shows trend left in by detrending.
The "bai" class has as.bai() and methods for [, subset(), time(), window(), summary() and plot(). chron(), detrend() and the crossdating functions take it without a warning; functions that want ring widths warn.
window() methods for rwl, rwi, bai and crn objects: window(x, 1800, 1900).
[ and subset() methods for rwl and rwi objects keep the class and the records, and trim years no series covers.
A new vignette, "Getting Started with dplR".