NEWS.md

plyr (development version)

plyr 1.8.9

• Fixes for R CMD check

plyr 1.8.8

• Update so R CMD check passes cleanly in future R-devel.

plyr 1.8.7

• Update so R CMD check passes cleanly in future R-devel.

plyr 1.8.6

• Update so R CMD check passes cleanly on R and R-devel.

plyr 1.8.5

• Update so R CMD check passes cleanly on R and R-devel.

Version 1.8.4

• Update so R CMD check passes cleanly on R and R-devel.

Version 1.8.3

• Revert to C version of loop_apply() as Rcpp version was appears to be having PROTECTion problems. (Also fixes #256)

Version 1.8.2

• Update for changes in R namespace best-practices.

• New parameter .id to adply() that specifies the name(s) of the index column(s). (Thanks to Kirill Müller, #191)

• Fix bug in split_indices() when n isn't supplied.

• Fix bug in .id parameter to ldply() and rdply() allowing for .id = NULL to work as described in the help. (Thanks to Doug Mitarotonda, #207, and Marek, #224 and #225)

• Deprecate exotic functions liply() and isplit2(), remove unused and unexported functions dots() and parallel_fe() (Thanks to Kirill Müller, #242, #248)

• Warn on duplicate names that cause certain array functions to fail. (Thanks to Kirill Müller, #211)

• Parameter .inform is now honored for ?_ply() calls. (Thanks to Kirill Müller, #209)

Version 1.8.1

• New parameter .id to ldply() and rdply() that specifies the name of the index column. (Thanks to Kirill Müller, #107, #140, #142)

• The .id column in ldply() is generated as a factor to preserve the sort order, but only if the new .id parameter is set. (Thanks to Kirill Müller, #137)

• rbind.fill now silently drops NULL inputs (#138)

• rbind.fill avoids array copying which had produced quadratic time complexity. *dply of large numbers of groups should be faster. (Contributed by Peter Meilstrup)

• rbind.fill handles non-numeric matrix columns (i.e. factor arrays, character arrays, list arrays); also arrays with more than 2 dimensions can be used. Dimnames of array columns are now preserved. (Contributed by Peter Meilstrup)

• rbind.fill(x,y) converts factor columns of Y to character when columns of X are character. join(x,y) and match_df(x,y) now work when the key column in X is character and Y is factor. (Contributed by Peter Meilstrup)

• Fix faulty array allocation which caused problems when using split_indices with large (> 2^24) vectors. (Fixes #131)

• list_to_array() incorrectly determined dimensions if column of labels contained any missing values (#169).

• r*ply expression is evaluated exactly .n times, evaluation results are consistent with side effects. (#158, thanks to Kirill Müller)

Version 1.8

New features and functions

• **ply gain a .inform argument (previously only available in llply) - this gives more useful debugging information at the cost of some speed. (Thanks to Brian Diggs, #57)

• if .dims = TRUE alply's output gains dimensions and dimnames, similar to apply. Sequential indexing of a list produced by alply should be unaffected. (Peter Meilstrup)

• colwise, numcolwise and catcolwise now all accept additional arguments in .... (Thanks to Stavros Macrakis, #62)

• here makes it possible to use **ply + a function that uses non-standard evaluation (e.g. summarise, mutate, subset, arrange) inside a function. (Thanks to Peter Meilstrup, #3)

• join_all recursively joins a list of data frames. (Fixes #29)

• name_rows provides a convenient way of saving and then restoring row names so that you can preserve them if you need to. (#61)

• progress_time (used with .progress = "time") estimates the amount of time remaining before the job is completed. (Thanks to Mike Lawrence, #78)

• summarise now works iteratively so that later columns can refer to earlier. (Thanks to Jim Hester, #44)

• take makes it easy to subset along an arbitrary dimension.

• Improved documentation thanks to patches from Tim Bates.

Parallel plyr

• **ply gains a .paropts argument, a list of options that is passed onto foreach for controlling parallel computation.

• *_ply now accepts .parallel argument to enable parallel processing. (Fixes #60)

• Progress bars are disabled when using parallel plyr (Fixes #32)

Performance improvements

• a*ply: 25x speedup when indexing array objects, 3x speedup when indexing data frames. This should substantially reduce the overhead of using a*ply

• d*ply subsetting has been considerably optimised: this will have a small impact unless you have a very large number of groups, in which case it will be considerably faster.

• idata.frame: Subsetting immutable data frames with [.idf is now faster (Peter Meilstrup)

• quickdf is around 20% faster

• split_indices, which powers much internal splitting code (like vaggregate, join and d*ply) is about 2x faster. It was already incredibly fast ~0.2s for 1,000,000 obs, so this won't have much impact on overall performance

Bug fixes

• *aply functions now bind list mode results into a list-array (Peter Meilstrup)

• *aply now accepts 0-dimension arrays as inputs. (#88)

• count now works correctly for factor and Date inputs. (Fixes #130)

• *dply now deals better with matrix results, converting them to data frames, rather than vectors. (Fixes #12)

• d*ply will now preserve factor levels input if drop = FALSE (#81)

• join works correctly when there are no common rows (Fixes #74), or when one input has no rows (Fixes #48). It also consistently orders the columns: common columns, then x cols, then y cols (Fixes #40).

• quickdf correctly handles NA variable names. (Fixes #66. Thanks to Scott Kostyshak)

• rbind.fill and rbind.fill.matrix work consistently with matrices and data frames with zero rows. Fixes #79. (Peter Meilstrup)

• rbind.fill now stops if inputs are not data frames. (Fixes #51)

• rbind.fill now works consistently with 0 column data frames

• round_any now works with POSIXct objects, thanks to Jean-Olivier Irisson (#76)

Version 1.7.1

• Fix bug in id, using numeric instead of integer

Version 1.7

• rbind.fill: if a column contains both factors and characters (in different inputs), the resulting column will be coerced to character

• When there are more than 2^31 distinct combinations id, switches to a slower fallback strategy using strings (inspired by merge) that guarantees correct results. This fixes problems with join when joining across many columns. (Fixes #63)

• split_indices checks input more aggressively to prevent segfaults. Fixes #43.

• fix small bug in loop_apply which lead to segfaults in certain circumstances. (Thanks to Pål Westermark for patch)

• itertools and iterators moved to suggests from imports so that plyr now only depends on base R.

Version 1.6

• documentation improved using new features of roxygen2

• fixed namespacing issue which lead to lost labels when subsetting the results of *lply

• colwise automatically strips off split variables.

• rlply now correctly deals with rlply(4, NULL) (thanks to bug report from Eric Goldlust)

• rbind.fill tries harder to keep attributes, retaining the attributes from the first occurrence of each column it finds. It also now works with variables of class POSIXlt and preserves the ordered status of factors.

• arrange now works with one column data frames

Version 1.5.2

• d*ply returns correct number of rows when function returns vector

• fix NAMESPACE bug which was causing problems with ggplot2

Version 1.5.1

• rbind.fill now treats 1d arrays in the same way as rbind (i.e. it turns them into ordinary vectors)

• fix bug in rename when renaming multiple columns

Version 1.5 (2011-03-02)

New features

• new strip_splits function removes splitting variables from the data frames returned by ddply.

• rename moved in from reshape, and rewritten.

• new match_df function makes it easy to subset a data frame to only contain values matching another data frame. Inspired by http://stackoverflow.com/questions/4693849.

Bug fixes

• **ply now works when passed a list of functions

• *dply now correctly names output even when some output combinations are missing (NULL) (Thanks to bug report from Karl Ove Hufthammer)

• *dply preserves the class of many more object types.

• a*ply now correctly works with zero length margins, operating on the entire object (Thanks to bug report from Stavros Macrakis)

• join now implements joins in a more SQL like way, returning all possible matches, not just the first one. It is still a (little) faster than merge. The previous behaviour is accessible with match = "first".

• join is now more symmetric so that join(x, y, "left") is closer to join(y, x, "right"), modulo column ordering

• named.quoted failed when quoted expressions were longer than 50 characters. (Thanks to bug report from Eric Goldlust)

• rbind.fill now correctly maintains POSIXct tzone attributes and preserves missing factor levels

• split_labels correctly preserves empty factor levels, which means that drop = FALSE should work in more places. Use base::droplevels to remove levels that don't occur in the data, and drop = T to remove combinations of levels that don't occur.

• vaggregate now passes ... to the aggregation function when working out the output type (thanks to bug report by Pavan Racherla)

Version 1.4.1 (2011-04-05)

• Add citation to JSS article

Version 1.4 (2011-01-03)

• count now takes an additional parameter wt_var which allows you to compute weighted sums. This is as fast, or faster than, tapply or xtabs.

• Really fix bug in names.quoted

• . now captures the environment in which it was evaluated. This should fix an esoteric class of bugs which no-one probably ever encountered, but will form the basis for an improved version of ggplot2::aes.

Version 1.3.1 (2010-12-30)

• Fix bug in names.quoted that interfered with ggplot2

Version 1.3 (2010-12-28)

New features

• new function mutate that works like transform to add new columns or overwrite existing columns, but computes new columns iteratively so later transformations can use columns created by earlier transformations. (It's also about 10x faster) (Fixes #21)

Bug fixes

• split column names are no longer coerced to valid R names.

• quickdf now adds names if missing

• summarise preserves variable names if explicit names not provided (Fixes #17)

• arrays with names should be sorted correctly once again (also fixed a bug in the test case that prevented me from catching this automatically)

• m_ply no longer possesses .parallel argument (mistakenly added)

• ldply (and hence adply and ddply) now correctly passes on .parallel argument (Fixes #16)

• id uses a better strategy for converting to integers, making it possible to use for cases with larger potential numbers of combinations

Version 1.2.1 (2010-09-10)

• Fix bug in llply fast path that causes problems with ggplot2.

Version 1.2 (2010-09-09)

New features

• l*ply, d*ply, a*ply and m*ply all gain a .parallel argument that when TRUE, applies functions in parallel using a parallel backend registered with the foreach package:

  x <- seq_len(20)
  wait <- function(i) Sys.sleep(0.1)
  system.time(llply(x, wait))
  #  user  system elapsed
  # 0.007   0.005   2.005
  
  doParallel::registerDoParallel(2)
  system.time(llply(x, wait, .parallel = TRUE))
  #  user  system elapsed
  # 0.020   0.011   1.038

  This work has been generously supported by BD (Becton Dickinson).

Minor changes

• aply and mply gain an .expand argument that controls whether data frames produce a single output dimension (one element for each row), or an output dimension for each variable.

• new vaggregate (vector aggregate) function, which is equivalent to tapply, but much faster (~ 10x), since it avoids copying the data.

• llply: for simple lists and vectors, with no progress bar, no extra info, and no parallelisation, llply calls lapply directly to avoid all the overhead associated with those unused extra features.

• llply: in serial case, for loop replaced with custom C function that takes about 40% less time (or about 20% less time than lapply). Note that as a whole, llply still has much more overhead than lapply.

• round_any now lives in plyr instead of reshape

Bug fixes

• list_to_array works correct even when there are missing values in the array. This is particularly important for daply.

Version 1.1 (2010-07-19)

• *dply deals more gracefully with the case when all results are NULL (fixes #10)

• *aply correctly orders output regardless of dimension names (fixes #11)

• join gains type = "full" which preserves all x and y rows

Version 1.0 (2010-07-02)

New functions

• arrange, a new helper method for reordering a data frame.
• count, a version of table that returns data frames immediately and that is much much faster for high-dimensional data.
• desc makes it easy to sort any vector in descending order
• join, works like merge but can be much faster and has a somewhat simpler syntax drawing from SQL terminology
• rbind.fill.matrix is like rbind.fill but works for matrices, code contributed by C. Beleites

Speed improvements

• experimental immutable data frame (idata.frame) that vastly speeds up subsetting - for large datasets with large numbers of groups, this can yield 10-fold speed ups. See examples in ?idata.frame to see how to use it.

• rbind.fill rewritten again to increase speed and work with more data types

• d*ply now much faster with nested groups

  This work has been generously supported by BD (Becton Dickinson).

Version 0.2

New features:

• d*ply now accepts NULL for splitting variables, indicating that the data should not be split
• plyr no longer exports internal functions, many of which were causing clashes with other packages
• rbind.fill now works with data frame columns that are lists or matrices
• test suite ensures that plyr behaviour is correct and will remain correct as I make future improvements.

Bug fixes:

• **ply: if zero splits, empty list(), data.frame() or logical() returned, as appropriate for the output type
• **ply: leaving .fun as NULL now always returns list (thanks to Stavros Macrakis for the bug report)
• a*ply: labels now respect options(stringAsFactors)
• each: scoping bug fixed, thanks to Yasuhisa Yoshida for the bug report
• list_to_dataframe is more consistent when processing a single data frame
• NAs preserved in more places
• progress bars: guaranteed to terminate even if **ply prematurely terminates
• progress bars: misspelling gives informative warning, instead of uninformative error
• splitter_d: fixed ordering bug when .drop = FALSE

Version 0.1.9 (2009-06-23)

• fix bug in rbind.fill when NULLs present in list
• improve each to recognise when all elements are numeric
• fix labelling bug in d*ply when .drop = FALSE
• additional methods for quoted objects
• add summarise helper - this function is like transform, but creates a new data frame rather than reusing the old (thanks to Brendan O'Connor for the neat idea)

Version 0.1.8 (2009-04-20)

• made rbind a little faster (~20%) using an idea from Richard Raubertas
• daply now works correctly when splitting variables that contain empty factor levels

Version 0.1.7 (2009-04-15)

• Version of rbind.fill that copies attributes.

Version 0.1.6 (2009-04-15)

Improvements:

• all ply functions deal more elegantly when given function names: can supply a vector of function names, and name is used as label in output
• failwith and each now work with function names as well as functions (i.e. "nrow" instead of nrow)
• each now accepts a list of functions or a vector of function names
• l*ply will use list names where present
• if .inform is TRUE, error messages will give you information about where errors within your data - hopefully this will make problems easier to track down
• d*ply no longer converts splitting variables to factors when drop = T (thanks to bug report from Charlotte Wickham)

Speed-ups

• massive speed ups for splitting large arrays
• fixed typo that was causing a 50% speed penalty for d*ply
• rewritten rbind.fill is considerably (> 4x) faster for many data frames
• colwise about twice as fast

Bug fixes:

• daply: now works when the data frame is split by multiple variables
• aaply: now works with vectors
• ddply: first variable now varies slowest as you'd expect

Version 0.1.5 (2009-02-23)

• colwise now accepts a quoted list as its second argument. This allows you to specify the names of columns to work on: colwise(mean, .(lat, long))
• d_ply and a_ply now correctly pass ... to the function

Version 0.1.4 (2008-12-12)

• Greatly improved speed (> 10x faster) and memory usage (50%) for splitting data frames with many combinations
• Splitting variables containing missing values now handled consistently

Version 0.1.3 (2008-11-19)

• Fixed problem where when splitting by a variable that contained missing values, missing combinations would be drop, and labels wouldn't match up

Version 0.1.2 (2008-11-18)

• a*ply now works correctly with array-lists
• drop. -> .drop
• r*ply now works with ...
• use inherits instead of is so method package doesn't need to be loaded
• fix bug with using formulas

Version 0.1.1 (2008-10-08)

• argument names now start with . (instead of ending with it) - this should prevent name clashes with arguments of the called function
• return informative error if .fun is not a function
• use full names in all internal calls to avoid argument name clashes