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Known issues: https://github.com/PredictiveEcology/SpaDES.core/issues

version 0.2.3

package dependencies

  • add RandomFields to Suggests, as it is in the Suggests of SpaDES.tools and used in examples/tests.

new features

  • simList internals changed. It now inherits from environment. Amongst other things, this means that tab autocomplete in RStudio now works for objects in the simList. Also, we removed several associated methods, $, [[, ls, ls.str, objects, as the defaults for environments work correctly with the simList now
  • debug arg in spades call can now take numeric, currently 1 or 2, giving a few pre-packaged informative messaging each event
  • new function elapsedTime which gives a summary of the clock time used by each module or event
  • most metadata entries now have accessor of same name, e.g., inputObjects(sim) returns the inputObjects data.frame.
  • new function citation replaces utils::citation with an S4 generic. If package arg is a character, it dispatches utils::citation; if a simList, it gives the citation for the module(s)
  • improved messaging when GLPK not installed (e.g., on macOS)
  • downloadModule() now prints the module version downloaded (#77)

bugfixes

  • resolved .inputObjects() name conflict (internal .inputObjects renamed to ._inputObjectsDF; .outputObjects renamed to ._outputObjectsDF)
  • module .inputObjects evaluated based on module load order (#72)
  • .robustDigest fix for simLists -- needed to omit ._startClockTime and .timestamp

version 0.2.2

package dependencies

  • remove sp from imports

new features

  • none

bugfixes

  • fix issues with failing tests on macOS

version 0.2.1

package dependencies

  • requires new version of reproducible (>=0.2.2)

new features

  • new option spades.useRequire: a logical which causes simInit to load packages with Require or require. Lower case is generally faster, but will not handle the case of uninstalled packages, so should only be used once all packages are installed.

      • new option spades.keepCompleted: a logical which causes spades() to keep (TRUE) or not keep a record of completed events. Keeping track of completed events when they are many (>1e5) gets slow enough that it may be worth turning it off.

  • more robust and faster tests are used now, care of helper functions in tests

  • all.equal.simList now removes all time dependent attributes, e.g., ._startClockTime and .timestamp

  • speed enhancements for Discrete Event Simulator; now overhead is 1.3 seconds for 5000 events or, per event, 260 microseconds (185 microseconds if options("spades.keepCompleted" = FALSE)

bugfixes

  • Improvements to caching of functions with simList objects:

    • Cached functions with a simList in the arguments would erroneously return cached copies of functions. These now are copied through from argument simList, rather than cached simList. This means that changes to the function definitions in a module will persist (e.g., debugging via browser() will work correctly)
    • functions with simList in arguments that return a simList will now do a post digest of the output. This will be compared with the predigest, and only those object which changed in the simList will be modified.
    • caching of .inputObjects function was incorrect. Fixed.

version 0.2.0

new features

  • module metadata now in named lists inside depends(sim)

  • new debugging -- if debug is not FALSE, then any error will trigger a browser() call inside the event function. User can continue (c) or quit (Q) as per normal. c will trigger a reparse and events will continue as scheduled.

  • introduction of code checking for modules, currently turned on or off by an option spades.moduleCodeChecks, which is TRUE by default. Code checking includes various types:

    • use codetools to check for various code problems
    • detects conflicts with known common functions (raster::level, raster::scale, quickPlot::Plot)
    • use checkCodeEnv on every function inside a module
    • checking for sim$xxx occurrences in modules, comparing to outputObjects in metadata if used in assignment (i.e., left hand side of assign operator), or comparing to inputObjects if used on the right hand side
    • check that all objects declared in inputObjects have default values assigned in the .inputObjects function
    • messages colour coded, and separated by file with absolute path explicit

  • option spades.debug set to TRUE by default, instead of FALSE. This is better for new users.

  • moduleMetadata argument order changed, so sim is first, more consistent with all other simList accessors.

  • downloadData has changed dramatically, now it is a wrapper around reproducible::prepInputs which does more checking.

  • extractURL will extract the sourceURL from metadata, given an object name.

  • makeMemoiseable and unmakeMemoisable, new methods, each the inverse of the other, to deal with imperfect memoised returns under some cases of simList.

  • new option, spades.keepCompleted, TRUE by default, which can be useful for dramatically speeding up the DES when there are many (>10,000) events.

deprecated, defunct, and removed features

  • remove fileExt -- use tools::file_ext instead

bug fixes

  • fix tests based on data.table changes (@mattdowle, #64).
  • re-export start and end.
  • newModule template modified slightly based on workshop feedback.
  • setPaths now only sets the directories that are passed into it.
  • all.equal.simList method strips a small number of attributes that are used internally that create false failures.
  • speed enhancements.
  • other minor bug fixes.

package dependency changes

  • add package imports tools, pryr.
  • removed package imports rgeos, RCurl and googledrive.

version 0.1.1

  • uses reproducible::Require instead of SpaDES.core::loadPackages to load required packages. Currently, does not use version control for packages, but does use installing (from CRAN or GitHub), and loading (via require). This means a module can indicate a github package, e.g,. achubaty/amc@development

  • environments in modules are now as follows:

    • Functions defined in a module are sourced into an environment located here: sim@.envir$<moduleName>, and it is a is a child of sim@.envir. Functions can be found in this environment, but prefixing functions is not necessary, because modules functions are within this environment already.
    • sim@.envir is a child of SpaDES.core

  • scoping from within a function that is defined in a module is thus:

    • sim@.envir$<moduleName> --> sim@.envir --> SpaDES.core --> all imported packages including base --> .GlobalEnv --> search()

  • speed improvements:

    • the core DES is now built around lists, rather than data.table objects. For small objects (e.g., the eventQueue) that have fewer than 200 objects, lists are faster. Accessors (e.g., events(sim), completed(sim)) of the event queues still show data.table objects, but these are made on the fly.
    • .parseModule and .parseModuePartial now put their parsed content into a temporary environment (sim@.envir$.parsedFiles$<Full Filename>) during the simInit, which gets re-used. Previously, files were parsed multiple times in a given simInit call. Several functions now have envir argument to pass this through (including moduleVersion, packages, checkParams)

  • parsing of modules is now more intelligent, allowing for modules to contain functions (the current norm) and but they can also create objects at the module level. These can use the sim object in their definition. These objects can, for example, be used to help define parameters, for example, e.g., startSimPlus1 <- start(sim) + 1 can be defined in the module and used in defineModule

  • remove grDevices from Imports as it was not used (#1)

  • remove chron and CircStats dependencies

  • remove functions dwrpnorm2 and move to package SpaDES.tools

  • remove unused function F() due to conflicts with F/FALSE.

  • improved download of module data: added new quickCheck argument

  • improved download of modules: use fuzzy matching

  • new option: spades.switchPkgNamespaces which allows the user to turn off the SpaDES feature that loads and unloads libraries specific to each module. While useful, it slows down computations, in some cases, by a lot.

  • bug fixes:

    • in zipModule that omitted the checksum file from being included when data = FALSE (#3)
    • caching of .inputObjects functions was evaluating outputObjects instead of inputObjects. Now corrected.

  • If .inputObjects contains arguments other than just sim, these will be evaluated as function inputs by the Cache mechanism (via .useCache), therefore correctly assessing when those inputs changed, e.g., if they are files and the arg is wrapped in asPath, then any change to the underlying file will cause a re-cache. e.g., .inputObjects <- function(sim, importantFile = asPath(file.path(inputPath(sim), "theFile.rdata"))) { ... }

  • default debug option in spades() now uses the package option spades.debug and default is set to FALSE (#5)

  • various other speed improvements and bug fixes

  • convert P to a function, rather than S4 generic and method, for speed.

  • importFrom only used functions from utils due to name conflicts with raster::stack and utils::stack

  • new function remoteFileSize to check the size of remote files

  • new namespaced function dataPath will return file.path(modulePath(sim), currentModule(sim), "data"), which will return a different path, depending on which module it is placed inside.

  • add crayon to imports -- now messages are more colour coded

  • bug fix in 'inputs' for the case of loading objects from the global environment, either from the same object to the same object, or from different global objects overwriting on the same simList object

version 0.1.0

  • A new package, which takes all core DES functionality out of the SpaDES package:

    • see ?SpaDES.core for an overview

  • various speed improvements and bug fixes