Diversity Dynamics using Fossil Sampling Data

Functions to describe sampling and diversity dynamics of fossil occurrence datasets (e.g. from the Paleobiology Database). The package includes methods to calculate range- and occurrence-based metrics of taxonomic richness, extinction and origination rates, along with traditional sampling measures. A powerful subsampling tool is also included that implements frequently used sampling standardization methods in a multiple bin-framework. The plotting of time series and the occurrence data can be simplified by the functions incorporated in the package, as well other calculations, such as environmental affinities and extinction selectivity testing. Details can be found in: Kocsis, A.T.; Reddin, C.J.; Alroy, J. and Kiessling, W. (2019) .


News

Change log of the R package 'divDyn'

[0.7.1 (build 670)] - 2019.02.18

Added

  • A lot of people reported problems with the direction of time in the divDyn() function. A startup message is added as a reminder of the arbitrary decision I had to make when designing the function.
  • The affinity() function is extended with the 'na.rm' argument. Setting this argument to TRUE will remove all NAs found in relevant columns of the data table. Otherwise the function will halt if these are found.
  • The "binom" method of the affinity() function is now generalized to more than two entry types. Binomial tests are run for that type that has the highest odds ratio of occurrences when contrasted to the reference dataset ('dat' or 'reldat').
  • The 'bycoll' argument is now added to the affinity() function. This allows the calculation of affinities based on the collection rather than occurrence counts.
  • Some code was added to the tsplot() function to correctly plot the labels of the time scale boxes when the boundaries of the plot do not coincide with those of the boxes. The plotting of the labels of these partially drawn boxes can be switched on and off with the added 'rtlab' and 'ltlab' arguments.

Changed

  • Package suggested citation now directs to the paper in Methods in Ecology and Evolution.
  • The default of the 'coll' argument in the affinity() function is now set to NULL.

Fixed

  • The main divDyn() function produced warnings ('In cbind(bin = aubi$z, dCountsAndMetrics)'') when the automatic binning was used ('breaks 'argument) and when the provided interval had younger parts than the occurrence data. The results are the same, the warnings are no longer produced.
  • Problems with the 'reldat' argument of the affinity() function

[0.7.0 (build 642)] - 2019.01.08

Added

  • the georange() function for geographic range estimation from a set of coordinates (suggesting the vegan and the icosa packages)
  • the tabinate() function for iterating procedures on taxon/time slice subsets of the data

Changed

  • the internals of the binning procedure of divDyn()
  • updated ddPhanero vignette
  • To make the contents of the 'stages' object consistent with its name, the former geochronological entries are replaced with their chronostratigraphic counterparts. The columns per, period and periodCol were replaced with 'sys', 'system' and 'systemCol', table entries with 'Early' and 'Late' qualifiers were replaced with 'Lower' and 'Upper', respectively. The vignettes are adjusted to work with these changes.

[0.6.3] - 2018.12.12

Added

  • The modeltab() function
  • the fill() utility function
  • proper NEWS file
  • the 'ages' argument to the divDyn() function
  • the 'misspell', 'subgenera' and 'stems' are added to the spCleanse() function, which was renamed to cleansp()
  • warnings to some functions that signs the presence of "" empty quotes taxa

Changed/Fixed

  • instead of zeros, the divDyn() function now outputs NAs where counting patterns are not applicable
  • bin processing in divDyn() had potential issues with negative integer bin numbers

Deleted

  • The inf argument of divDyn(), that an unncessary complication

[0.6.2] - 2018.10.22

Added

  • The collapse() and seqduplicated() utility functions.
  • The 'zerodur' argumnet to the fadlad() function
  • Hexadecimal colour values to the 'stages' table.
  • The 'boxes.col' argumnet is added to the tsplot() function to plot these colours.
  • The 'labels' argument to the the tsplot() function, that allows the user not to plot the labels within the boxes.

Changed/Fixed

  • The stage identification 'Thanetian' was changed to 'Selandian-Thanetian in the 'stages' object to better reflect what the interval really is. It also had a typo in the 'per' column, at the Ordovician/Silurian boundary. The abbreviation of the Bartonian stage was changed to 'Brt' as 'Bar' was already assigned to the Barremian, causing plotting errors.
  • Bug in the 'noNAStart' argument of the binstat() function, causing inappropriate function return
  • tsplot() now allows y-axis reversal, e.g. ylim=c(4,-1)
  • fix of bug in subsample() that resulted in an error message when the first randomly chosen species had higher adjusted frequency than the quorum

[0.6.1] - 2018.10.01

Added

  • the singletons() function to quickly return single-occurrence, single-reference, single-interval and similar taxa
  • citation file

Changed

  • typo correction in the 'stages' table: 'Ordiovician' entries in the 'period' column were corrected to 'Ordovician'
  • minor changes in help files.

[0.6.0] - 2018.09.17

Added

  • the indices() function to calculate some basic diversity indices within the package. Please feel encouraged to use the rest from the 'vegan' package.
  • the binstat() and sumstat() functions. Binstat calculates bin-specific indices and sampling metrics, sumstat() calculates those relevant for the entire occurrence database. Most functionality of the deprecated sampstat() function is in binstat.
  • forgotten proper cleanup of dynamic libraries upon package unload

Changed

  • material in the sampstat() function was reorganized to two separate functions, see above

Deleted

  • the deprecated crDD() function and the old plotTS() functions were deleted from the package

[0.5.2] - 2018.09.02

Added

  • x argument for sampstat() to calculate maximum quotas with OxW subsampling.
  • the "none" subsampling type to subsample(). This argument will skip the subsampling part, but reruns the applied function in the trials, nevertheless.

Changed

  • the map() function was renamed to categorize() to better reflect its intended use

[0.5.1] - 2018.08.31

Changed

  • example bin identifier changes (from 'slc' to 'stg')
  • the subsample(), subtrialCR(), subtrialOXW(), subtrialSQS() functions now automatically omit rows that have NA entries in the 'bin' variables.
  • the 'stages' object now contains dates from Ogg et al. 2016
  • bin durations were added to both the 'stages' and 'bins' objects
  • the 'stratkeys' and 'keys' objects were updated to version 0.9.2

[0.5.0-1] - 2018.08.29

Changed

  • stratigraphic assignment objects (in 'keys') now have a -1 entries for empty strings

[0.5.0] - 2018.08.20

Added

  • bug fix that made R crash randomly
  • subsampling trial functions (subtrialCR(), subtrialOXW(), subtrialSQS()) and cleaned help files for 'subsample()'
  • multiple bin entry support for 'ranges()'
  • proper Description in description file

Changed

  • the functions 'plotTS()' and 'fadLad()' were renamed to 'tsplot()' and 'fadlad()' for easier typing.
  • 'stratkeys' and the corresponding 'keys' updated to v0.9.1
  • the 'sampstat()' function no longer outputs empty variables when the argument columns are set to NULL

Deleted

  • the 'exact' method implementation for SQS as it was slow and and incorrect. The 'inexact' method was confirmed with the iNEXT package.

[0.4.2] - 2018.07.24

Added

  • the ranges() function to plot occurrence data and stratigraphic ranges over time (see examples)
  • fadLad(): function defenses
  • fadLad(): two bin columns are now allowed as input (for age uncertainty estimation)
  • fadLad(): the ages argument for inverting the time axis
  • fixes to conform to the CRAN requirements

Changed

  • plotTS() now allows "no-boxes" plotting, and multiple layers of boxes

[0.4.1] - 2018.07.07

Added

  • function defenses
  • fixes to conform to the CRAN requirements

Changed

  • default settings for the sampstat() and subsample() functions to increase flexibility and user-friendliness
  • the intact argument of subsample() was separated to the rem and keep arguments, to enable negative time-slice identifiers.

[0.4.0] - 2018.06.29

Added

  • the first vignette is now included
  • bug fix for the parts() function. Due to the overplotting of polygons, the RGBA colours were not appropriately visualized
  • bug fix to the omit() function's binref method.
  • the "total" method for the sampstat() function
  • documentation to the built in datasets
  • the map() function to resolve information downloaded from the PaleoDB
  • 'keys' to the stratigraphic and environmental resolution, based on the FossilWorks dynamic timescale ?keys
  • the 10 million year timescale of the Paleobiology Database, ?bin

Changed

  • The sampstat() function now outputs a data.frame, instead of a matrix.
  • the 'method' argument of subsample() was renamed to 'type' to avoid problems with argument distribution with the frequent 'method' argument name

Deleted

  • The previously added bayesian method from the affinity() function. The method had problems and is under investigation.

[0.3.1] - 2018.06.04

Added

  • method argument for the affinity() function, allows implementation of a simple majority rule (method="majority") or the Bayesian approach of Simpson and Harnik (2009, method="bayesian")

Changed

  • the affinity() function was also completely reprogrammed

[0.3.0] - 2018.06.01

Added

  • continuous time entry is now possible for the divDyn() function. (does not yet work with subsampling!!!!)
  • the breaks argument to the divDyn() function

Changed

  • the examples and defaults match the current download from the Paleobiology Database
  • the previous 'scleractinia' example dataset was renamed to 'corals' for the sake of simplicity

[0.2.12] - 2018.05.17

Added

  • na.rm argument for the shades() function to omit gaps in plotting of the time series
  • bug fix for the shades() function, single rows bounded by rows of NAs (gaps) from above and below do not crash the function anymore

[0.2.11] - 2018.05.17

Added

  • bug fix for the plotTS() function, enables log scaling of y axis with plot.args=list(log="y")
  • the parts() function for efficient plotting of proportion/count data over time

[0.2.10] - 2018.05.13

Added

  • proportional extinction and origination rates to the divDyn() function
  • the omit() function for culling occurrence datasets (kind of slow yet)

Changed

  • argumentation of the divDyn function was extended to accomodate the omission of occurrences within the function (optional)

[0.2.9] - 2018.05.09

Changed

  • the 'cr' method of the subsample() function was rewritten in C++ and with Rcpp classes for faster performance
  • fixed bug in the subsample() function, when custom functions produce vector output

[0.2.8] - 2018.05.01

Added

  • multiple versions of the shareholder quorum subsampling (SQS) routine to subsample()
  • the sampstat() function, that outputs basic sampling stats for the time slices
  • useFailed argument to subsample(). Changes output depending on whether the subsampling quota/quorum is reached.
  • bug fix for the CR method in subsampling

Changes

  • argument distribution in the subsample() function, FUN argument simplified to a single function

Planned

  • the subsampling routines will be remodularized so that their argument becomes the dataset, rather than the individual columns. This will allow the support for custom subsampling functions.

[0.2.7] - 2018.02.01

Changes

  • bug (due to output changes in fadLad) and speed fixes for the affinity() function. The interface also changed, it now outputs a single vector instead of a data.frame.
  • bug fix in the ratesplit() function argument distribution. The "combine" version works properly now.

Change log

[0.2.6] - 2018.01.26

Added

  • John Alroy's (2015) second-for-third extinction/origination proportions/rates to the divDyn() function

[0.2.5] - 2018.01.22

Added

  • survivors() function to calculate survivorship probabilities

Changes

  • the 'subseries()' function was renamed to 'subsample()' for easier application
  • the 'fadLad()' function was redrafted for speed

[0.2.4] - 2018.01.15

Added

  • the the "oxw" method for the subseries() function. This implements occurrence-weighted by list subsampling.

[0.2.3] - 2018.01.08

Added

  • the subseries() function to execute certain functions with subsampling applied.

[0.2.2] - 2017.12.18

Added

  • the shades() function for plotting distributions of values arranged in a time series

[0.2.1] - 2017.12.12

Added

  • the ratesplit() function for selectivity tests
  • period abbreviations for the 'stages' object

Changes

  • plotTS() function default changes

[0.2.0] - 2017.12.11

Changes

  • added Rccp import
  • divDyn() updated to v2, ca. 150x faster
  • installation changes

[0.1.6] - 2017-12-04

Added

  • the plotTS() time scale plotting function
  • examples were updated

[0.1.5] - 2017-11-27

Added

  • the streaklog() and whichmaxstreak() functions

[0.1.4] - 2017-11-22

Changes

  • documentation

[0.1.3] - 2017-11-21

Changes

  • output variable names in the divDyn() function

Added

  • the first version of the crDD() function is added.

Notes

Pre-open versions were not registered.

Reference manual

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install.packages("divDyn")

0.8.0 by Adam T. Kocsis, 3 months ago


Report a bug at https://github.com/divDyn/r_package/issues


Browse source code at https://github.com/cran/divDyn


Authors: Adam T. Kocsis , John Alroy , Carl J. Reddin , Wolfgang Kiessling


Documentation:   PDF Manual  


CC BY 4.0 license


Imports Rcpp, stats, graphics, grDevices

Suggests knitr, rmarkdown, vegan, icosa

Linking to Rcpp


See at CRAN