divDyn 0.8.2 - 2022-09-05
CRAN release: 2022-09-05
Added
- the matchtime() function from chronosphere 0.4
- defense against trying to use divDyn() as applied function in subsample() when bin=NULL
- the probs argument to modeltab() following Reddin et al. 2021
Changed
- subsample() will produce warnings instead of halting when the variables ‘tax’ or ‘bin’ has NAs in them. The corresponding rows are omitted automatically.
- changed bitwise and to boolean in Engine.cpp
- regenerated documentation for compatibility to HTML5, corrected some entries
- Fixed mismatching data object keys$lat, which indicated intervals for absolute paleolatitudes instead of actual paleolatitudes.
- Fixed error, when parts() was invoked for "" category.
divDyn 0.8.0 - 2019-06-12
CRAN release: 2019-06-12
Added
- Support for ‘tibble’ type input data.frames.
- The tsbars() function.
- The ‘age’ argument for the divDyn() and fadlad() functions. With the previous composite time argument (‘bin’) it was difficult to handle both contiunous age and discrete bin entries, as the two implied different direction of time and applicability in the package functions. The argument ‘bin’ is now reserved for discrete entries, where bin number increases from earlier to later intervals. The argument ‘age’ is used for continuous, automatically binned time, where time flows from higher to lower numbers. The ‘age’ argument will be added to the binstat() function in future versions.
- You can reverse this pattern by toggling the added ‘revtime’ argument.
- The repmatch() function is now exported from the package namespace. This is the function that is called to match and average the subsampling output. You will probably not need this, but just in case.
- The ‘bin=NULL’ option is now valid for the subsample() function, specifying subsampling processes that are not iterated over mutliple time bins. This allows the application of sampling-based rarefaction, SQS and so on. With this configuration, the function can also accept vectors as the primary argument.
- The ‘na.rm’ argument is added to the subsample() function. The inclusion of this argument is part of a more scrutinous checking protocol for missing values.
- The slice() function is now exported from the package namespace. This function is used by the divDyn() function for discretizing (slicing) the continuous time dimension. Doing this separately is a prerequisite of running subsample() on the data.
- The ‘depenv’ element to the ‘keys’ data object. This addition maps entries in the ‘environment’ field of the Paleobiology Database to “onshore” or “offshore” settings.
- Option to supress loop counting output in the subsample() function (‘counter=FALSE’).
Changes
- The divDyn() and binstat() functions both output the names of the ‘bins’ in the a column that has the ‘bin’/‘age’ argument as a name. Note that in previous versions this was a hard-coded ‘“bin”’ character string. The occasional empty rows that result from using largen than 1- bin numbers now have the bin numbers in the
column instead of NAs. - The subsample() function is updated to version 2.0, with a lot of additions. The output of the subsample() function is constrained to match the output of the FUN argument function.
numbers are no longer NA, when FUN=divDyn, and when bins fail the subsampling trials (too low quota) and the output table dimensions do not change, even if bins are omitted from the start or end of the series. THe reorganized function allows additional improvements that will be added in the next version of the package. - The divDyn() and binstat() functions have a rownames variable that is a replicate of
column. - The ‘zerodur’ argument of the fadlad() function is renamed to ‘diffbin’ and is restricted to be used with binned entries.
- If ‘bin!=NULL’ then ‘output=list’ option of subsample() returns the failed bins (accessible as failed).Thelistcontainingtrialresultscanbeaccessedas′results’.
- If the last bin is supplied as ‘rem’, the dimensions of the output of subsample() will not change, because the interval will be included in the prototype calculation.
- The abbreviation for the Triassic in the ‘stages’ internal data.frame is changed from ‘T’ to ‘Tr’ (suggestion by V. Roden)
- The ‘bins’ internal time scale object was renamed to ‘tens’. The columns
and were also replaced with ‘ten’ to avoid confusion. - All functions of the package now use the conventional ‘x’ as the primary function argument, typically denoting the occurrence database. This change was necessary to streamline the passing of function objects. Accordingly, the rarely used x-exponent of the OxW subsampling method was changed from ‘x’ to ‘xexp’.
- The default ‘xlab’ of the tsplot() function was changed to “Age (ma)” from “age (ma)”.
- Some default arguments of the omit() function were changed from the Paleobiology Database defaults, ensuring proper argument flow.
- The package now depends on R versions that are newer than 3.5.0.
Deleted
- The ‘ages’ argument of the divDyn() and fadlad() functions was removed due to the re-organization of the time-argumentation.
Fixed
- The function subsample() crashed when FUN was set to ‘divDyn’, and the output resulting from its application on the subsample trial dataset did not have have the same dimensions as the result of divDyn() when it was applied to the total dataset. Note that this matching of the ‘trial results’ is only viable when the data.frame output of FUN has a ‘rownames’ attribute.
divDyn 0.7.1 (build 670) - 2019-02-18
CRAN release: 2019-02-19
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
divDyn 0.7.0 (build 642)- 2019-01-08
CRAN release: 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.
divDyn 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
divDyn 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
divDyn 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
divDyn 0.5.2 - 2018-09-02
divDyn 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
divDyn 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
divDyn 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
divDyn 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
divDyn 0.3.1 - 2018-06-04
divDyn 0.3.0 - 2018-06-01
divDyn 0.2.10 - 2018-05-13
divDyn 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