SIMBA VERSIONS
Version 0.3-5
* Bug fix to the NAMESPACE (upon user request)
* Bug fix to mama()
* Argument waist added to batons
Version 0.3-4
* auc has been moved to package flux.
* There is a NAMESPACE now
* New start function
* Minor bug fixes to diffmean and mama
Version 0.3-3
* Bugfixes to function mps.f. Further the function is now
named mos.f
* New function mos.ft for the calculation of the (dis)similarity
of a focal plot to the pooled surrounding plots. This, like mos.f
represents measures of singularity
* New function CqN for the calculation of Chao et al.s probabilistic
multiple plot similarity indices.
* New function trudi for the calculation of true diversity on gamma,
alpha and beta scale
* New plotting function batonplot ---
* Bug fixes and updates to pcol and all related functions (the
functionality of permcor and mancor is now integrated in pcol
and permcor2 is now mantl and does the permutations). Thus, two
functions pcol (doing the handling) and mantl (doing the calculations)
remain.
* Deprecated: dfcor. The functionality is easy to be achieved using
lapply. An example is included in the help for mantl.
Version 0.3-2
* Added a neighbor definition possibility to rin. Now, also a number
of k nearest neighbors can be defined.
* Fixed some issues with many of the documentations especially
for pdf.
* Fixed a missing documentation: the data set bernina was undocumented.
* Now gives version number when loading.
Version 0.3-1
* rin, mps, mpd, mps.ave, mps.f, sos: A bunch of new functions
for the calculation of multiple plot similarity coefficients with
rin a wrapper function that allows for the application of all
other functions in a moving window across an array of plots.
* The older functions het2nbs, sim.het, sim.pat, sim.rel, sim.relt,
simn, sima that provided parts of that functionality in a different
way, have been removed from the package.
* symbol.size, new helper function. enables to easily create
something like bubble plots through all plot.xy methods
* auc, new function for integrating the area under a curve (line)
* bb2num, new function for translation of Braun-Blanquet scale
abundance values to cover percentages and vice versa.
* simbadocs, new function to view some documentation details
to the package
* ads.fbg, new function to maximize the relation with the
prescribed gradient and the resulting gradient when creating
an artificial species matrix with either ads, ads.hot or makead.
* fixed a bug in mama that caused an error if input was not well defined.
The function is now more robust. Updated documentation accordingly.
* fixed a bug in liste that has caused an error if the input
data.frame object had no rownames.
* fixed a bug in diffslope and expanded the function. Now also the
difference in intercept can be calculated (function diffic).
(take care with resc.y!!) accordingly a print function has
been added.
* New documentations for the new functions as well as updates
and bug fixes to many of the existent documentations
Version 0.2-5
* sim.yo, new function to create and calculate your own
similarity coefficient. data preparation as in sim but you
can give your own formula.
* dist.tmp, new function to calulate distance between the
variables or instances of a data-set in time. The two recordings
are to be given as two distinct matrices.
* updating an cleaning documentation and data-sets
* some functions (e.g. meanea, medea) were skipped
Version 0.2-4
* ads.hot, new function to create artificial data-set with
hotpots of species richness
* update to occ.time (printing methods)
* com.sim, new function to compare similarities between subsets
* sim: added some similarity measures (most of them found in
Shi 1993. the help was updated accordingly.
* ads.ternaries: new data-set, which contains artificial data
for the construction of ternary plots to inspect the behavior
of the asymmetric similarity indices in sim.
* updated the possibilities of neighbor definition in sim.pat,
sim.rel, sim.het, and sim. In a addition to specifying a radius
it is now possible to give two radiuses which define a ring
around each plot. All other plots falling into the ring are
considered as neighbors.
Version 0.2-3
* sim.tmp: similarity of plots in time. all similarity indices
provided by sim can be used to calculate similarity not between
plots but between timesteps
* occ.time: new function which allows to track changes in
species composition in time. the basic function is occ.tmp which
is called by occ.time to calculate changes in species occurence
for various time steps at once.
* sim.relt: significance testing for sim.rel
* sim.pat: changes to underlying functions simn and sima lead
to minor changes in sim.pat as well. sima and simn changed
considerably and handle presence/absence data better now
* sim.relt: significance testing for sim.rel
* sim.rel: new function for calculating additive partitioning
and relative similarity sensu Whittaker
* sim.het: significance testing for het2nbs. Furthermore a bug in
the underlying function was fixed
Version 0.2-2
* Updated and added documentation files
* Some for-loops are replaced by faster apply-functions.
* simdist is now obsolet. sim takes over its functionality.
If you give geographic coordinates the geographic distances
and related things are calculated in addition to similarities.
* sim.pat: new function for calculating similarity between a
focal unit and its neighbours.
* het2nbs: automatic calculation of mean similarity between
a focal unit and its neighbours (including the variation in
the single values)
* aslopect: calculate the similarity of sampling units regarding
their aspect and slope at the same time. follows the idea, that,
the more shallow the slope the less important are differences in
aspect in an ecological sense
Version 0.2-1
* meanea: new function for the calculation of running means, can
be applied to vectors as well as to data.frames, subsetter must
be given
* medea: new function for the calculation of running medeans, can
be applied to vectors as well as to data.frames, subsetter must
be given
* aslopect: calculate the similarity of sampling units regarding
their aspect and slope at the same time. follows the idea, that,
the more shallow the slope the less important are differences in
aspect in an ecological sense
* dfcor: calculate permuted correlation between a vector and a
dataframe with columns each containing a vectorized similarity
or dissimilarity matrix.
* diffslope, permcor, permcor2: bug fixes
* direct, direct2: results are now given as dist-object
Version 0.2-0
* Rewritten documentation files
* bcoov: new function for the calculation of Bray-Curtis distance
for one variable
* pcol: is now also capable of calculating permuted correlation
of a distance matrix (or vector) against a subsetting object
(containing distance classes or similar). background function
permcor was rewritten and is now faster. permcor2 and mancor are
new written functions to handle the different possibilities of
pcol.
* diffmean: new functions to calculate the difference in mean
and the F-value of two numeric vectors. Inference is obtained
by permutation.
* diffmich: new function to calculate the difference in the
parameters of Michaelis-Menten Kinetik fitted to PAM data
* diffslope: calculating and testing of significance the difference
in slope between two regressions.
* The most of the functions have now print and plot methods to
obtain nice output and plots.
Version 0.1-1
* Fixed bugs in documentation
* bcoov: new function for the calculation of Bray-Curtis distance
for one variable
* pcol: calculate permuted correlation on levels or strata. The results
are written to a data.frame which then contains for each level the
correlation estimate, the significance after permutation and the number
of cases which made up the level
* direct and direct2: calculation of direction classes for geographic
coordinates with two different class-divisions. classes are fixed and
cannot be set by the user (which might come in the future)
Version 0.1-0
* The first version. Could still be unstable.