goeveg 0.7.9
syntable(): Fixes in fidelity calculation when using
the u-value; added Fishers’s exact test to exclude non-significant
fidelity
syntable(): Added options for standardization of sample
group size
hcr_resampling(): Added checks for groups limits
- Harmonized terminology between
synsort() and
syntable(): Both refer to groups instead of clusters
now.
goeveg 0.7.8.
- New function
hcr_resampling() to perform
heterogeneity-constrained random (HCR) resampling (Lengyel, Chytrý &
Tichý, 2011)
syntable(): Added new options of fidelity calculation
(u-value and Ochiai index); improved speed using more vectorised
computations
syntable(): Added option to calculate synoptic tables
from long-format vegetation data; implemented with
data.table for faster performance on large databases.
synsort(): Added method = "totalfreq"
(order species by overall frequency) and method = "manual"
(order by a user-supplied vector).
synsort(): The species–sample matrix is no longer
returned by default (for faster performance on large datasets); set
samples = TRUE to include it.
synsort(): Added cluster_order to select
and order cluster columns; columns not listed are omitted.
goeveg 0.7.6
per2cov(): Fixed a mistake leading to wrong cover value
assignments in specific cases
goeveg 0.7.5
syntable(): Added argument to define number of decimal
places in results
clean_matrix(): Empty cell values are transformed to 0;
fixed to work correctly with non-numeric values in data tables
goeveg 0.7.4
cov2per and per2cov: Added option to
transform with individual scales per sample
trans_matrix(): Added option rmchar to
remove the first character of the original column names
goeveg 0.7.3
- New function
clean_matrix() to remove species without
occurrences (frequency = 0) and samples without species from a species
matrix in one simple step
- New function
trans_matrix() to transpose a species
matrix, while preserving correct species and sample names.
- Simplified function
merge_taxa() with increased
performance
- Added option
backtransform to decide whether
cover-abundance values should be kept as percentage cover or
back-transformed into original cover-abundance values
- Option
drop_zero renamed to clean_matrix
and set on FALSE by default
cov2per: Fixed an error when providing a data frame
with only one column as community data
syntable: Fixed an unnecessary warning message
occurring at cover value transformation
goeveg 0.7.2
- Cover-abundance scales:
- Added scale “niwap” from Lower Saxony species survey programmes
(Schacherer 2001)
- Added
x-value to presence/absence scale
merge_taxa():
- returns names of merged taxa only once (not for each relevé)
- added option
drop_zero to decide whether species
without occurrences or empty samples should be removed or kept
- fixed an error when providing individual scales for each sample
syntable() and merge_taxa() automatically
repair imported tables with empty character values (““)
goeveg 0.7.1
syntable() can now handle factorial variables for
defining clusters, e.g. to summarize relevés according to pre-defined
categories and is more flexible regarding the format of the community
matrix
- Terminology was harmonized between different functions
goeveg 0.7.0
- New functions added:
merge_taxa() for merging taxa/species with identical
names
cov2per() and per2cov() for conversion
between cover-abundance codes and percentage cover
dimcheckMDS() is renamed into
screeplot_NMDS() with enhanced description and progress
bar
goeveg 0.6.5
- Fixed wrong species labeling in
racurve() when
freq = TRUE
goeveg 0.6.4
- Added functions
deg2rad() and rad2deg()
for conversion between radians and degrees
- Updated data table
schedenenv
goeveg 0.6.3
- Fixed wrong p-value calculation for GLMs in
specresponse()
- Fixed problem with NAs in
specresponse() when showing
point values
goeveg 0.6.2
- Added na.action argument to
specresponse()
goeveg 0.6.1
- Explained deviances and p-values are now printed in
specresponse(). Full model results are returned in an
(invisible) object.
- Added functionality to select the least abundant (rarest) species in
ordiselect()
goeveg 0.6.0
- (Re-)added functions for calculation and sorting of synoptic tables:
syntable() and synsort()
- Comprehensive update for
ordiselect(). Now returns
exact proportion of selected species. Correction in selection to axis
fit limits. Variable fit now only works with factor centroids.
- Updated help pages
goeveg 0.5.1
- Fixes in references and value tags
goeveg 0.5.0
- Removal of functions
synsort() and
syntable() due to unsolved incompatibilities
goeveg 0.4.4
- Added lwd argument for
specresponse()
goeveg 0.4.3
- Added xlim & ylim arguments for
racurve()
- Added na.rm argument for
ordiselect()
goeveg 0.4.2
- Small fixes, fixed package dependencies
- Spell checking
goeveg 0.4.1
- Added new functions for calculation and sorting of synoptic tables:
syntable() and synsort()
goeveg 0.3.3
goeveg 0.3.2
- Merged
specresponses()/specresponse() into
one single function specresponse()
- Better selection method of polynomial GLMs and GAMs in
specresponse()
goeveg 0.3.1
- Fixed use of external functions (
gam(),
rdist())
- Max. of 3 polynomials in automatic GLM selection of
specresponse()
goeveg 0.3.0
- Fixed and renewed function
specresponse()/specresponses(): now works also
with NMDS, includes zero values and is based on presence/absence data
(logistic regression). Instead of cubic smoothing splines the function
now uses GLMs/GAMs.
goeveg 0.2.0
- Added functionality to use frequencies in
racurve()
- Added functionality to label species in
racurve()
- New (invisible) output in
racurve()
- Package checked and tested on OS X
goeveg 0.1.7
- Added functionality for labeling species in
racurve()
- Corrected spelling mistakes
goeveg 0.1.6