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Version 4.33
(Committed 2025-03-21) ->
CRAN
Modified functions:
- Fav
- added ‘inv’ argument to compute instead probability from
favourability
Other modified files:
- NEWS
- reformatted and converted to .md to work with news()
Version 4.32
(Committed 2025-02-24)
New functions:
Modified functions:
- cleanCoords
- fixed bug when input data is SpatVector
- ‘coord.cols’ ignored with warning if provided and input is
SpatVector
Version 4.31
(Committed 2024-12-27)
Modified functions:
- partialResp
- fixed bug when only one variable in model
- polygon instead of lines for confidence interval
- new argument se.mult, default 1.96 for the 95% confidence interval,
but can be changed e.g. to 1 (for just the SE) or 0 (for no CI)
- initial plot with type=“n” and points added if plot.points=TRUE,
removing boilerplate code
- added args ‘reset.par’ and ‘…’ for plot()
- selectAbsences
- moved “Absences not enough…” section upwards, avoiding unnecessary
remaining computations
- distPres
- removed double loop to increase efficiency
- new default method “auto”
- option to use faster methods like haversine and cosine distance if
packageVersion(“terra”) >= “1.8.7”
Version 4.30
(Committed 2024-12-16)
New functions:
Version 4.29
(Committed 2024-12-12) ->
CRAN
Modified functions:
- getRegion
- added ‘dist_mat’ argument
- changed default ‘weight’ to FALSE, as it looked too restrictive
Version 4.28
(Committed 2024-12-05)
Modified functions:
- cleanCoords
- added ‘extend’ argument, default 0.1 to increase the output plot
extent by 10% of the input coordinates range
Version 4.27
(Committed 2024-11-22)
Modified functions:
- fuzzyOverlay
- fixed bug for raster inputs with NA pixels (reported by Jakub
Nowosad:
https://github.com/AMBarbosa/fuzzySim/issues/2#issue-2679366909)
Other modified files:
- getRegion.Rd
- selectAbsences.Rd
- added example with bias layer
Version 4.26
(Committed 2024-10-29) ->
CRAN
Modified functions:
- gridRecords
- output is SpatVector only if input is too
- selectAbsences
- added data.frame() to fix error when input SpatVector
Version 4.25
(Committed 2024-10-24)
Modified functions:
- selectAbsences
- ‘bias’ can now be a raster layer
- modelTrim
- implement categorical variables in phylolm models
Version 4.24
(Committed 2024-10-03)
Modified functions:
- fuzSim, simMat, fuzzyOverlay, modOverlap, fuzzyRangeChange
- simMat
Other modified files:
- fuzzyOverlay.Rd
- ‘op’ argument itemized list of options
- NAMESPACE
- removed import of utils::installed.packages() [now using
.packages(all.available = TRUE) instead]
Version 4.23
(Committed 2024-09-27)
Modified functions:
- getRegion
- labels now appear for all clusters in plot
- gridRecords, selectAbsences
- output plot SpatVector when ‘terra’ available
Version 4.22
(Committed 2024-09-26)
Modified functions:
- getRegion
- hclust() now with method = “single”
- cutree() with h = clust_dist (new argument)
- fixed bug in ‘weight’, which wasn’t correctly ordered (replaced
merge with match)
- ‘weight’ argument now also applies to type=“width”
Version 4.21
(Committed 2024-09-25)
Modified functions:
- distPres, selectAbsences
- add ‘CRS’ argument; if provided, terra::distance() is used
- distPres
- getRegion
- fix plotting error, now specifying ‘terra::’ before plot() and
text()
Version 4.20
(Committed 2024-09-24)
New functions:
Version 4.13
(Committed 2024-09-17)
Modified functions:
- modelTrim
- implemented for ‘phylolm’ models
- added ‘phy’ and ‘verbosity’ arguments
- changed ‘if (class(model) %in% c(“glm”, “lm”))’ to ‘if
(all(class(model) %in% c(“glm”, “lm”)))’, otherwise CRAN check
error
Other modified files:
Version 4.12
(Committed 2024-06-03)
New functions:
Version 4.11.1
(Committed 2024-03-07)
Modified functions:
- FDR, multGLM, corSelect
- added argument ‘test’ (default “Chisq” for back-compatibility;
future default probably “Rao” score as in SPSS)
- stepByStep
- message and NA outputs if model has no variables
Version 4.11
(Committed 2024-03-06)
Modified functions:
- stepByStep
- added option select=“p.value” and associated arguments
Other modified files:
- stepwise.Rd
- changed ‘sp.col’ in Examples, for a model where a variable is
included and then dropped
Version 4.10.8
(Committed 2024-03-05)
Modified functions:
- appendData
- ‘data1’ and ‘data2’ coerced to data.frame (to work e.g. for
SpatVectors)
- stepByStep
- ‘data’ can now be a ‘glm’ model object, from which the order of the
variables will be taken
Version 4.10.7
(Committed 2024-01-24) ->
CRAN
Modified functions:
- selectAbsences
- added ‘dist.mat’ argument for ‘distPres’
- updated help file to reflect this
Other modified files:
- distPres.Rd
- corrected typo “euclidian” -> “euclidean”
- mention that (external) spherical distance is recommended for large
extents
- mention that ‘method’ is only used if ‘dist.mat’ is not
provided
Version 4.10.6
(Committed 2023-11-02)
Modified functions:
- corSelect
- fixed incorrect use of all.equal() to compare results between
different ‘select’ criteria (thanks to bug report by Jose Carlos
Guerrero)
Other modified files:
- corSelect.Rd
- mention {collinear} pkg under “See also”
- mention that method ‘pearson’ is recommended for >30 rows,
‘spearman’ for >10 rows (as in ?collinear::collinear)
- fuzSim.Rd
- mention fuzzy Jaccard = weighted Jaccard (Ioffe 2010), overlap,
coincidence, consistence (Real et al. 2010)
Version 4.10.5
(Committed 2023-10-04) ->
CRAN
Modified functions:
- corSelect
- added ‘cor’ to ‘select’ criteria
- getPreds
- replaced ‘requireNamespace(raster)’ with ‘raster %in%
rownames(installed.packages())’, to avoid loading the pkg if
unnecessary
== # Version 4.10.4 ### (Committed 2023-09-28) ==
Modified functions:
- cleanCoords
- added ‘year.min’ and ‘year.na.pass’ arguments
== # Version 4.10.3 ### (Committed 2023-09-25) ==
Modified functions:
- appendData
- added ‘add.source’ argument
- x and y arguments renamed to data1 and data2
- warning when no matching columns
- out data frame created empty, instead of taking data1 values and
then converting to NA
- gridRecords
- replaced ‘requireNamespace(raster)’ with ‘raster %in%
rownames(installed.packages())’, to avoid loading ‘sp’ and triggering
all the deprecation warnings
Other modified files:
- cleanCoords.Rd
- now states that row names are carried from input dataframe
== # Version 4.10.2 ### (Committed 2023-09-23) ==
New functions:
== # Version 4.10.1 ### (Committed 2023-07-04) ==
Modified functions:
- cleanCoords
- added ‘terra::’ before plot() on SpatVector objects, to prevent
newly appeared error
Other modified files:
- Fav.Rd
- now states that ‘model’ or ‘pred’ must have been obtained with
weights=NULL
- corSelect.Rd
- added “however” references against dropping correlated
variables
== # Version 4.10 ### (Committed 2023-05-24) ==
Modified functions:
- multGLM
- added ‘coeff’ argument to pass to ‘corSelect’, and changed
‘cor.thresh’ default accordingly
- precluded error when no variables pass corSelect
== # Version 4.9.13 ### (Committed 2023-05-22) ==
Modified functions:
- corSelect
- fixed bug that didn’t allow correctly reporting the selected
variables when coeff=FALSE
== # Version 4.9.12 ### (Committed 2023-05-21) ==
Modified functions:
- corSelect
- added ‘coeff’ argument; if FALSE, high correlations are identified
based on p-value (not coefficient) of correlation
- ‘p.value’ column added to ‘high.correlations’ output table
- fixed bug when there’s >1 categorical variable to exclude a
priori
== # Version 4.9.11 ### (Committed 2023-05-17) ==
Modified functions:
- multGLM
- warning emitted if select=“p.value” and trim=TRUE
- started implementation of ‘block.cols’ argument (still not
useable)
== # Version 4.9.10 ### (Committed 2023-04-21) ==
Modified functions:
- corSelect
- ‘select’ default now VIF if ‘sp.cols’ is null
- ‘select’ can now be null
- message displayed saying what ‘select’ criterion was used
- help file updated accordingly
== # Version 4.9.9 ### (Committed 2023-04-14) -> CRAN ==
Modified functions:
- cleanCoords
- added arguments ‘rm.abs’ and ‘abs.col’
- when all records are removed, return ‘data’ with zero rows instead
of error
- input ‘data’ can also be a SpatVector of points, in which case
output is too
- ‘coord.cols’ default now NULL, can be taken from ‘data’ if class
‘SpatVector’
- ‘coord.cols’ can be NULL, in which case only the other removal
criteria (absences, coordinate uncertainty) are applied
- gridRecords
- input ‘pres.coords’ and ‘abs.coords’ can also be SpatVector of
points
== # Version 4.9.8 ### (Committed 2023-03-06) -> CRAN ==
Modified files:
- CITATION
- removed old-style personList(), and replaced citEntry() with
bibentry(), as per new CRAN requirements
Version 4.9.8
(Committed 2023-02-22)
Modified functions:
- selectAbsences
- added ‘df’ argument
- output df now ordered by as.integer(rownames) rather than character
rownames (1, 10, 100, 2, …)
- points now plotted in this order: unselected absences, selected
absences, presences on top
- gridRecords
- points now plotted in this order: absences, presences on top
Version 4.9.7
(Committed 2023-01-25)
Modified functions:
- cleanCoords
- added ‘plot’ argument
- changed default ‘uncert.limit’ from Inf to 50000
Version 4.9.6
(Committed 2023-01-24)
New functions:
Modified functions:
- cleanCoords
- fixed bug in ‘rm.imprecise’
Version 4.9.5
(Committed 2023-01-20)
New functions:
Modified functions:
- fuzzyRangeChange
- added argument ‘plot.type’
- default ‘plot.type’ now “lollipop”
- entropy
- added argument ‘plot.type’
- default ‘plot.type’ now “lollipop”
Version 4.9.4
(Committed 2023-01-12)
Modified functions:
- pairwiseRangemaps
- replaced ‘PBSmapping’ (and consequently ‘sp’ and ‘maptools’) with
‘terra’ (future-proof and much faster)
Other modified files:
- DESCRIPTION
- packages ‘PBSmapping’, ‘sp’ and ‘maptools’ removed from
‘Suggests’
Version 4.9.3
(Committed 2023-01-09)
Modified functions:
- gridRecords
- corSelect
- non-numeric variables excluded with warning (instead of causing
error)
- multGLM
- corrected bug that miscounted the variables excluded by FDR when
FDR.first=FALSE (affecting only console messages)
- total N variables now reported when TSA=TRUE (i.e. “… 46 with the
spatial trend variable” instead of just “…plus the spatial trend
variable”)
- modelTrim
- added family <- family(model) when method = “summary”, as per bug
report by J.C.Guerrero email 30/12/2022
Version 4.9.2
(Committed 2022-10-27)
Modified functions:
- multGLM
- added ‘FDR.first’ argument
Other modified files:
- multGLM.Rd
- added recommendation to set trim=FALSE when select=“p.value”
- added JCG funding acknowledgment to Note
- fuzSim.Rd
- help file now mentions Jaccard and Sorensen also as recommended
metrics for model evaluation
Version 4.9.1
(Committed 2022-10-13)
Modified functions:
- corSelect
- added ‘verbosity’ argument
- message emitted saying how many vars selected and excluded (like in
‘FDR’) if verbosity > 0
- message emitted saying which vars selected and excluded if verbosity
> 1
- FDR
- argument ‘verbose’ replaced with ‘verbosity’ (with warnings)
- message emitted saying which vars selected and excluded if verbosity
> 1
- multGLM
- argument ‘verbose’ for ‘FDR’ replaced with ‘verbosity’ (as per ‘FDR’
change above)
- argument ‘select’ now accepts additional criterion “p.value”, in
which case ‘stepwise’ used instead of ‘step’
- added arguments test.in, test.out, p.in and p.out to pass to
‘stepwise’
- trim=TRUE reverts back to using ‘modelTrim’ (rather than ‘stepwise’
with direcction=‘backward’ as in previous experimental versions)
- argument trim.fun (added in previous experimental versions)
removed
Version 4.9
(Committed 2022-10-11)
Modified functions:
- summaryWald
- fixed bug when model has no variables
- stepwise
- break loop when a variable simultanously meets the criteria for
inclusion and exclusion
Other modified files:
- stepwise
- help file with new references (two against AIC, and one more against
stepwise)
Version 4.8.1
(Committed 2022-08-01)
Modified functions:
- gridRecords
- moved if(na.rm) uppward to go back to using 5:ncol(result) instead
of names(result), which was causing problems with some raster names (bug
report by Alba Estrada)
- ordered result by ‘cell’ and removed (confusing) row names
- help file Examples now includes mapping multi-species gridded
presences
Other modified files:
- multGLM
- help file notes that ‘TSA’ uses “type=”Y” and is included in FDR,
corSelect, etc.
Version 4.8
(Committed 2022-07-21)
Modified functions:
- gridRecords
- warning if ‘species’ (not character or) has leading/trailing
spaces
- added check.names=FALSE to data.frame call, so that output column
names are exactly as the unique values of ‘species’ (even if they are
numbers), and the first species name doesn’t come out different from the
rest
- added last argument in abs.coords <- terra::crds(rst, df=TRUE,
na.rm=FALSE), otherwise some rows with missing data in some variables
would be missing from the result (bug report by Alba Estrada)
Other modified files:
- multGLM
- help file notes that ‘modelTrim’ and ‘stepwise’ have different
default significance thresholds, to explain why ‘stepwise’ may leave
more variables in the model
Version 4.7
(Committed 2022-07-07)
Modified functions:
- multGLM
- fixed message about N variables excluded by ‘modelTrim’ (now by
trim.fun)
- set trace=0 for ‘stepwise’
- fuzzyConsensus
- changed default biplot to FALSE, as it makes function much
slower
- fuzzyRangeChange
- changed “Stable presence” and “Stable absence” to “Stable positive”
and “Stable negative” to avoid erroneous interpretations
- added y axis label
Version 4.6
(Committed 2022-07-05)
New functions:
Modified functions:
- fuzzyRangeChange
- added ‘x.lab=TRUE’ argument, so user can set to FALSE and add labels
differently
- stepByStep
- added warning(“‘Favourability’ is only applicable when
family=binomial(link=‘logit’), so it was automatically set to
FALSE.”)
- multGLM
- added argument trim.fun=“modelTrim”, which can be changed to
“stepwise”
Version 4.5
(Committed 2022-06-15)
Modified functions:
- stepByStep
- added ‘k’ argument to pass to ‘step’ (allows approaching p<0.05;
https://www.researchgate.net/post/Why-stepAIC-gives-a-model-with-insignificant-variables-in-the-summarymodel)
- added ‘direction’ argument to pass to ‘step’ (implementation by Alba
Estrada)
Version 4.4
(Committed 2022-06-14)
Modified functions:
- fuzzyConsensus
- ‘cat’ message now mentions the number of input vectors
- multGLM
- added ‘cor.method’ argument (for ‘cor’ via ‘corSelect’; default
“pearson”)
- stepByStep
- ‘sp.col’ and ‘var.cols’ can now be column names, not just index
numbers
Version 4.3
(Committed 2022-06-01) ->
CRAN
Modified functions:
- fuzzyConsensus
- ‘data’ can also be SpatRaster
- removed unnecessary argument ‘fav.cols’ (as no other ’*.cols’
argument exists)
Version 4.2
(Committed 2022-05-31)
New functions:
Modified functions:
- Fav
- stops with error if any ‘pred’ is outside the [0,1] interval
(matching ‘fuzzyConsensus’)
Other modified files:
- DESCRIPTION
- added reference about the method, as suggested by Uwe Ligges after
previous CRAN submission
Version 4.1
(Committed 2022-05-15)
Modified functions:
- modOverlap
- improved help file and removed reference to requiring GLM
predictions
Version 4.0
(Committed 2022-05-02) ->
CRAN
New functions:
- prevalence (copied from ‘modEvA’ pkg)
Modified functions:
- bioThreat
- “white” changed to “grey” for 0-values to be visible on the map
- corSelect, FDR, fuzzyOverlay, integerCols, multConvert, multGLM,
multicol, multTSA, simMat, splist2presabs, stepByStep, transpose
- added data=as.data.frame(data), to avoid errors when input is
tibble
- bioThreat, Fav, favClass, fuzSim, fuzzyRangeChange, modOverlap,
sharedFav, spCodes
- added ‘unlist’ to avoid obscure error when input is one-column
tibble instead of vector
Version 3.96
(Committed 2022-03-22)
Modified functions:
- sharedFav
- improved help file and corrected a mistake (bug report by Alba
Estrada)
- replaced ‘main’ argument with ‘…’ for barplot (to accept also
‘las’)
- plot now produced in phases as computations are made, to have
something plotted even in case of error
- ‘conf’ can be set to NA, to avoid error and still get values and
plot (without CIs)
- returned value now includes ‘FOvI’ and ‘bins_table’
Version 3.95
(Committed 2022-03-22)
New functions:
rarity
vulnerability
entropy
Modified functions:
- spCodes
- added ‘verbosity’ argument
- ‘cat’ now used instead of red ‘message’ when OK no dupl codes
- corSelect
- replaced ‘…’ with arguments ‘use’ and ‘method’, the former
defaulting to “pairwise.complete.obs”
- simMat
- added ‘na.omit’ to ‘data’ in ‘stopifnot’, to avoid error when
NAs
- sharedFav
- added ‘bin_interval’ argument, currently accepting ‘0.1’ (the
default, for back-compatibility) or ‘quantiles’
- added Note to help file about possible error when overly small
bins
Version 3.9
(Committed 2022-03-13)
Modified functions:
- gridRecords
- result now ordered by “cells” column, instead of presences then
absences
- help file “Examples” changed to “elev” raster for more clarity
- included also example with multiple species
- corSelect
- added ‘family’ argument (to pass to FDR when ‘sp.col’ is not
NULL)
- fixed NA ‘excluded.vars’ output when input ‘var.cols’ is
character
- FDR
- added ‘Gamma’ for positive non-integer responses when
family=“auto”
Version 3.8
(Committed 2022-02-05)
Modified functions:
- gridRecords
- added ‘species’ argument for multi-species gridding
- ‘pres.coords’ (and ‘abs.coords’ if not NULL) automatically converted
with ‘as.data.frame’
- changed ‘raster’ to ‘terra’ in help file “Examples”
- fixed bug that did not grid abs.coords (if not NULL)
Version 3.7
(Committed 2022-01-21) ->
CRAN
Modified functions:
- corSelect
- fixed new CRAN check error (with ‘all.equal’ in ‘corSelect’) on
r-devel-linux-x86_64-fedora-clang and r-devel-linux-x86_64-fedora-gcc
(by manually setting the ‘tolerance’ argument for ‘all.equal’)
- Fav
- added import modEvA::mod2obspred
Other modified files:
- fuzsim.Rd
- updated Sorensen wikipedia link with ‘https’
Version 3.6
(Committed 2021-09-29)
Modified functions:
- Fav
- ‘model’ argument can now be of class ‘glm’, ‘gam’, ‘gbm’,
‘randomForest’ or ‘bart’
- ‘pred’ can now also be a ‘SpatRaster’ (‘terra’ pkg) object
- gridRecords
- ‘rst’ can now also be a ‘SpatRaster’ (‘terra’ pkg) object
- Raster* ‘rst’ coerced to SpatRaster if ‘terra’ pkg is installed
Version 3.5
(Committed 2021-09-04)
Modified functions:
- FDR
- fixed bug when using ‘pvalues’ as input (following bug report by
Stephen via modTools contact form)
Version 3.4
(Committed 2021-09-02)
Modified functions:
- gridRecords
- fixed bug when only one raster layer [ , drop = FALSE]
Version 3.3
(Committed 2021-04-24)
Modified functions:
- simMat
- added ‘verbosity’ argument
- replaced “25%-50%-75% done” with ‘utils::txtProgressBar’
- multTSA
- added ‘verbosity’ argument
- getPreds
- added ‘verbosity’ argument
- ‘data’ can now also be a RasterBrick (not only dataframe or a
RasterStack)
- Fav
- added ‘verbosity’ argument
- ‘pred’ can now also be a RasterLayer (not only a numeric
vector)
Version 3.2
(Committed 2020-12-12)
Modified functions:
- favClass (benefitting also bioThreat)
- added ‘is.na(fav) |’ to ‘stopifnot’ to avoid NA fail
Other changes:
- added Linero et al. (2020) to references of papers using fuzzySim
Version 3.1
(Committed 2020-09-18)
Modified functions:
- gridRecords
- added ‘absences’ logical argument
Version 3.0
(Committed 2020-02-03) ->
CRAN
Modified functions:
- gridRecords
- added ‘na.rm’ argument (default TRUE)
- fixed bug when no gridded absences (i.e. no absence AND not
presence)
Other changes:
- clarifications and typo/format corrections in the manual
Version 2.5
(Committed 2020-01-31)
Modified files:
Version 2.2.4
(Committed 2020-01-30)
New functions:
Modified functions:
- getPreds:
- replaced ‘if(“raster” %in% class(data))’ (no longer working) with
‘if (is(data, “RasterStack”))’
- added ‘Imports: methods’ to DESCRIPTION and ‘importFrom(“methods”,
“is”)’ to NAMESPACE
- if ‘data’ are raster, added ‘raster::’ before ‘stack’
Version 2.2.3
(Committed 2020-01-06)
Modified functions:
- multGLM:
- fixed id.col name in ‘predictions’ when id.col input as
character
Other changes:
- added ‘inst’ folder with article citation information
- removed ‘onAttach’ function with citation message on load
- added package URLs to DESCRIPTION file
Version 2.2.2
(Committed 2020-01-03)
Modified functions:
- multGLM:
- output now includes list of selected variables per model
- sp.cols, var.cols and id.col can now optionally be input as column
names rather than index numbers
Other changes:
- fixed length of some lines along the PDF manual
Version 2.2.1
(Committed 2019-10-18)
Modified functions:
- modOverlap:
- corrected typo in na.rm closing parentheses (reported by Heidi K.
Mod)
- Fav:
- slightly reduced probabilities of exactly 1, which would cause
division by zero (resulting Fav is still 1)
Version 2.2
(Committed 2019-03-10)
New functions:
Version 2.1
(Committed 2019-03-07)
New functions:
Modified functions:
- multGLM:
- spatial_trend variable in models (when TSA=TRUE and the spatial
trend is selected) now named after the response variable
(e.g. ‘sptrend_giraffe’)
- getPreds:
- fixed new bug by replacing ‘if (class(data) == “RasterStack”)’ with
‘if (“RasterStack” %in% class(data))’
Modified .Rd files:
- multGLM:
- added example with TSA=TRUE
Other changes:
- updated maintainer e-mail address
Version 2.0
(Committed 2018-12-05) ->
CRAN
Modified functions:
- multTSA:
- resulting model object now named ‘models’ rather than
‘TSA.models’
- corrected bug in coordinate polynomial names (if save.models =
TRUE)
Version 1.9
(Committed 2018-11-20)
Modified functions:
- distPres
- ‘inv’ now subtracts from 1 (after standardizing) rather than
dividing by 1
- multTSA:
- added ‘criterion’ argument, which can be ‘AIC’ (to use ‘step’) or
‘significance’ (to use ‘modelTrim’)
- added ‘…’ argument to pass to modelTrim
- introduced more informative coordinate polynomial names (visible if
‘save.models = TRUE’)
- added ‘simple = TRUE’ to ‘poly’ for speedup
- modelTrim:
- added ‘data’ argument to ‘update’, to avoid ‘attach’
- multGLM:
- added arguments ‘verbosity’, ‘TSA’ and ‘coord.cols’
- added ‘data = train.data’ to ‘step’, and ‘with(train.data’ to
‘model.formula’, so finally got rid of ‘attach’
- “Building model 1…” ‘message’ instances replaced with ‘cat’ so that
they are saved if ‘sink’ is used
Version 1.8.3
(Committed 2018-07-06)
Modified functions:
- multTSA:
- added argument ‘type’ which can be “Y”, “P” (the default, for
back-compatibility) or “F” (which substitutes the deprecated argument
below)
- deprecated argument ‘Favourability = FALSE’
Modified .Rd files:
- multTSA:
- documented argument changes described above
- pairwiseRangemaps:
- updated literature reference
webpage:
- added additional article citing fuzzySim
Version 1.8.2
(Committed 2018-05-23)
Modified functions:
- getPreds:
- ‘data’ can now be a RasterStack
Version 1.8.1
(Committed 2018-05-15)
Modified functions:
- multTSA:
- fixed bug when only one species was used
webpage:
- added articles citing fuzzySim
Version 1.8.0
(Committed 2017-07-07)
Modified functions:
Version 1.7.9
(Committed 2017-03-27)
Modified functions:
- multGLM:
- fixed bug when only one variabe passed to corSelect
- corSelect:
- added check that ‘data’ is not missing and is a data frame
- help file now states that corSelect is included as option in
multGLM
- added ‘use = “pairwise.complete.obs”’ to examples
- PDF manual:
- reduced several code line lengths to avoid overboard
Version 1.7.8
(Committed 2016-09-15)
Removed empty sections
from .Rd files
Modified functions:
- fuzzyRangeChange:
- underscore replaced with space in measure names
- x axis labels plotted instead of legend
- ‘col’ no longer supplied by default
Version 1.7.7
(Committed 2016-08-01)
Modified functions:
- pairwiseRangemaps:
- argument ‘chunks’ replaced with ‘nchunks’ for operative reasons
- added ‘subchunks’ argument for continuing interrupted runs
Version 1.7.6
(Committed 2016-05-05)
Modified functions:
- corSelect:
- removed error when no corrs above threshold
- sp.cols now NULL by default (to avoid error when missing)
- multGLM:
- FDR correction reverted to “fdr” by default
Version 1.7.5
(Committed 2016-04-26)
Modified functions:
- FDR:
- corSelect:
- BIC now included as selection criterion
- multGLM:
- added “select” argument (for ‘step’) - AIC or BIC
Version 1.7.4
(Committed 2016-04-15)
Modified functions:
- multGLM:
- FDR correction now “BY” by default
Version 1.7.3
(Committed 2016-04-12)
Modified functions:
- corSelect:
- error message when length(sp.cols) > 1
- message about excluded missing data
- added option sp.cols=NULL to get only high.cor.mat
- multGLM:
- added ‘correction’ argument to pass to ‘FDR’
Version 1.7.2
(Committed 2016-03-22)
Modified functions:
- fuzzyRangeChange:
- user can now choose which measures to calculate
- ‘loss’ now reported as originally negative
- results provided also as a barplot
Version 1.7.1
(Committed 2016-03-17)
Modified functions:
- multTSA:
- eliminated call to ‘attach’
Version 1.7
(Committed 2016-02-12)
New functions:
Version 1.6.3
(Committed 2015-12-02)
Modified functions:
- FDR:
- now uses only finite sp.col values
Version 1.6.2
(Committed 2015-11-23)
Modified functions:
- fuzzyRangeChange:
- corrected proportional changes to be relative to reference range
size, not total study area
- replaced “stable” with “stable presence” and added (fuzzy equivalent
of) “stable absence”
- replaced “change” with “balance” (overall loss/gain, not amount of
changed cells)
- result is now data frame, not named vector
- distPres:
Version 1.6.1
(Committed 2015-11-13)
Modified functions:
- fuzzyOverlay:
- added arguments ‘prop = TRUE’ and ‘overlay.cols = 1:ncol(data)’
- result now includes 4 (not 8) values, either sum or proportion
- result is now a named vector instead of a list
- ‘na.rm’ now TRUE by default
- fuzSim:
- added argument ‘na.rm = TRUE’
- multGLM:
- bug corrected in corSelect (was reporting but not really eliminating
variables)
- suppressMessages in corSelect
Modified help files:
fuzzyOverlay: modifications reflecting function changes
modOverlap: example now provided
fuzzyOverlay, fuzzyRangeChange, modOverlap:
- examples containing ‘jitter’ corrected to avoid values outside the
[0, 1] interval
fuzSim:
- examples now provided also for similarity between fuzzy data
- tables of significance for Jaccard and Baroni’s indices now
referred
Version 1.6
(Committed 2015-11-03)
New functions:
fuzzyOverlay (calculate row-wise intersection, union, expansion,
contraction or consensus among continuous model predictions)
fuzzyRangeChange (calculate overal loss, gain, and maintenance of
favourability between models)
Version 1.5
(Committed 2015-10-29)
New functions:
Modified functions:
- multGLM:
- ‘corSelect’ now included as additional option for variable
selection
- FDR:
- AIC now also calculated
- ‘model.type’ deprecated
- ‘family = “auto”’ by default
- ‘simplif’ argument added
Version 1.4
… and previous (edits I can
remember)
Modified functions:
- multicol:
- ‘model’ argument added (user can provide a model object instead of a
set of variables)
- variables in output are now ordered according to VIF
- simFromSetOps:
- the similarity index used is now mentioned in a message
- FDR:
- data input format changed, with former parameters ‘response’ and
‘predictors’ replaced with ‘data’, ‘sp.cols’ and ‘var.cols’ (for
coherence and compatibility with ‘multGLM’ function)
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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