Package: NEff
Type: Package
Title: Calculating Effective Sizes Based on Known Demographic
Parameters of a Population
Version: 1.1
Date: 2015-05-04
Author: Annegret Grimm, Bernd Gruber & Klaus Henle
Maintainer: Annegret Grimm <annegret.grimm@ufz.de>
Depends: msm, bit
Description: Effective population sizes (often abbreviated as "Neff") are essential in biodiversity monitoring and conservation. For the first time, calculating effective sizes with data obtained within less than a generation but considering demographic parameters is possible. This individual based model uses demographic parameters of a population to calculate annual effective sizes and effective population sizes (per generation). A defined number of alleles and loci will be used to simulate the genotypes of the individuals. Stepwise mutation rates can be included. Variations in life history parameters (sex ratio, sex-specific survival, recruitment rate, reproductive skew) are possible. These results will help managers to define existing populations as viable or not.
License: GPL-2
Packaged: 2015-05-15 10:22:28 UTC; grimm
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-15 21:42:41
Package: ff
Version: 2.2-13
Date: 2012-03-29
Title: memory-efficient storage of large data on disk and fast access
functions
Author: Daniel Adler <dadler@uni-goettingen.de>,
Christian Gläser <christian_glaeser@gmx.de>,
Oleg Nenadic <onenadi@uni-goettingen.de>,
Jens Oehlschlägel <Jens.Oehlschlaegel@truecluster.com>,
Walter Zucchini <wzucchi@uni-goettingen.de>
Maintainer: Jens Oehlschlägel <Jens.Oehlschlaegel@truecluster.com>
Depends: R (>= 2.10.1), bit (>= 1.1-12), utils
Suggests: biglm
Description: The ff package provides data structures that are stored on
disk but behave (almost) as if they were in RAM by transparently
mapping only a section (pagesize) in main memory - the effective
virtual memory consumption per ff object. ff supports R's standard
atomic data types 'double', 'logical', 'raw' and 'integer' and
non-standard atomic types boolean (1 bit), quad (2 bit unsigned),
nibble (4 bit unsigned), byte (1 byte signed with NAs), ubyte (1 byte
unsigned), short (2 byte signed with NAs), ushort (2 byte unsigned),
single (4 byte float with NAs). For example 'quad' allows efficient
storage of genomic data as an 'A','T','G','C' factor. The unsigned
types support 'circular' arithmetic. There is also support for
close-to-atomic types 'factor', 'ordered', 'POSIXct', 'Date' and
custom close-to-atomic types.
ff not only has native C-support for vectors, matrices and arrays
with flexible dimorder (major column-order, major row-order and
generalizations for arrays). There is also a ffdf class not unlike
data.frames and import/export filters for csv files.
ff objects store raw data in binary flat files in native encoding,
and complement this with metadata stored in R as physical and virtual
attributes. ff objects have well-defined hybrid copying semantics,
which gives rise to certain performance improvements through
virtualization. ff objects can be stored and reopened across R
sessions. ff files can be shared by multiple ff R objects
(using different data en/de-coding schemes) in the same process
or from multiple R processes to exploit parallelism. A wide choice of
finalizer options allows to work with 'permanent' files as well as
creating/removing 'temporary' ff files completely transparent to the
user. On certain OS/Filesystem combinations, creating the ff files
works without notable delay thanks to using sparse file allocation.
Several access optimization techniques such as Hybrid Index
Preprocessing and Virtualization are implemented to achieve good
performance even with large datasets, for example virtual matrix
transpose without touching a single byte on disk. Further, to reduce
disk I/O, 'logicals' and non-standard data types get stored native and
compact on binary flat files i.e. logicals take up exactly 2 bits to
represent TRUE, FALSE and NA.
Beyond basic access functions, the ff package also provides
compatibility functions that facilitate writing code for ff and ram
objects and support for batch processing on ff objects (e.g. as.ram,
as.ff, ffapply). ff interfaces closely with functionality from package
'bit': chunked looping, fast bit operations and coercions between
different objects that can store subscript information ('bit',
'bitwhich', ff 'boolean', ri range index, hi hybrid index). This allows
to work interactively with selections of large datasets and quickly
modify selection criteria.
Further high-performance enhancements can be made available upon request.
License: GPL-2 | file LICENSE
LazyLoad: yes
ByteCompile: yes
Encoding: latin1
URL: http://ff.r-forge.r-project.org/
Packaged: 2014-04-07 21:16:45 UTC; root
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-04-09 09:54:20
Package: bit64
Type: Package
Title: A S3 Class for Vectors of 64bit Integers
Version: 0.9-5
Date: 2015-06-24
Author: Jens Oehlschlägel <Jens.Oehlschlaegel@truecluster.com>
Maintainer: Jens Oehlschlägel <Jens.Oehlschlaegel@truecluster.com>
Depends: R (>= 3.0.1), bit (>= 1.1-12), utils, methods, stats
Description:
Package 'bit64' provides serializable S3 atomic 64bit (signed) integers
that can be used in vectors, matrices, arrays and data.frames. Methods are
available for coercion from and to logicals, integers, doubles, characters
and factors as well as many elementwise and summary functions. Many fast
algorithmic operations such as 'match' and 'order' support interactive data
exploration and manipulation and optionally leverage caching.
License: GPL-2
LazyLoad: yes
ByteCompile: yes
URL: http://ff.r-forge.r-project.org/
Encoding: latin1
Packaged: 2015-07-04 09:58:24 UTC; jo
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-07-05 09:24:32
Package: TOC
Type: Package
Title: Total Operating Characteristic Curve and ROC Curve
Version: 0.0-4
Date: 2015-12-29
Author: Robert G. Pontius <rpontius@clarku.edu>, Alí Santacruz, Amin Tayyebi, Benoit Parmentier, Kangping Si
Maintainer: Alí Santacruz <amsantac@unal.edu.co>
Depends: R (>= 2.14.0), raster, bit, rgdal, methods
Imports: graphics, grDevices, utils
Description: Construction of the Total Operating Characteristic (TOC) Curve and the Receiver (aka Relative) Operating Characteristic (ROC) Curve for spatial and non-spatial data. The TOC method is a modification of the ROC method which measures the ability of an index variable to diagnose either presence or absence of a characteristic. The diagnosis depends on whether the value of an index variable is above a threshold. Each threshold generates a two-by-two contingency table, which contains four entries: hits (H), misses (M), false alarms (FA), and correct rejections (CR). While ROC shows for each threshold only two ratios, H/(H + M) and FA/(FA + CR), TOC reveals the size of every entry in the contingency table for each threshold (Pontius Jr., R.G., Si, K. 2014. The total operating characteristic to measure diagnostic ability for multiple thresholds. Int. J. Geogr. Inf. Sci. 28 (3), 570-583).
License: GPL (>= 2)
URL: http://amsantac.co/software.html
Encoding: latin1
NeedsCompilation: no
Packaged: 2015-12-29 20:06:12 UTC; Alí
Repository: CRAN
Date/Publication: 2015-12-29 21:58:08
Package: tabplot
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
License: GPL-3
Title: Tableplot, a Visualization of Large Datasets
Type: Package
LazyLoad: yes
Author: Martijn Tennekes and Edwin de Jonge
Description: A tableplot is a visualisation of a (large)
dataset with a dozen of variables, both numeric and
categorical. Each column represents a variable and each
row bin is an aggregate of a certain number of records.
Numeric variables are visualized as bar charts, and
categorical variables as stacked bar charts. Missing
values are taken into account. Also supports large ffdf
datasets from the ff package.
Version: 1.3
URL: https://github.com/mtennekes/tabplot
Date: 2016-03-25
Depends: bit, ff, ffbase (>= 0.12.2)
Imports: grid
VignetteBuilder: knitr
Suggests: shiny (>= 0.6), knitr, classInt, ggplot2
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-03-25 19:36:12 UTC; vt
Repository: CRAN
Date/Publication: 2016-03-26 15:47:38
providing 
.