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r-sybil
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public |
This Systems Biology Package (Gelius-Dietrich et. al. (2012) <doi:10.1186/1752-0509-7-125>) implements algorithms for constraint based analyses of metabolic networks, e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis. The package is easily extendable for additional algorithms. Most of the current LP/MILP solvers are supported via additional packages.
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2023-06-16 |
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r-swirl
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public |
Use the R console as an interactive learning environment. Users receive immediate feedback as they are guided through self-paced lessons in data science and R programming.
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2023-06-16 |
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r-suncalc
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public |
Get sun position, sunlight phases (times for sunrise, sunset, dusk, etc.), moon position and lunar phase for the given location and time. Most calculations are based on the formulas given in Astronomy Answers articles about position of the sun and the planets : <https://www.aa.quae.nl/en/reken/zonpositie.html>.
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2023-06-16 |
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r-subpathwaygmir
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public |
Routines for identifying metabolic subpathways mediated by microRNAs (miRNAs) through topologically locating miRNAs and genes within reconstructed Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway graphs embedded by miRNAs. (1) This package can obtain the reconstructed KEGG metabolic pathway graphs with genes and miRNAs as nodes, through converting KEGG metabolic pathways to graphs with genes as nodes and compounds as edges, and then integrating miRNA-target interactions verified by low-throughput experiments from four databases (TarBase, miRecords, mirTarBase and miR2Disease) into converted pathway graphs. (2) This package can locate metabolic subpathways mediated by miRNAs by topologically analyzing the "lenient distance" of miRNAs and genes within reconstructed KEGG metabolic pathway graphs.(3) This package can identify significantly enriched miRNA-mediated metabolic subpathways based on located subpathways by hypergenomic test. (4) This package can support six species for metabolic subpathway identification, such as caenorhabditis elegans, drosophila melanogaster, danio rerio, homo sapiens, mus musculus and rattus norvegicus, and user only need to update interested organism-specific environment variables.
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2023-06-16 |
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r-subgroup
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public |
Produces various measures of expected treatment effect heterogeneity under an assumption of homogeneity across subgroups. Graphical presentations are created to compare these expected differences with the observed differences.
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2023-06-16 |
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r-stripless
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public |
For making Trellis-type conditioning plots without strip labels. This is useful for displaying the structure of results from factorial designs and other studies when many conditioning variables would clutter the display with layers of redundant strip labels. Settings of the variables are encoded by layout and spacing in the trellis array and decoded by a separate legend. The functionality is implemented by a single S3 generic strucplot() function that is a wrapper for the Lattice package's xyplot() function. This allows access to all Lattice graphics capabilities in the usual way.
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2023-06-16 |
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r-sticky
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public |
In base R, object attributes are lost when objects are modified by common data operations such as subset, filter, slice, append, extract etc. This packages allows objects to be marked as 'sticky' and have attributes persisted during these operations or when inserted into or extracted from recursive (i.e. list- or table-like) objects.
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2023-06-16 |
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r-stevedore
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public |
Work with containers over the Docker API. Rather than using system calls to interact with a docker client, using the API directly means that we can receive richer information from docker. The interface in the package is automatically generated using the 'OpenAPI' (a.k.a., 'swagger') specification, and all return values are checked in order to make them type stable.
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2023-06-16 |
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r-steinernet
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public |
A set of functions for finding and analysing Steiner trees. It has applications in biological pathway network analysis. Sadeghi (2013) <doi:10.1186/1471-2105-14-144>.
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2023-06-16 |
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r-statgraph
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public |
Contains statistical methods to analyze graphs, such as graph parameter estimation, model selection based on the GIC (Graph Information Criterion), statistical tests to discriminate two or more populations of graphs (ANOGVA -Analysis of Graph Variability), correlation between graphs, and clustering of graphs.
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2023-06-16 |
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r-standardizetext
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public |
Standardizes text according to a template; particularly useful for country names.
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2023-06-16 |
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r-umoments
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public |
Calculates one-sample unbiased central moment estimates and two-sample pooled estimates up to 6th order, including unbiased estimates of powers and products of central moments. Provides the machinery for obtaining unbiased central moment estimators beyond 6th order.
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2023-06-16 |
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r-ucbthesis
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public |
This package contains latex, knitr and R Markdown templates that adhere to the UC Berkeley Graduate Division's thesis guidelines. The templates are located in the inst/ directory.
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2023-06-16 |
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r-twostepclogit
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public |
Conditional logistic regression with longitudinal follow up and individual-level random coefficients: A stable and efficient two-step estimation method.
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2023-06-16 |
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r-tufte
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public |
Provides R Markdown output formats to use Tufte styles for PDF and HTML output.
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2023-06-16 |
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r-tttplot
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public |
Implementation of Time to Target plot based on the work of Ribeiro and Rosseti (2015) <DOI:10.1007/s11590-014-0760-8>, that describe a numerical method that gives the probability of an algorithm A finds a solution at least as good as a given target value in smaller computation time than algorithm B.
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2023-06-16 |
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r-trimcluster
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public |
Trimmed k-means clustering.
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2023-06-16 |
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r-trekfont
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public |
Provides a collection of true type and open type Star Trek-themed fonts.
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2023-06-16 |
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r-trading
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public |
Contains trades from the five major assets classes and also functionality to use pricing curves, rating tables, CSAs and add-on tables. The implementation follows an object oriented logic whereby each trade inherits from more abstract classes while also the curves/tables are objects. There is a lot of functionality focusing on the counterparty credit risk calculations however the package can be used for trading applications in general.
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2023-06-16 |
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r-tnet
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public |
R package for analyzing weighted, two-mode, and longitudinal networks.
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2023-06-16 |
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r-titan
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public |
GUI to analyze mass spectrometric data on the relative abundance of two substances from a titration series.
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2023-06-16 |
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r-tickexec
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public |
Functions to execute orders in backtesting using tick data. A testing platform was established by the four major execution functions, namely 'LimitBuy', 'LimitSell', 'MarketBuy' and 'MarketSell', which enclosed all tedious aspects (such as queueing for order executions and calculate actual executed volumes) for order execution using tick data. Such that one can focus on the logic of strategies, rather than its execution.
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2023-06-16 |
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r-thankyoustars
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public |
A tool for starring GitHub repositories.
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2023-06-16 |
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r-tfx
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public |
Connects R to TrueFX(tm) for free streaming real-time and historical tick-by-tick market data for dealable interbank foreign exchange rates with millisecond detail.
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2023-06-16 |
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r-tfse
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public |
A collection of useful tools for programming and writing-scripts. Several functions are simple wrappers around base R functions that extend their functionality while also providing some convenient properties–regular expression functions that automatically detect look-ahead and look-behind statements, a read-line function that suppresses incomplete-final-line warnings and automatically opens and closes connections, a version of substrings that starts from the end of strings, etc. Other functions are useful for checking whether packages are installed, omitting missing data, and showing in-use connections.
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2023-06-16 |
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r-textshape
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public |
Tools that can be used to reshape and restructure text data.
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2023-06-16 |
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r-textrank
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public |
The 'textrank' algorithm is an extension of the 'Pagerank' algorithm for text. The algorithm allows to summarize text by calculating how sentences are related to one another. This is done by looking at overlapping terminology used in sentences in order to set up links between sentences. The resulting sentence network is next plugged into the 'Pagerank' algorithm which identifies the most important sentences in your text and ranks them. In a similar way 'textrank' can also be used to extract keywords. A word network is constructed by looking if words are following one another. On top of that network the 'Pagerank' algorithm is applied to extract relevant words after which relevant words which are following one another are combined to get keywords. More information can be found in the paper from Mihalcea, Rada & Tarau, Paul (2004) <http://www.aclweb.org/anthology/W04-3252>.
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2023-06-16 |
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r-tensor
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public |
The tensor product of two arrays is notionally an outer product of the arrays collapsed in specific extents by summing along the appropriate diagonals.
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2023-06-16 |
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r-tejapi
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public |
Functions for interacting directly with the Taiwan Economic Journal API to offer data in R. For more information go to <https://api.tej.com.tw>.
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2023-06-16 |
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r-teachnet
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public |
Can fit neural networks with up to two hidden layer and two different error functions. Also able to handle a weight decay. But just able to compute one output neuron and very slow.
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2023-06-16 |
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r-tangram
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public |
Provides an extensible formula system to quickly and easily create production quality tables. The steps of the process are formula parser, statistical content generation from data, to rendering. Each step of the process is separate and user definable thus creating a set of building blocks for highly extensible table generation. A user is not limited by any of the choices of the package creator other than the formula grammar. For example, one could chose to add a different S3 rendering function and output a format not provided in the default package. Or possibly one would rather have Gini coefficients for their statistical content. Routines to achieve New England Journal of Medicine style, Lancet style and Hmisc::summaryM() statistics are provided. The package contains rendering for HTML5, Rmarkdown and an indexing format for use in tracing and tracking are provided.
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2023-06-16 |
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r-subcopem2d
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public |
Calculate empirical subcopula and dependence measures from a given bivariate sample, and Bernstein copula approximations.
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2023-06-16 |
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r-stringformattr
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public |
Pass named and unnamed character vectors into specified positions in strings. This represents an attempt to replicate some of python's string formatting.
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2023-06-16 |
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r-stmgp
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public |
Rapidly build accurate genetic prediction models for genome-wide association or whole-genome sequencing study data by smooth-threshold multivariate genetic prediction (STMGP) method. Variable selection is performed using marginal association test p-values with an optimal p-value cutoff selected by Cp-type criterion. Quantitative and binary traits are modeled respectively via linear and logistic regression models. A function that works through PLINK software (Purcell et al. 2007 <DOI:10.1086/519795>, Chang et al. 2015 <DOI:10.1186/s13742-015-0047-8>) <https://www.cog-genomics.org/plink2> is provided. Covariates can be included in regression model.
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2023-06-16 |
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r-stellar
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public |
A package to manage and display stellar tracks and isochrones from Pisa low-mass database. Includes tools for isochrones construction and tracks interpolation.
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2023-06-16 |
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r-startupmsg
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public |
Provides utilities to create or suppress start-up messages.
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2023-06-16 |
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r-stargazer
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public |
Produces LaTeX code, HTML/CSS code and ASCII text for well-formatted tables that hold regression analysis results from several models side-by-side, as well as summary statistics.
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2023-06-16 |
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r-stakeholderanalysis
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public |
Proposes an original instrument for measuring stakeholder influence on the development of an infrastructure project that is carried through by a municipality, drawing on stakeholder classifications (Mitchell, Agle, & Wood, 1997) and input-output modelling (Hester & Adams, 2013). Mitchell R., Agle B.R., & Wood D.J. <doi:10.2307/259247> Hester, P.T., & Adams, K.M. (2013) <doi:10.1016/j.procs.2013.09.282>.
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2023-06-16 |
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r-ssize.fdr
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public |
This package contains a set of functions that calculates appropriate sample sizes for one-sample t-tests, two-sample t-tests, and F-tests for microarray experiments based on desired power while controlling for false discovery rates. For all tests, the standard deviations (variances) among genes can be assumed fixed or random. This is also true for effect sizes among genes in one-sample and two sample experiments. Functions also output a chart of power versus sample size, a table of power at different sample sizes, and a table of critical test values at different sample sizes.
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2023-06-16 |
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r-srttools
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public |
Srt file is a common subtitle format for videos, it contains subtitle and when the subtitle showed. This package is for align time of srt file, and also change color, style and position of subtitle in videos, the srt file will be read as a vector into R, and can be write into srt file after modified using this package.
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2023-06-16 |
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r-urbin
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public |
Calculate unified measures that quantify the effect of a covariate on a binary dependent variable (e.g., for meta-analyses). This can be particularly important if the estimation results are obtained with different models/estimators (e.g., linear probability model, logit, probit, ...) and/or with different transformations of the explanatory variable of interest (e.g., linear, quadratic, interval-coded, ...). The calculated unified measures are: (a) semi-elasticities of linear, quadratic, or interval-coded covariates and (b) effects of linear, quadratic, interval-coded, or categorical covariates when a linear or quadratic covariate changes between distinct intervals, the reference category of a categorical variable or the reference interval of an interval-coded variable needs to be changed, or some categories of a categorical covariate or some intervals of an interval-coded covariate need to be grouped together. Approximate standard errors of the unified measures are also calculated. All methods that are implemented in this package are described in the 'vignette' "Extracting and Unifying Semi-Elasticities and Effect Sizes from Studies with Binary Dependent Variables" that is included in this package.
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2023-06-16 |
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r-upsvarapprox
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public |
Variance approximations for the Horvitz-Thompson total estimator in Unequal Probability Sampling using only first-order inclusion probabilities. See Matei and Tillé (2005) and Haziza, Mecatti and Rao (2008) for details.
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2023-06-16 |
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r-uncdecomp
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public |
If a procedure consists of several stages and there are several scenarios that can be selected for each stage, uncertainty of the procedure can be decomposed by stages or scenarios. cum_uncertainty() is used to decompose uncertainty based on the cumulative uncertainty. stage_uncertainty() and scenario_uncertainty() is used to decompose uncertainty based on the second order interaction ANOVA model. In stage_uncertainty() and scenario_uncertainty(), the uncertainty from interaction effect from two stages is distributed equally to each stage.
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2023-06-16 |
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r-tsetools
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public |
Tools for downloading and organizing data from Tehran Stock Exchange (TSE) <http://new.tse.ir/en/>. It also performs some descriptive data analysis for assets.
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2023-06-16 |
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r-trendchange
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public |
Innovative Trend Analysis is a graphical method to examine the trends in time series data. Sequential Mann-Kendall test uses the intersection of prograde and retrograde series to indicate the possible change point in time series data. Distribution free cumulative sum charts indicate location and significance of the change point in time series. Zekai, S. (2011). <doi:10.1061/(ASCE)HE.1943-5584.0000556>. Grayson, R. B. et al. (1996). Hydrological Recipes: Estimation Techniques in Australian Hydrology. Cooperative Research Centre for Catchment Hydrology, Australia, p. 125. Sneyers, S. (1990). On the statistical analysis of series of observations. Technical note no 5 143, WMO No 725 415. Secretariat of the World Meteorological Organization, Geneva, 192 pp.
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2023-06-16 |
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r-toxtestd
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public |
Calculates sample size and dose allocation for binary toxicity tests, using the Fish Embryo Toxicity Test as example. An optimal test design is obtained by running (i) spoD (calculate the number of individuals to test under control conditions), (ii) setD (estimate the minimal sample size per treatment given the users precision requirements) and (iii) doseD (construct an individual dose scheme).
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2023-06-16 |
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r-toordinal
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public |
Language specific cardinal to ordinal number conversion.
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2023-06-16 |
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r-tnc
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public |
Node centrality measures for temporal networks. Available measures are temporal degree centrality, temporal closeness centrality and temporal betweenness centrality defined by Kim and Anderson (2012) <doi:10.1103/PhysRevE.85.026107>. Applying the REN algorithm by Hanke and Foraita (2017) <doi:10.1186/s12859-017-1677-x> when calculating the centrality measures keeps the computational running time linear in the number of graph snapshots. Further, all methods can run in parallel up to the number of nodes in the network.
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2023-06-16 |
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r-tmdb
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public |
Provides an R-interface to the TMDb API (see TMDb API on <http://docs.themoviedb.apiary.io/#>). The Movie Database (TMDb) is a popular user editable database for movies and TV shows (see <https://www.themoviedb.org>).
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2023-06-16 |
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r-textutils
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public |
Utilities for handling character vectors that store human-readable text (either plain or with markup, such as HTML or LaTeX). The package provides, in particular, functions that help with the preparation of plain-text reports (e.g. for expanding and aligning strings that form the lines of such reports); the package also provides generic functions for transforming R objects to HTML and to plain text.
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2023-06-16 |
