Showing 44 of total 44 results (show query)
itsleeds
od:Manipulate and Map Origin-Destination Data
The aim of 'od' is to provide tools and example datasets for working with origin-destination ('OD') datasets of the type used to describe aggregate urban mobility patterns (Carey et al. 1981) <doi:10.1287/trsc.15.1.32>. The package builds on functions for working with 'OD' data in the package 'stplanr', (Lovelace and Ellison 2018) <doi:10.32614/RJ-2018-053> with a focus on computational efficiency and support for the 'sf' class system (Pebesma 2018) <doi:10.32614/RJ-2018-009>. With few dependencies and a simple class system based on data frames, the package is intended to facilitate efficient analysis of 'OD' datasets and to provide a place for developing new functions. The package enables the creation and analysis of geographic entities representing large scale mobility patterns, from daily travel between zones in cities to migration between countries.
Maintained by Robin Lovelace. Last updated 5 months ago.
86.9 match 33 stars 8.50 score 96 scripts 6 dependents
hsvab
odbr:Download Data from Brazil's Origin Destination Surveys
Download data from Brazil's Origin Destination Surveys. The package covers both data from household travel surveys, dictionaries of variables, and the spatial geometries of surveys conducted in different years and across various urban areas in Brazil. For some cities, the package will include enhanced versions of the data sets with variables "harmonized" across different years.
Maintained by Haydee Svab. Last updated 1 months ago.
34.1 match 16 stars 5.85 score 11 scripts
ropensci
stplanr:Sustainable Transport Planning
Tools for transport planning with an emphasis on spatial transport data and non-motorized modes. The package was originally developed to support the 'Propensity to Cycle Tool', a publicly available strategic cycle network planning tool (Lovelace et al. 2017) <doi:10.5198/jtlu.2016.862>, but has since been extended to support public transport routing and accessibility analysis (Moreno-Monroy et al. 2017) <doi:10.1016/j.jtrangeo.2017.08.012> and routing with locally hosted routing engines such as 'OSRM' (Lowans et al. 2023) <doi:10.1016/j.enconman.2023.117337>. The main functions are for creating and manipulating geographic "desire lines" from origin-destination (OD) data (building on the 'od' package); calculating routes on the transport network locally and via interfaces to routing services such as <https://cyclestreets.net/> (Desjardins et al. 2021) <doi:10.1007/s11116-021-10197-1>; and calculating route segment attributes such as bearing. The package implements the 'travel flow aggregration' method described in Morgan and Lovelace (2020) <doi:10.1177/2399808320942779> and the 'OD jittering' method described in Lovelace et al. (2022) <doi:10.32866/001c.33873>. Further information on the package's aim and scope can be found in the vignettes and in a paper in the R Journal (Lovelace and Ellison 2018) <doi:10.32614/RJ-2018-053>, and in a paper outlining the landscape of open source software for geographic methods in transport planning (Lovelace, 2021) <doi:10.1007/s10109-020-00342-2>.
Maintained by Robin Lovelace. Last updated 7 months ago.
cyclecyclingdesire-linesorigin-destinationpeer-reviewedpubic-transportroute-networkroutesroutingspatialtransporttransport-planningtransportationwalking
15.9 match 427 stars 12.31 score 684 scripts 3 dependentsropensci
readODS:Read and Write ODS Files
Read ODS (OpenDocument Spreadsheet) into R as data frame. Also support writing data frame into ODS file.
Maintained by Chung-hong Chan. Last updated 2 months ago.
12.1 match 55 stars 12.74 score 808 scripts 26 dependents
mattkerlogue
tidyods:Read cells from ODS files
Import cells from ODS files. Identify a cell's postion, value types and formulas, and provide methods to "rectify" cells back to a 2-dimensional data.frame.
Maintained by Matt Kerlogue. Last updated 2 years ago.
odsods-filesopendocumentopendocument-spreadsheetspreadsheettidytidy-data
28.5 match 4 stars 3.30 score 5 scripts
a-b-street
abstr:R Interface to the A/B Street Transport System Simulation Software
Provides functions to convert origin-destination data, represented as straight 'desire lines' in the 'sf' Simple Features class system, into JSON files that can be directly imported into A/B Street <https://www.abstreet.org>, a free and open source tool for simulating urban transport systems and scenarios of change <doi:10.1007/s10109-020-00342-2>.
Maintained by Nathanael Sheehan. Last updated 3 years ago.
10.0 match 34 stars 6.87 score 27 scripts
nanxstats
enpls:Ensemble Partial Least Squares Regression
An algorithmic framework for measuring feature importance, outlier detection, model applicability domain evaluation, and ensemble predictive modeling with (sparse) partial least squares regressions.
Maintained by Nan Xiao. Last updated 3 years ago.
chemometricsdimensionality-reductionensemble-learningmachine-learningoutlier-detectionpartial-least-squares-regression
12.0 match 18 stars 5.56 score 40 scripts
robinlovelace
simodels:Flexible Framework for Developing Spatial Interaction Models
Develop spatial interaction models (SIMs). SIMs predict the amount of interaction, for example number of trips per day, between geographic entities representing trip origins and destinations. Contains functions for creating origin-destination datasets from geographic input datasets and calculating movement between origin-destination pairs with constrained, production-constrained, and attraction-constrained models (Wilson 1979) <doi:10.1068/a030001>.
Maintained by Robin Lovelace. Last updated 9 days ago.
9.4 match 18 stars 6.90 score 11 scriptsitsleeds
pct:Propensity to Cycle Tool
Functions and example data to teach and increase the reproducibility of the methods and code underlying the Propensity to Cycle Tool (PCT), a research project and web application hosted at <https://www.pct.bike/>. For an academic paper on the methods, see Lovelace et al (2017) <doi:10.5198/jtlu.2016.862>.
Maintained by Robin Lovelace. Last updated 12 days ago.
7.5 match 20 stars 6.54 score
patnik
CIM:Compositional Impact of Migration
Produces statistical indicators of the impact of migration on the socio-demographic composition of an area. Three measures can be used: ratios, percentages and the Duncan index of dissimilarity. The input data files are assumed to be in an origin-destination matrix format, with each cell representing a flow count between an origin and a destination area. Columns are expected to represent origins, and rows are expected to represent destinations. The first row and column are assumed to contain labels for each area. See Rodriguez-Vignoli and Rowe (2018) <doi:10.1080/00324728.2017.1416155> for technical details.
Maintained by Nikos Patias. Last updated 6 years ago.
24.1 match 2.00 score 4 scripts
jmsigner
amt:Animal Movement Tools
Manage and analyze animal movement data. The functionality of 'amt' includes methods to calculate home ranges, track statistics (e.g. step lengths, speed, or turning angles), prepare data for fitting habitat selection analyses, and simulation of space-use from fitted step-selection functions.
Maintained by Johannes Signer. Last updated 4 months ago.
3.3 match 41 stars 10.54 score 418 scripts
cran
ELISAtools:ELISA Data Analysis with Batch Correction
To run data analysis for enzyme-link immunosorbent assays (ELISAs). Either the five- or four-parameter logistic model will be fitted for data of single ELISA. Moreover, the batch effect correction/normalization will be carried out, when there are more than one batches of ELISAs. Feng (2018) <doi:10.1101/483800>.
Maintained by Feng Feng. Last updated 4 years ago.
9.6 match 1 stars 3.29 score 39 scriptsropensci
skynet:Generates Networks from BTS Data
A flexible tool that allows generating bespoke air transport statistics for urban studies based on publicly available data from the Bureau of Transport Statistics (BTS) in the United States <https://www.transtats.bts.gov/databases.asp?Z1qr_VQ=E&Z1qr_Qr5p=N8vn6v10&f7owrp6_VQF=D>.
Maintained by Filipe Teixeira. Last updated 6 months ago.
air-transportbtsbureau-of-transport-statisticsdb1bpeer-reviewedritaskynett100transtats
6.0 match 11 stars 4.67 score 43 scripts
nhs-r-community
NHSRtools:NHS-R Tools
Provides tools commonly used by Analysts within the NHS.
Maintained by Tom Jemmett. Last updated 4 years ago.
10.3 match 2 stars 2.00 score 1 scripts
r-spatial
stars:Spatiotemporal Arrays, Raster and Vector Data Cubes
Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in 'R', using 'GDAL' bindings provided by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'.
Maintained by Edzer Pebesma. Last updated 30 days ago.
1.1 match 571 stars 18.27 score 7.2k scripts 137 dependentsropensci
tidyqpcr:Quantitative PCR Analysis with the Tidyverse
For reproducible quantitative PCR (qPCR) analysis building on packages from the ’tidyverse’, notably ’dplyr’ and ’ggplot2’. It normalizes (by ddCq), summarizes, and plots pre-calculated Cq data, and plots raw amplification and melt curves from Roche Lightcycler (tm) machines. It does NOT (yet) calculate Cq data from amplification curves.
Maintained by Edward Wallace. Last updated 11 months ago.
miqeqpcrqpcr-analysistidyverse
3.4 match 54 stars 5.64 score 20 scripts
mpadge
spatialcluster:R port of redcap
R port of redcap (Regionalization with dynamically constrained agglomerative clustering and partitioning).
Maintained by Mark Padgham. Last updated 2 months ago.
clusterclustering-algorithmspatialcpp
2.5 match 31 stars 4.97 score 1 scripts
bioc
autonomics:Unified Statistical Modeling of Omics Data
This package unifies access to Statistal Modeling of Omics Data. Across linear modeling engines (lm, lme, lmer, limma, and wilcoxon). Across coding systems (treatment, difference, deviation, etc). Across model formulae (with/without intercept, random effect, interaction or nesting). Across omics platforms (microarray, rnaseq, msproteomics, affinity proteomics, metabolomics). Across projection methods (pca, pls, sma, lda, spls, opls). Across clustering methods (hclust, pam, cmeans). It provides a fast enrichment analysis implementation. And an intuitive contrastogram visualisation to summarize contrast effects in complex designs.
Maintained by Aditya Bhagwat. Last updated 2 months ago.
softwaredataimportpreprocessingdimensionreductionprincipalcomponentregressiondifferentialexpressiongenesetenrichmenttranscriptomicstranscriptiongeneexpressionrnaseqmicroarrayproteomicsmetabolomicsmassspectrometry
2.0 match 5.95 score 5 scripts
uribo
ssrn:Scan Statistics for Railway Network
Implement the algorithm provided in scan for estimating the transmission route on railway network using passenger volume. It is a generalization of the scan statistic approach for railway network to identify the hot railway route for transmitting infectious diseases.
Maintained by Shinya Uryu. Last updated 5 years ago.
3.5 match 2 stars 3.00 score 5 scripts
ssa-statistical-team-projects
povmap:Extension to the 'emdi' Package
The R package 'povmap' supports small area estimation of means and poverty headcount rates. It adds several new features to the 'emdi' package (see "The R Package emdi for Estimating and Mapping Regionally Disaggregated Indicators" by Kreutzmann et al. (2019) <doi:10.18637/jss.v091.i07>). These include new options for incorporating survey weights, ex-post benchmarking of estimates, two additional transformations, several new convenient functions to assist with reporting results, and a wrapper function to facilitate access from 'Stata'.
Maintained by Ifeanyi Edochie. Last updated 5 months ago.
2.3 match 1 stars 4.60 score 10 scripts
uscbiostats
cit:Causal Inference Test
A likelihood-based hypothesis testing approach is implemented for assessing causal mediation. Described in Millstein, Chen, and Breton (2016), <DOI:10.1093/bioinformatics/btw135>, it could be used to test for mediation of a known causal association between a DNA variant, the 'instrumental variable', and a clinical outcome or phenotype by gene expression or DNA methylation, the potential mediator. Another example would be testing mediation of the effect of a drug on a clinical outcome by the molecular target. The hypothesis test generates a p-value or permutation-based FDR value with confidence intervals to quantify uncertainty in the causal inference. The outcome can be represented by either a continuous or binary variable, the potential mediator is continuous, and the instrumental variable can be continuous or binary and is not limited to a single variable but may be a design matrix representing multiple variables.
Maintained by Joshua Millstein. Last updated 9 months ago.
2.3 match 2 stars 3.81 score 32 scripts
jancaha
CzechData:Download various datasets (including spatial data) for the Czech Republic
Download various datasets (including spatial data) for the Czech Republic.
Maintained by Jan Caha. Last updated 1 years ago.
1.8 match 7 stars 4.70 score 16 scripts 1 dependents
epivec
TDLM:Systematic Comparison of Trip Distribution Laws and Models
The main purpose of this package is to propose a rigorous framework to fairly compare trip distribution laws and models as described in Lenormand et al. (2016) <doi:10.1016/j.jtrangeo.2015.12.008>.
Maintained by Maxime Lenormand. Last updated 10 days ago.
1.7 match 2 stars 4.85 score 3 scripts
rabilon
merror:Accuracy and Precision of Measurements
N>=3 methods are used to measure each of n items. The data are used to estimate simultaneously systematic error (bias) and random error (imprecision). Observed measurements for each method or device are assumed to be linear functions of the unknown true values and the errors are assumed normally distributed. Pairwise calibration curves and plots can be easily generated. Unlike the 'ncb.od' function, the 'omx' function builds a one-factor measurement error model using 'OpenMx' and allows missing values, uses full information maximum likelihood to estimate parameters, and provides both likelihood-based and bootstrapped confidence intervals for all parameters, in addition to Wald-type intervals.
Maintained by Richard A. Bilonick. Last updated 2 years ago.
6.5 match 1.23 score 17 scripts
kwb-r
kwb.geosalz:R Package for Documenting Workflow Used in Project "geosalz"
R Package for Documenting Workflow Used in Project "geosalz".
Maintained by Michael Rustler. Last updated 12 months ago.
data-cleaningdata-importdata-visualisationexcelproject-fakinproject-geosalzspreadsheets
3.4 match 2.30 score 3 scriptscran
spnaf:Spatial Network Autocorrelation for Flow Data
Identify statistically significant flow clusters using the local spatial network autocorrelation statistic G_ij* proposed by 'Berglund' and 'Karlström' (1999) <doi:10.1007/s101090050013>. The metric, an extended statistic of 'Getis/Ord' G ('Getis' and 'Ord' 1992) <doi:10.1111/j.1538-4632.1992.tb00261.x>, detects a group of flows having similar traits in terms of directionality. You provide OD data and the associated polygon to get results with several parameters, some of which are defined by spdep package.
Maintained by Youngbin Lee. Last updated 8 months ago.
2.2 match 3.18 score 2 scripts
sth1402
ICODS:Data Analysis for ODS and Case-Cohort Designs with Interval-Censoring
Sieve semiparametric likelihood methods for analyzing interval-censored failure time data from an outcome-dependent sampling (ODS) design and from a case-cohort design. Zhou, Q., Cai, J., and Zhou, H. (2018) <doi:10.1111/biom.12744>; Zhou, Q., Zhou, H., and Cai, J. (2017) <doi:10.1093/biomet/asw067>.
Maintained by Shannon T. Holloway. Last updated 3 years ago.
6.8 match 1.00 score
zuchaoshen
anomo:Analysis of Moderation, Statistical Power, and Optimal Design for Studies Detecting Difference and Equivalence
Analysis of moderation (ANOMO) method conceptualizes the difference and equivalence tests as a moderation problem to test the difference and equivalence of two means (or two effects in two studies).
Maintained by Zuchao Shen. Last updated 22 days ago.
2.0 match 3.30 score 10 scripts
kaiaragaki
ezmtt:Easy MTT Assay Tidying and Plotting
This package automates the analysis and plotting of standard MTT workflows.
Maintained by Kai Aragaki. Last updated 4 months ago.
1.8 match 3.30 score 3 scriptsropensci
ReLTER:An Interface for the eLTER Community
ReLTER provides access to DEIMS-SDR (https://deims.org/), and allows interaction with data and software implemented by eLTER Research Infrastructure (RI) thus improving data sharing among European LTER projects. ReLTER uses the R language to access and interact with the DEIMS-SDR archive of information shared by the Long Term Ecological Research (LTER) network. This package grew within eLTER H2020 as a major project that will help advance the development of European Long-Term Ecosystem Research Infrastructures (eLTER RI - https://elter-ri.eu). The ReLTER package functions in particular allow to: - retrieve the information about entities (e.g. sites, datasets, and activities) shared by DEIMS-SDR (see e.g. get_site_info function); - interact with the [ODSEurope](maps.opendatascience.eu) starting with the dataset shared by [DEIMS-SDR](https://deims.org/) (see e.g. [get_site_ODS](https://docs.ropensci.org/ReLTER/reference/get_site_ODS.html) function); - use the eLTER site informations to download and crop geospatial data from other platforms (see e.g. get_site_ODS function); - improve the quality of the dataset (see e.g. get_id_worms). Functions currently implemented are derived from discussions of the needs among the eLTER users community. The ReLTER package will continue to follow the progress of eLTER-RI and evolve, adding new tools and improvements as required.
Maintained by Alessandro Oggioni. Last updated 1 years ago.
biodiversity-informaticsdata-scienceecologyelterresearch-infrastructure
1.7 match 12 stars 3.38 score 4 scripts
raim
dpseg:Piecewise Linear Segmentation by Dynamic Programming
Piecewise linear segmentation of ordered data by a dynamic programming algorithm. The algorithm was developed for time series data, e.g. growth curves, and for genome-wide read-count data from next generation sequencing, but is broadly applicable. Generic implementations of dynamic programming routines allow to scan for optimal segmentation parameters and test custom segmentation criteria ("scoring functions").
Maintained by Rainer Machne. Last updated 26 days ago.
1.1 match 4.71 score 17 scripts 1 dependents
ecuris
SARP.moodle:XML Output Functions for Easy Creation of Moodle Questions
Provides a set of basic functions for creating Moodle XML output files suited for importing questions in Moodle (a learning management system, see <https://moodle.org/> for more information).
Maintained by Emmanuel Curis. Last updated 2 years ago.
3.9 match 1.20 score 16 scriptscran
ssMRCD:Spatially Smoothed MRCD Estimator
Estimation of the Spatially Smoothed Minimum Regularized Determinant (ssMRCD) estimator and its usage in an ssMRCD-based outlier detection method as described in Puchhammer and Filzmoser (2023) <doi:10.1080/10618600.2023.2277875> and for sparse robust PCA for multi-source data described in Puchhammer, Wilms and Filzmoser (2024) <doi:10.48550/arXiv.2407.16299>. Included are also complementary visualization and parameter tuning tools.
Maintained by Patricia Puchhammer. Last updated 7 months ago.
2.3 match 2.00 score 3 scripts
ropenspain
spanishoddata:Get Spanish Origin-Destination Data
Gain seamless access to origin-destination (OD) data from the Spanish Ministry of Transport, hosted at <https://www.transportes.gob.es/ministerio/proyectos-singulares/estudios-de-movilidad-con-big-data/opendata-movilidad>. This package simplifies the management of these large datasets by providing tools to download zone boundaries, handle associated origin-destination data, and process it efficiently with the 'duckdb' database interface. Local caching minimizes repeated downloads, streamlining workflows for researchers and analysts. Extensive documentation is available at <https://ropenspain.github.io/spanishoddata/index.html>, offering guides on creating static and dynamic mobility flow visualizations and transforming large datasets into analysis-ready formats.
Maintained by Egor Kotov. Last updated 7 days ago.
cdrdatadata-packagemobile-telephone-datamobilityorigin-destination
0.5 match 35 stars 7.89 score 14 scripts
smorenoa
ODMeans:OD-Means: k-Means for Origin-Destination
OD-means is a hierarchical adaptive k-means algorithm based on origin-destination pairs. In the first layer of the hierarchy, the clusters are separated automatically based on the variation of the within-cluster distance of each cluster until convergence. The second layer of the hierarchy corresponds to the sub clustering process of small clusters based on the distance between the origin and destination of each cluster.
Maintained by Sebastian Moreno. Last updated 12 months ago.
3.4 match 1.00 scorebioc
odseq:Outlier detection in multiple sequence alignments
Performs outlier detection of sequences in a multiple sequence alignment using bootstrap of predefined distance metrics. Outlier sequences can make downstream analyses unreliable or make the alignments less accurate while they are being constructed. This package implements the OD-seq algorithm proposed by Jehl et al (doi 10.1186/s12859-015-0702-1) for aligned sequences and a variant using string kernels for unaligned sequences.
Maintained by José Jiménez. Last updated 5 months ago.
alignmentmultiplesequencealignment
0.5 match 4.18 score 25 scripts 1 dependents
jaytimm
puremoe:Pubmed Unified REtrieval for Multi-Output Exploration
Access a variety of 'PubMed' data through a single, user-friendly interface, including abstracts <https://pubmed.ncbi.nlm.nih.gov/>, bibliometrics from 'iCite' <https://icite.od.nih.gov/>, pubtations from 'PubTator3' <https://www.ncbi.nlm.nih.gov/research/pubtator3/>, and full-text records from 'PMC' <https://www.ncbi.nlm.nih.gov/pmc/>.
Maintained by Jason Timm. Last updated 1 months ago.
0.5 match 2 stars 3.95 score
chockemeyer
CDSS:Course-Dependent Skill Structures
Deriving skill structures from skill assignment data for courses (sets of learning objects).
Maintained by Cord Hockemeyer. Last updated 1 years ago.
1.7 match 1.00 score
jingzhuzhuzhu
bfboinet:Backfill Bayesian Optimal Interval Design Using Efficacy and Toxicity
The backfill Bayesian optimal interval design using efficacy and toxicity outcomes for dose optimization (BF-BOIN-ET) design is a novel clinical trial design to allow patients to be backfilled at lower doses during a dose-finding trial while prioritizing the dose-escalation cohort to explore a higher dose. The advantages compared to the other designs in terms of the percentage of correct optimal dose (OD) selection, reducing the sample size, and shortening the duration of the trial, in various realistic setting.
Maintained by Jing Zhu. Last updated 1 months ago.
0.5 match 1.30 score