Tools Developed by the Long Term Ecological Research Community

Set of the data science tools created by various members of the Long Term Ecological Research (LTER) community. These functions were initially written largely as standalone operations and have later been aggregated into this package.

Estimation of the Number of Fatalities from Carcass Searches

The number of bird or bat fatalities from collisions with buildings, towers or wind energy turbines can be estimated based on carcass searches and experimentally assessed carcass persistence times and searcher efficiency. Functions for estimating the probability that a bird or bat that died is found by a searcher are provided. Further functions calculate the posterior distribution of the number of fatalities based on the number of carcasses found and the estimated detection probability.

Advanced Analysis of Longitudinal Data Using the Concordance Correlation Coefficient

Methods for assessing agreement between repeated measurements obtained by two or more methods using the longitudinal concordance correlation coefficient (LCC). Polynomial mixed-effects models (via 'nlme') describe how concordance, Pearson correlation and accuracy evolve over time. Functions are provided for model fitting, diagnostic plots, extraction of summaries, and non-parametric bootstrap confidence intervals (including parallel computation), following Oliveira et al. (2018) .

Create Network Connections Based on Chess Moves

Provides functions to work with directed (asymmetric) and undirected (symmetric) spatial networks. It makes the creation of connectivity matrices easier, i.e. a binary matrix of dimension n x n, where n is the number of nodes (sampling units) indicating the presence (1) or the absence (0) of an edge (link) between pairs of nodes. Different network objects can be produced by 'chessboard': node list, neighbor list, edge list, connectivity matrix. It can also produce objects that will be used later in Moran's Eigenvector Maps (Dray et al. (2006) ) and Asymetric Eigenvector Maps (Blanchet et al. (2008) ), methods available in the package 'adespatial' (Dray et al. (2023) < https://CRAN.R-project.org/package=adespatial>). This work is part of the FRB-CESAB working group Bridge < https://www.fondationbiodiversite.fr/en/the-frb-in-action/programs-and-projects/le-cesab/bridge/>.

Download Official Spatial Data Sets of Brazil

Easy access to official spatial data sets of Brazil. The package offers a wide range of spatial data sets available at various geographic scales and for various years with harmonized attributes, projection and fixed topology. All functions allow for seamless integration sf, DuckDB and Arrow.

Make 'Mirai' 'Promises'

Allows 'mirai' objects encapsulating asynchronous computations, from the 'mirai' package by Gao (2023) , to be used interchangeably with 'promise' objects from the 'promises' package by Cheng (2021) < https://CRAN.R-project.org/package=promises>. This facilitates their use with packages 'plumber' by Schloerke and Allen (2022) < https://CRAN.R-project.org/package=plumber> and 'shiny' by Cheng, Allaire, Sievert, Schloerke, Xie, Allen, McPherson, Dipert and Borges (2022) < https://CRAN.R-project.org/package=shiny>.

Procrustes Matching for Latent Space Item Response Model

Procrustes matching of the posterior samples of person and item latent positions from latent space item response models. The methods implemented in this package are based on work by Borg, I., Groenen, P. (1997, ISBN:978-0-387-94845-4), Jeon, M., Jin, I. H., Schweinberger, M., Baugh, S. (2021) , and Andrew, D. M., Kevin M. Q., Jong Hee Park. (2011) .

Multiple Imputation for Proteomics

A framework for multiple imputation for proteomics is proposed by Marie Chion, Christine Carapito and Frederic Bertrand (2021) . It is dedicated to dealing with multiple imputation for proteomics.

Analysis and Identification of Raman Spectra of Microplastics

Pre-processing and polymer identification of Raman spectra of plastics. Pre-processing includes normalisation functions, peak identification based on local maxima, smoothing process and removal of spectral region of no interest. Polymer identification can be performed using Pearson correlation coefficient or Euclidean distance (Renner et al. (2019), ), and the comparison can be done with a user-defined database or with the database already implemented in the package, which currently includes 356 spectra, with several spectra of plastic colorants.

Methods for Fixed-Income Valuation, Risk and Return

Bond Pricing and Fixed-Income Valuation of Selected Securities included here serve as a quick reference of Quantitative Methods for undergraduate courses on Fixed-Income and CFA Level I Readings on Fixed-Income Valuation, Risk and Return. CFA Institute ("CFA Program Curriculum 2020 Level I Volumes 1-6. (Vol. 5, pp. 107-151, pp. 237-299)", 2019, ISBN: 9781119593577). Barbara S. Petitt ("Fixed Income Analysis", 2019, ISBN: 9781119628132). Frank J. Fabozzi ("Handbook of Finance: Financial Markets and Instruments", 2008, ISBN: 9780470078143). Frank J. Fabozzi ("Fixed Income Analysis", 2007, ISBN: 9780470052211).