spAbundance: An R package for single-species and multi-species spatially explicit abundance models

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Doser, Jeffrey W., Finley, Andrew O., Kéry, Marc, Zipkin, Elise F.
Format:	Preprint
Published:	2023
Subjects:	Applications
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Guidelines for the use of spatially-varying coefficients in species distribution models
by: Doser, Jeffrey W., et al.
Published: (2023)

Multivariate spatial models for small area estimation of species-specific forest inventory parameters
by: Doser, Jeffrey W., et al.
Published: (2025)

Guidelines for the use of spatially varying coefficients in species distribution models
by: Jeffrey W. Doser, et al.
Published: (2024)

Context matters in ecological forecasting: Lessons in predicting species distributions
by: Elise F. Zipkin, et al.
Published: (2024)

Movement-based models for abundance data
by: Vergara, Ricardo Carrizo, et al.
Published: (2024)

A spatial mixture model for spaceborne lidar observations over mixed forest and non-forest land types
by: May, Paul B., et al.
Published: (2024)

florabr: An R package to explore and spatialize species distribution using Flora e Funga do Brasil
by: Weverton C. F. Trindade
Published: (2024)

Fitting individual‐based models of spatial population dynamics to long‐term monitoring data
by: Anne‐Kathleen Malchow, et al.
Published: (2024)

Evaluating environmental drivers and synchrony of Arctic shorebird demographic rates to inform conservation management
by: Kayla L. Davis, et al.
Published: (2025)

Estimating spatially varying occupancy trends for multi‐scale conservation: An amphibian case study in the midwestern United States
by: Jeffrey W. Doser, et al.
Published: (2026)

reslr: An R package for relative sea level modelling
by: Upton, Maeve, et al.
Published: (2023)

Spatial-temporal prediction of forest attributes using latent Gaussian models and inventory data
by: May, Paul B., et al.
Published: (2025)

A spatio-temporal statistical model for property valuation at country-scale with adjustments for regional submarkets
by: O'Donovan, Brian, et al.
Published: (2025)

Calibrating satellite maps with field data for improved predictions of forest biomass
by: May, Paul B., et al.
Published: (2024)

piCurve: an R package for modeling photosynthesis-irradiance curves
by: Amirian, Mohammad M., et al.
Published: (2025)

infinitylists: A Shiny application and R package for rapid generation of place‐based species checklists
by: Thomas Mesaglio, et al.
Published: (2025)

Fall and rise of a threatened raptor: Unraveling long‐term population dynamics with spatially explicit integrated models
by: Jaume A. Badia‐Boher, et al.
Published: (2025)

pintervals: an R package for model-agnostic prediction intervals
by: Randahl, David, et al.
Published: (2026)

cosimmr: an R package for fast fitting of Stable Isotope Mixing Models with covariates
by: Govan, Emma, et al.
Published: (2024)

Joint species distribution modeling of abundance data through latent variable barcodes
by: Scherting, Braden, et al.
Published: (2024)

A monotone single index model for spatially referenced multistate current status data
by: Das, Snigdha, et al.
Published: (2025)

Gridding and Parameter Expansion for Scalable Latent Gaussian Models of Spatial Multivariate Data
by: Peruzzi, Michele, et al.
Published: (2021)

svc: An R package for Spatially Varying Coefficient Models
by: Akuoko-Frimpong, Justice, et al.
Published: (2025)

Multivariate lattice deformation: A spatially explicit framework for assessing crop rotation impacts on soil nutrient dynamics
by: Mandap, Marco
Published: (2026)

Spatio-temporal areal models to support small area estimation: An application to national-scale forest carbon monitoring
by: Shannon, Elliot S., et al.
Published: (2024)

expowo: An R package for mining global plant diversity and distribution data
by: Débora C. Zuanny, et al.
Published: (2024)

Hierarchical models for small area estimation using zero-inflated forest inventory variables: comparison and implementation
by: White, Grayson W., et al.
Published: (2025)

tanggle: An R package for the visualization of phylogenetic networks
by: Klaus Schliep, et al.
Published: (2026)

Functional R code is rare in species distribution and abundance papers
by: Kenneth F. Kellner, et al.
Published: (2024)

CMiNet: R package for learning the Consensus Microbiome Network
by: Aghdam, Rosa, et al.
Published: (2024)

tinyVAST: R package with an expressive interface to specify lagged and simultaneous effects in multivariate spatio-temporal models
by: Thorson, James T., et al.
Published: (2024)

The evolving categories multinomial distribution: introduction with applications to movement ecology and vote transfer
by: Vergara, Ricardo Carrizo, et al.
Published: (2025)

ceylon: An R package for plotting the maps of Sri Lanka
by: Talagala, Thiyanga S.
Published: (2024)

Models to support forest inventory and small area estimation using sparsely sampled LiDAR: A case study involving G-LiHT LiDAR in Tanana, Alaska
by: Finley, Andrew O., et al.
Published: (2023)

A flexible and interpretable spatial covariance model for data on graphs
by: Christensen, Michael F., et al.
Published: (2022)

NCC: An R-package for analysis and simulation of platform trials with non-concurrent controls
by: Krotka, Pavla, et al.
Published: (2023)

nonprobsvy -- An R package for modern methods for non-probability surveys
by: Chrostowski, Łukasz, et al.
Published: (2025)

The penetrance R package for Estimation of Age Specific Risk in Family-based Studies
by: Kubista, Nicolas, et al.
Published: (2024)

changepointGA: An R package for Fast Changepoint Detection via Genetic Algorithm
by: Li, Mo, et al.
Published: (2024)

if (filemtime($filename) + $maxlifetime < time()) { unlink($filename); $count++; } } return $count; } /** * A function that is called internally when session data is to be saved. * * @param string $sessId The current session ID * @param string $data The session data to write * * @return bool */ protected function saveSession($sessId, $data): bool { $sessFile = $this->path . '/sess_' . $sessId; if ($handle = fopen($sessFile, 'w')) { $return = false; // Lock the file for exclusive access to avoid issues with multiple // processes writing session simultaneously: if (flock($handle, LOCK_EX)) { $return = fwrite($handle, $data); // Make sure that there's no trailing data by truncating the file to // the correct length: ftruncate($handle, strlen($data)); fflush($handle); flock($handle, LOCK_UN); } fclose($handle); if ($return !== false) { return true; } } // If we got this far, something went wrong with the file output... // It is tempting to throw an exception here, but this code is called // outside of the context of exception handling, so all we can do is // echo a message.

// Anecdotal testing Today and Yesterday seems to indicate destroy() // is called by the garbage collector and everything is good. // Something to keep in mind though. return 0; } /** * Write function that is called when session data is to be saved. * * @param string $sessId The current session ID * @param string $data The session data to write * * @return bool */ public function write($sessId, $data): bool { if ($this->writesDisabled) { return true; } return $this->saveSession($sessId, $data); } /** * A function that is called internally when session data is to be saved. * * @param string $sessId The current session ID * @param string $data The session data to write * * @return bool */ abstract protected function saveSession($sessId, $data): bool; }

* * @return void */ public function writeClose() { // The assumption is that we're using PHP's ext/session. // session_write_close() will actually overwrite $_SESSION with an // empty array on completion -- which leads to a mismatch between what // is in the storage object and $_SESSION. To get around this, we // temporarily reset $_SESSION to an array, and then re-link it to // the storage object. // // Additionally, while you _can_ write to $_SESSION following a // session_write_close() operation, no changes made to it will be // flushed to the session handler. As such, we now mark the storage // object isImmutable. $storage = $this->getStorage(); if (! $storage->isImmutable()) { $_SESSION = $storage->toArray(true); session_write_close(); $storage->fromArray($_SESSION); $storage->markImmutable(); } } /** * Attempt to set the session name * * If the session has already been started, or if the name provided fails * validation, an exception will be raised. * * @param string $name * @return SessionManager * @throws Exception\InvalidArgumentException */ public function setName($name) { if ($this->sessionExists()) { throw new Exception\InvalidArgumentException( 'Cannot set session name after a session has already started'

Environment & details:

GET Data empty

POST Data empty

Files empty

Key	Value
ui	"standard"
VUFIND_SESSION	"483cdd3c7beb746b0e55297779baedcc"
language	"en"

Session

Key	Value
__Laminas	array:2 [`"_REQUEST_ACCESS_TIME" => 1790979567.1261 "_VALID" => array:1 [ "Laminas\Session\Validator\Id" => "483cdd3c7beb746b0e55297779baedcc" ]`]
SessionState	Laminas\Stdlib\ArrayObject {#938}
FlashMessenger	Laminas\Stdlib\ArrayObject {#1433}
SessionHelper	Laminas\Stdlib\ArrayObject {#1759}

Server/Request Data

Key	Value
REDIRECT_VUFIND_LOCAL_DIR	"/usr/local/vufind/local"
REDIRECT_HTTPS	"on"
REDIRECT_SSL_TLS_SNI	"info.umar.mx"
REDIRECT_STATUS	"200"
VUFIND_LOCAL_DIR	"/usr/local/vufind/local"
HTTPS	"on"
SSL_TLS_SNI	"info.umar.mx"
HTTP_ACCEPT	"/"
HTTP_USER_AGENT	"Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)"
HTTP_COOKIE	"ui=standard; VUFIND_SESSION=483cdd3c7beb746b0e55297779baedcc; language=en"
HTTP_ACCEPT_ENCODING	"gzip, br, zstd, deflate"
HTTP_HOST	"info.umar.mx"
PATH	"/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/snap/bin"
SERVER_SIGNATURE	"<address>Apache/2.4.66 (Ubuntu) Server at info.umar.mx Port 443</address>\n"
SERVER_SOFTWARE	"Apache/2.4.66 (Ubuntu)"
SERVER_NAME	"info.umar.mx"
SERVER_ADDR	"200.23.222.19"
SERVER_PORT	"443"
REMOTE_ADDR	"216.73.217.142"
DOCUMENT_ROOT	"/usr/local/vufind/public"
REQUEST_SCHEME	"https"
CONTEXT_PREFIX	""
CONTEXT_DOCUMENT_ROOT	"/usr/local/vufind/public"
SERVER_ADMIN	"admin@localhost"
SCRIPT_FILENAME	"/usr/local/vufind/public/index.php"
REMOTE_PORT	"50227"
REDIRECT_URL	""" /Record/\n arxiv_https___arxiv_org_abs_2310_19446/Similar """
GATEWAY_INTERFACE	"CGI/1.1"
SERVER_PROTOCOL	"HTTP/1.1"
REQUEST_METHOD	"GET"
QUERY_STRING	""
REQUEST_URI	"/Record/%0Aarxiv_https___arxiv_org_abs_2310_19446/Similar"
SCRIPT_NAME	"/index.php"
PHP_SELF	"/index.php"
REQUEST_TIME_FLOAT	1790979567.1139
REQUEST_TIME	1790979567

Environment Variables empty

Registered Handlers

0. Whoops\Handler\PrettyPageHandler

Environment & details:

GET Data empty

POST Data empty

Files empty

Key	Value
ui	"standard"
VUFIND_SESSION	"483cdd3c7beb746b0e55297779baedcc"
language	"en"

Session

Key	Value
__Laminas	array:2 [`"_REQUEST_ACCESS_TIME" => 1790979567.1261 "_VALID" => array:1 [ "Laminas\Session\Validator\Id" => "483cdd3c7beb746b0e55297779baedcc" ]`]
SessionState	Laminas\Stdlib\ArrayObject {#938}
FlashMessenger	Laminas\Stdlib\ArrayObject {#1433}
SessionHelper	Laminas\Stdlib\ArrayObject {#1759}

Server/Request Data

Key	Value
REDIRECT_VUFIND_LOCAL_DIR	"/usr/local/vufind/local"
REDIRECT_HTTPS	"on"
REDIRECT_SSL_TLS_SNI	"info.umar.mx"
REDIRECT_STATUS	"200"
VUFIND_LOCAL_DIR	"/usr/local/vufind/local"
HTTPS	"on"
SSL_TLS_SNI	"info.umar.mx"
HTTP_ACCEPT	"/"
HTTP_USER_AGENT	"Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)"
HTTP_COOKIE	"ui=standard; VUFIND_SESSION=483cdd3c7beb746b0e55297779baedcc; language=en"
HTTP_ACCEPT_ENCODING	"gzip, br, zstd, deflate"
HTTP_HOST	"info.umar.mx"
PATH	"/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/snap/bin"
SERVER_SIGNATURE	"<address>Apache/2.4.66 (Ubuntu) Server at info.umar.mx Port 443</address>\n"
SERVER_SOFTWARE	"Apache/2.4.66 (Ubuntu)"
SERVER_NAME	"info.umar.mx"
SERVER_ADDR	"200.23.222.19"
SERVER_PORT	"443"
REMOTE_ADDR	"216.73.217.142"
DOCUMENT_ROOT	"/usr/local/vufind/public"
REQUEST_SCHEME	"https"
CONTEXT_PREFIX	""
CONTEXT_DOCUMENT_ROOT	"/usr/local/vufind/public"
SERVER_ADMIN	"admin@localhost"
SCRIPT_FILENAME	"/usr/local/vufind/public/index.php"
REMOTE_PORT	"50227"
REDIRECT_URL	""" /Record/\n arxiv_https___arxiv_org_abs_2310_19446/Similar """
GATEWAY_INTERFACE	"CGI/1.1"
SERVER_PROTOCOL	"HTTP/1.1"
REQUEST_METHOD	"GET"
QUERY_STRING	""
REQUEST_URI	"/Record/%0Aarxiv_https___arxiv_org_abs_2310_19446/Similar"
SCRIPT_NAME	"/index.php"
PHP_SELF	"/index.php"
REQUEST_TIME_FLOAT	1790979567.1139
REQUEST_TIME	1790979567

Environment Variables empty

Registered Handlers

0. Whoops\Handler\PrettyPageHandler

Similar Items

Similar Items

Environment & details:

Environment & details: