R/TrendNPS.r
In LAStarcevich/TrendNPS: NPS Trend Analyses for Complex Survey Designs
#' TrendNPS: An R package for trend analysis for data from complex survey
#' designs.
#'
#' @section Description: The TrendNPS package provides trend analysis tools for
#' complex survey designs. Please refer to the accompanying National Park
#' Service Natural Resource Report (NRR) series report Starcevich et al.
#' (2017) and Starcevich et al. (2018) for background on how and under what
#' circumstances to use the trend analysis methods. Example analyses are
#' provided using the tools offered in the TrendNPS R package.
#'
#' @section TrendNPS functions:
#' \code{TrendNPS_Cont}, \cr
#' \code{TrendNPS_Count}, \cr
#' \code{TrendNPS_Binary}, \cr
#' \code{LinearizationVar_StRS}, \cr
#' \code{LinearizationVar}, \cr
#' \code{PWIGLS_ALL}
#'
#' @docType package
#' @name TrendNPS
NULL
#' NPS lake chemistry monitoring data for sites with at least two visits. Data
#' have been merged with GRTS sampling design factors.
#'
#' @name LakeDataRep
#' @docType data
#' @usage data(LakeDataRep)
#' @format A data frame with 77 rows and 17 variables.
#'
#' \describe{ A dataset containing the Sierra Nevada Network lake chemistry data
#' from Sequoia-Kings Canyon and Yosemite National Parks. See Starcevich et al.
#' (2017) for more information. The variables are as follows:
#'
#' \itemize{
#' \item Site. Lake identifier.
#' \item Park. National Park used as stratification variable. (\code{SEKI} = Sequoia-Kings Canyon, \code{YOSE} = Yosemite)
#' \item Year. The observation year. (2008--2013)
#' \item WYear. The observation year minus 2008. (0--5)
#' \item xcoord. UTM easting.
#' \item ycoord. UTM northing.
#' \item mdcaty. Multi-density category representing cost class from the unequal probability sample draw.
#' \item panel. Temporal revisit panel, or oversample when an oversample site was used.
#' \item wgt. Design weight from original GRTS sample draw.
#' \item lake_area. Lake area in square meters.
#' \item lake_perim. Lake perimeter in meters.
#' \item Elevation_m. Lake elevation in meters.
#' \item pH. pH measurement of lake.
#' \item Cl. Chloride measurement of lake.
#' \item EvalStatus. Evaluation status of lake relative to frame and nonresponse error.
#' \item AdjWgt. Design weight adjusted for frame error and nonresponse error.
#' \item PanelWt. Panel weight, or the inverse of the panel inclusion probability.
#' }
#' }
#' @keywords datasets
#' @references Heard, A. M., L. A. H. Starcevich, J. O. Sickman, M. Goldin Rose,
#' and D. W. Schweizer. 2012. Sierra Nevada Network lake monitoring protocol.
#' Natural Resource Report \cr NPS/SIEN/NRR-2012/551. National Park Service, Fort
#' Collins, Colorado.
#'
NULL
#' NPS lake chemistry monitoring data for all sites.
#'
#' @name LakeData_orig
#' @docType data
#' @usage data(LakeData_orig)
#' @format A data frame with 130 rows and 6 variables.
#'
#' \describe{ A dataset containing the Sierra Nevada Network lake chemistry data
#' from Sequoia-Kings Canyon and Yosemite National Parks. See Starcevich et al.
#' (2017) for more information. The variables are as follows:
#'
#' \itemize{
#' \item Site. Lake identifier.
#' \item Year. The observation year. (2008--2013)
#' \item Park. National Park used as stratification variable. (\code{SEKI} = Sequoia-Kings Canyon, \code{YOSE} = Yosemite)
#' \item Elevation_m. Lake elevation in meters.
#' \item pH. pH measurement of lake.
#' \item Cl. Chloride measurement of lake.
#' }
#' }
#' @keywords datasets
#' @references Heard, A. M., L. A. H. Starcevich, J. O. Sickman, M. Goldin Rose,
#' and D. W. Schweizer. 2012. Sierra Nevada Network lake monitoring protocol.
#' Natural Resource Report \cr NPS/SIEN/NRR-2012/551. National Park Service, Fort
#' Collins, Colorado.
#'
NULL
#' NPS lake chemistry GRTS sample.
#'
#' @name GRTSsample
#' @docType data
#' @usage data(GRTSsample)
#' @format A data frame with 461 rows and 10 variables.
#'
#' \describe{The design file containing the Sierra Nevada Network lake chemistry
#' GRTS sample draw. Sites were stratified by Park and unequal probability
#' sampling relative to a cost class (\code{mdcaty}) were drawn. The sample was
#' drawn using the \code{spsurvey} package (Kincaid and Olsen 2015). The
#' variables are as follows:
#'
#' \itemize{
#' \item siteID. Lake identifier.
#' \item Park. National Park used as stratification variable. (\code{SEKI} = Sequoia-Kings Canyon, \code{YOSE} = Yosemite)
#' \item WYear. The observation year minus 2008. (0--5)
#' \item xcoord. UTM easting.
#' \item ycoord. UTM northing.
#' \item mdcaty. Multi-density category representing cost class from the unequal probability sample draw.
#' \item panel. Temporal revisit panel, or oversample when an oversample site was used.
#' \item wgt. Design weight from original GRTS sample draw.
#' \item lake_area. Lake area in square meters.
#' \item lake_perim. Lake perimeter in meters.
#' }
#' }
#' @keywords datasets
#' @references Heard, A.M., L.A. H. Starcevich, J.O. Sickman, M. Goldin Rose,
#' and D.W. Schweizer. 2012. Sierra Nevada Network lake monitoring protocol.
#' Natural Resource Report NPS/SIEN/NRR-2012/551. National Park Service, Fort
#' Collins, Colorado.
#'
#' Kincaid, T. M. and Olsen, A. R. 2015. spsurvey: Spatial Survey Design and
#' Analysis. R package version 3.1. \url{http://www.epa.gov/nheerl/arm/}.
#'
NULL
#' Seastar count data.
#'
#' @name Seastar
#' @docType data
#' @usage data(Seastar)
#' @format A data frame with 65 rows and 10 variables.
#'
#' \describe{The file contains counts of \emph{Dermasterias imbricata} (leather
#' seastar) collected between 2009 and 2015 across two parks, Katmai National
#' Park (KATM) and Kenai Fjords National Park (KEFJ) in the Southwest Alaskan
#' Network. The variables are as follows:
#'
#' \itemize{
#' \item Site. Sampling unit selected with GRTS sampling.
#' \item Park. National Park. \code{KATM} = Katmai NP and \code{KEFJ} = Kenai Fjords NP.
#' \item Year. Survey year formatted as a factor for random effects estimation.
#' \item WYear. Scalar year covariate for trend analysis.
#' \item Gradient. Site gradient (degrees).
#' \item Long. Site longitude.
#' \item Lat. Site latitude.
#' \item Count. Number of sea stars observed.
#' \item wgt. Design weight from the sample draw.
#' \item PanelWt. Weight to account for temporal revisit design given sample inclusion.
#' }
#' }
#' @keywords datasets
#' @author Leigh Ann Starcevich of Western EcoSystems Technology, Inc.
#' @references Alaska Ocean Observing System Gulf of Alaska Data Integration
#' Portal. 2017. Nearshore: Intertidal Systems in Gulf of Alaska data
#' available at:
#' \url{http://portal.aoos.org/gulf-of-alaska.php#metadata/53c052b6-8874-46d1-b40a-acc615a3879a/project/files}.
#'
NULL
#' \emph{Acrosiphonia} binary cover data.
#'
#' @name Cover_Acro
#' @docType data
#' @usage data(Cover_Acro)
#' @format A data frame with 1794 rows and 11 variables.
#'
#' \describe{The file contains binary indicators of \emph{Acrosiphonia} cover
#' collected between 2009 and 2015 across two parks, Katmai National Park (KATM)
#' and Kenai Fjords National Park (KEFJ) in the Southwest Alaskan Network. Data
#' hierarchy includes Elevation class within Quadrat within Site. The variables
#' are as follows:
#'
#' \itemize{
#' \item Site. Sampling unit selected with GRTS sampling.
#' \item Park. National Park. \code{KATM} = Katmai NP and \code{KEFJ} = Kenai Fjords NP.
#' \item Quad. Quadrat within Site.
#' \item Elev. Elevation class within \code{Quad} Quadrat.
#' \item Year. Survey year formatted as a factor for random effects estimation.
#' \item WYear. Scalar year covariate for trend analysis.
#' \item Gradient. Site gradient (degrees).
#' \item Long. Site longitude.
#' \item Lat. Site latitude.
#' \item wgt. Design weight from the sample draw.
#' \item PanelWt. Weight to account for temporal revisit design given sample inclusion.
#' }
#' }
#' @keywords datasets
#' @author Leigh Ann Starcevich of Western EcoSystems Technology, Inc.
#' @references Alaska Ocean Observing System Gulf of Alaska Data Integration
#' Portal. 2017. Nearshore: Intertidal Systems in Gulf of Alaska data
#' available at:
#' \url{http://portal.aoos.org/gulf-of-alaska.php#metadata/53c052b6-8874-46d1-b40a-acc615a3879a/project/files}.
#'
NULL
#' Alaska Coastline 1:1,000,000 - Digital Chart of the World (DCW).
#'
#' @name mv_alaska_1mil_py
#' @docType data
#' @format A shapefile with 811 constituent polygons. To use, run
#'
#' \code{AK <- rgdal::readOGR(paste0(find.package("TrendNPS"),"/extdata"),"mv_alaska_1mil_py")}.
#'
#' \describe{The shapefile contains the polygonal extent of the US state of Alaska. This coverage was taken
#' from ESRI's Digital Chart of the World and clipped to the State of Alaska. The data was extracted from
#' the PONET coverage from each tile. For more information, see the DCW Data Dictionary.
#'
#' The attribute table contains the following variables, whose rows
#' contain the same data:
#'
#' \itemize{
#' \item TYPE. Uniformly "A" throughout. Unknown meaning.
#' \item REFRESH_01. Uniformly "2011-03-23" throughout. Unknown meaning.
#' \item POLNSTAT. Uniformly 0.0000 throughout. Unknown meaning.
#' \item POLNTYPE. Uniformly 0.0000 throughout. Unknown meaning.
#' }
#' }
#' @author Leigh Ann Starcevich of Western EcoSystems Technology, Inc.
#' @references Alaska Department of Natural Resources, Information Resource Management.
#'
#' Accessed January 13, 2017 and available at \url{http://asgdc.alaska.gov#2972}.
#'
NULL
LAStarcevich/TrendNPS documentation built on May 21, 2019, 9:19 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
#' TrendNPS: An R package for trend analysis for data from complex survey
#' designs.
#'
#' @section Description: The TrendNPS package provides trend analysis tools for
#' complex survey designs. Please refer to the accompanying National Park
#' Service Natural Resource Report (NRR) series report Starcevich et al.
#' (2017) and Starcevich et al. (2018) for background on how and under what
#' circumstances to use the trend analysis methods. Example analyses are
#' provided using the tools offered in the TrendNPS R package.
#'
#' @section TrendNPS functions:
#' \code{TrendNPS_Cont}, \cr
#' \code{TrendNPS_Count}, \cr
#' \code{TrendNPS_Binary}, \cr
#' \code{LinearizationVar_StRS}, \cr
#' \code{LinearizationVar}, \cr
#' \code{PWIGLS_ALL}
#'
#' @docType package
#' @name TrendNPS
NULL
#' NPS lake chemistry monitoring data for sites with at least two visits. Data
#' have been merged with GRTS sampling design factors.
#'
#' @name LakeDataRep
#' @docType data
#' @usage data(LakeDataRep)
#' @format A data frame with 77 rows and 17 variables.
#'
#' \describe{ A dataset containing the Sierra Nevada Network lake chemistry data
#' from Sequoia-Kings Canyon and Yosemite National Parks. See Starcevich et al.
#' (2017) for more information. The variables are as follows:
#'
#' \itemize{
#' \item Site. Lake identifier.
#' \item Park. National Park used as stratification variable. (\code{SEKI} = Sequoia-Kings Canyon, \code{YOSE} = Yosemite)
#' \item Year. The observation year. (2008--2013)
#' \item WYear. The observation year minus 2008. (0--5)
#' \item xcoord. UTM easting.
#' \item ycoord. UTM northing.
#' \item mdcaty. Multi-density category representing cost class from the unequal probability sample draw.
#' \item panel. Temporal revisit panel, or oversample when an oversample site was used.
#' \item wgt. Design weight from original GRTS sample draw.
#' \item lake_area. Lake area in square meters.
#' \item lake_perim. Lake perimeter in meters.
#' \item Elevation_m. Lake elevation in meters.
#' \item pH. pH measurement of lake.
#' \item Cl. Chloride measurement of lake.
#' \item EvalStatus. Evaluation status of lake relative to frame and nonresponse error.
#' \item AdjWgt. Design weight adjusted for frame error and nonresponse error.
#' \item PanelWt. Panel weight, or the inverse of the panel inclusion probability.
#' }
#' }
#' @keywords datasets
#' @references Heard, A. M., L. A. H. Starcevich, J. O. Sickman, M. Goldin Rose,
#' and D. W. Schweizer. 2012. Sierra Nevada Network lake monitoring protocol.
#' Natural Resource Report \cr NPS/SIEN/NRR-2012/551. National Park Service, Fort
#' Collins, Colorado.
#'
NULL
#' NPS lake chemistry monitoring data for all sites.
#'
#' @name LakeData_orig
#' @docType data
#' @usage data(LakeData_orig)
#' @format A data frame with 130 rows and 6 variables.
#'
#' \describe{ A dataset containing the Sierra Nevada Network lake chemistry data
#' from Sequoia-Kings Canyon and Yosemite National Parks. See Starcevich et al.
#' (2017) for more information. The variables are as follows:
#'
#' \itemize{
#' \item Site. Lake identifier.
#' \item Year. The observation year. (2008--2013)
#' \item Park. National Park used as stratification variable. (\code{SEKI} = Sequoia-Kings Canyon, \code{YOSE} = Yosemite)
#' \item Elevation_m. Lake elevation in meters.
#' \item pH. pH measurement of lake.
#' \item Cl. Chloride measurement of lake.
#' }
#' }
#' @keywords datasets
#' @references Heard, A. M., L. A. H. Starcevich, J. O. Sickman, M. Goldin Rose,
#' and D. W. Schweizer. 2012. Sierra Nevada Network lake monitoring protocol.
#' Natural Resource Report \cr NPS/SIEN/NRR-2012/551. National Park Service, Fort
#' Collins, Colorado.
#'
NULL
#' NPS lake chemistry GRTS sample.
#'
#' @name GRTSsample
#' @docType data
#' @usage data(GRTSsample)
#' @format A data frame with 461 rows and 10 variables.
#'
#' \describe{The design file containing the Sierra Nevada Network lake chemistry
#' GRTS sample draw. Sites were stratified by Park and unequal probability
#' sampling relative to a cost class (\code{mdcaty}) were drawn. The sample was
#' drawn using the \code{spsurvey} package (Kincaid and Olsen 2015). The
#' variables are as follows:
#'
#' \itemize{
#' \item siteID. Lake identifier.
#' \item Park. National Park used as stratification variable. (\code{SEKI} = Sequoia-Kings Canyon, \code{YOSE} = Yosemite)
#' \item WYear. The observation year minus 2008. (0--5)
#' \item xcoord. UTM easting.
#' \item ycoord. UTM northing.
#' \item mdcaty. Multi-density category representing cost class from the unequal probability sample draw.
#' \item panel. Temporal revisit panel, or oversample when an oversample site was used.
#' \item wgt. Design weight from original GRTS sample draw.
#' \item lake_area. Lake area in square meters.
#' \item lake_perim. Lake perimeter in meters.
#' }
#' }
#' @keywords datasets
#' @references Heard, A.M., L.A. H. Starcevich, J.O. Sickman, M. Goldin Rose,
#' and D.W. Schweizer. 2012. Sierra Nevada Network lake monitoring protocol.
#' Natural Resource Report NPS/SIEN/NRR-2012/551. National Park Service, Fort
#' Collins, Colorado.
#'
#' Kincaid, T. M. and Olsen, A. R. 2015. spsurvey: Spatial Survey Design and
#' Analysis. R package version 3.1. \url{http://www.epa.gov/nheerl/arm/}.
#'
NULL
#' Seastar count data.
#'
#' @name Seastar
#' @docType data
#' @usage data(Seastar)
#' @format A data frame with 65 rows and 10 variables.
#'
#' \describe{The file contains counts of \emph{Dermasterias imbricata} (leather
#' seastar) collected between 2009 and 2015 across two parks, Katmai National
#' Park (KATM) and Kenai Fjords National Park (KEFJ) in the Southwest Alaskan
#' Network. The variables are as follows:
#'
#' \itemize{
#' \item Site. Sampling unit selected with GRTS sampling.
#' \item Park. National Park. \code{KATM} = Katmai NP and \code{KEFJ} = Kenai Fjords NP.
#' \item Year. Survey year formatted as a factor for random effects estimation.
#' \item WYear. Scalar year covariate for trend analysis.
#' \item Gradient. Site gradient (degrees).
#' \item Long. Site longitude.
#' \item Lat. Site latitude.
#' \item Count. Number of sea stars observed.
#' \item wgt. Design weight from the sample draw.
#' \item PanelWt. Weight to account for temporal revisit design given sample inclusion.
#' }
#' }
#' @keywords datasets
#' @author Leigh Ann Starcevich of Western EcoSystems Technology, Inc.
#' @references Alaska Ocean Observing System Gulf of Alaska Data Integration
#' Portal. 2017. Nearshore: Intertidal Systems in Gulf of Alaska data
#' available at:
#' \url{http://portal.aoos.org/gulf-of-alaska.php#metadata/53c052b6-8874-46d1-b40a-acc615a3879a/project/files}.
#'
NULL
#' \emph{Acrosiphonia} binary cover data.
#'
#' @name Cover_Acro
#' @docType data
#' @usage data(Cover_Acro)
#' @format A data frame with 1794 rows and 11 variables.
#'
#' \describe{The file contains binary indicators of \emph{Acrosiphonia} cover
#' collected between 2009 and 2015 across two parks, Katmai National Park (KATM)
#' and Kenai Fjords National Park (KEFJ) in the Southwest Alaskan Network. Data
#' hierarchy includes Elevation class within Quadrat within Site. The variables
#' are as follows:
#'
#' \itemize{
#' \item Site. Sampling unit selected with GRTS sampling.
#' \item Park. National Park. \code{KATM} = Katmai NP and \code{KEFJ} = Kenai Fjords NP.
#' \item Quad. Quadrat within Site.
#' \item Elev. Elevation class within \code{Quad} Quadrat.
#' \item Year. Survey year formatted as a factor for random effects estimation.
#' \item WYear. Scalar year covariate for trend analysis.
#' \item Gradient. Site gradient (degrees).
#' \item Long. Site longitude.
#' \item Lat. Site latitude.
#' \item wgt. Design weight from the sample draw.
#' \item PanelWt. Weight to account for temporal revisit design given sample inclusion.
#' }
#' }
#' @keywords datasets
#' @author Leigh Ann Starcevich of Western EcoSystems Technology, Inc.
#' @references Alaska Ocean Observing System Gulf of Alaska Data Integration
#' Portal. 2017. Nearshore: Intertidal Systems in Gulf of Alaska data
#' available at:
#' \url{http://portal.aoos.org/gulf-of-alaska.php#metadata/53c052b6-8874-46d1-b40a-acc615a3879a/project/files}.
#'
NULL
#' Alaska Coastline 1:1,000,000 - Digital Chart of the World (DCW).
#'
#' @name mv_alaska_1mil_py
#' @docType data
#' @format A shapefile with 811 constituent polygons. To use, run
#'
#' \code{AK <- rgdal::readOGR(paste0(find.package("TrendNPS"),"/extdata"),"mv_alaska_1mil_py")}.
#'
#' \describe{The shapefile contains the polygonal extent of the US state of Alaska. This coverage was taken
#' from ESRI's Digital Chart of the World and clipped to the State of Alaska. The data was extracted from
#' the PONET coverage from each tile. For more information, see the DCW Data Dictionary.
#'
#' The attribute table contains the following variables, whose rows
#' contain the same data:
#'
#' \itemize{
#' \item TYPE. Uniformly "A" throughout. Unknown meaning.
#' \item REFRESH_01. Uniformly "2011-03-23" throughout. Unknown meaning.
#' \item POLNSTAT. Uniformly 0.0000 throughout. Unknown meaning.
#' \item POLNTYPE. Uniformly 0.0000 throughout. Unknown meaning.
#' }
#' }
#' @author Leigh Ann Starcevich of Western EcoSystems Technology, Inc.
#' @references Alaska Department of Natural Resources, Information Resource Management.
#'
#' Accessed January 13, 2017 and available at \url{http://asgdc.alaska.gov#2972}.
#'
NULL
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.