Title: Projecting Satellite-Derived Phenology in Space
Version: 2.0.1
Date: 2023-10-12
Maintainer: Christian John <cjohn@ucsb.edu>
Depends: R (≥ 4.1.0)
Imports: phenex, plyr, stringr, terra, doParallel
Description: This takes in a series of multi-layer raster files and returns a phenology projection raster, following methodologies described in John (2016) https://etda.libraries.psu.edu/catalog/13521clj5135.
License: GPL-3
URL: https://github.com/JepsonNomad/phenomap
BugReports: https://github.com/JepsonNomad/phenomap/issues
RoxygenNote: 7.1.2
NeedsCompilation: no
Packaged: 2023-10-12 21:22:27 UTC; christianjohn
Author: Christian John [aut, cre]
Repository: CRAN
Date/Publication: 2023-10-12 22:20:09 UTC

Convert a series of raster files to a single phenology raster.

Description

Convert a series of raster files to a single phenology raster.

Usage

mapPheno(
  File_List = NA,
  PhenoFactor = NA,
  phase = NA,
  threshold = NA,
  year = NA,
  NDVI = NA,
  VIQ = NA,
  DOY = NA,
  PR = NA,
  SnowExtent = NA,
  verbose = FALSE
)

Arguments

File_List

List of raster files

PhenoFactor

Character string; type of dataset to analyze (e.g., "VI", "Snow")

phase

Character string; name of phenophase to be measured (e.g., "greenup", "snowmelt", "senescence" or other arguments passed to phenex::phenophase())

threshold

Float threshold GWI value to be projected. Use only for VI option.

year

Integer Year (YYYY)

NDVI

Integer Band number of NDVI band in raster files

VIQ

Integer Band number of VI Quality layer in raster files

DOY

Integer Band number of Composite Day of Year layer in raster files

PR

Integer Band Number of PR layer in raster files

SnowExtent

Integer Band number of Maximum_Snow_Extent in raster files

verbose

TRUE or FALSE (Default = FALSE)

Value

Raster object with extent=extent(terra::rast(File_List)[1]) and CRS = crs(terra::rast(File_List)[1]). Digital numbers are expressed as Day of Year.

Examples


## Not run: 
fpath <- system.file("extdata", package="phenomap")
File_List <- paste(fpath, list.files(path = fpath, pattern=c("TinyCrop_")), sep="/")
File_List

PhenoFactor = "VI"
phase = "greenup"
threshold = 0.5
year = 2016
NDVI = 1
VIQ = 3
DOY = 4
PR = 5
verbose = TRUE

Sample.Greenup <- mapPheno(File_List = File_List, PhenoFactor = PhenoFactor,
                           phase = phase, threshold = threshold, year = year,
                           NDVI = NDVI, VIQ = VIQ, DOY = DOY, PR = PR,
                           SnowExtent=SnowExtent,
                           verbose = verbose)

## End(Not run)

Convert a series of phenology terra::raster files to a single long-term trend terra::raster.

Description

Convert a series of phenology terra::raster files to a single long-term trend terra::raster.

Usage

mapTrend(
  File_List,
  Year_List,
  parallel = FALSE,
  n.cores = NULL,
  verbose = FALSE
)

Arguments

File_List

List of phenology terra::raster files (i.e. those produced in 'mapPheno')

Year_List

Vector of Integer Year (YYYY) with length > 5

parallel

TRUE or FALSE (Default = FALSE) if TRUE, use parallel backend through plyr::aaply

n.cores

Integer number of cores to be used for parallel processing (only use if parallel = TRUE)

verbose

TRUE or FALSE (Default = FALSE)

Value

terra::raster object with extent=ext(rast(File_List)[1]) and CRS = crs(rast(File_List)[1]). Layer 1 is the slope estimate of the linear model relating green-up timing (Day of Year) to time (Year). Layer 2 is the p-value of the slope estimate. Layer 3 is the standard error of the slope estimate. Layer 4 is the r-squared value for the linear model.

Examples


## Not run: 

fpath <- system.file("extdata", package="phenomap")
File_List.Trend <- paste(fpath, list.files(path = fpath, pattern=c("Sample_Greenup_")), sep="/")

Year_List <- 2011:2016 # Tell it what years you're using
n.cores <- 4 # Set up parallel computing

phenotrend <- mapTrend(File_List = File_List.Trend,
                             Year_List = Year_List,
                             parallel = TRUE,
                             n.cores = n.cores,
                             verbose=TRUE)


## End(Not run)