hyfo 1.4.4

change package from rgdal to sf due to retirement of rdgal

.Rbuildignore

@@ -2,3 +2,5 @@
 ^\.Rproj\.user$
 ^data-raw$
 ^\.travis\.yml$
+^cran-comments\.md$
+^CRAN-SUBMISSION$

.Rhistory

@@ -1,66 +1,3 @@
-drizzle <- which(frc > minHindcastPreci & frc <= min(hindcast[hindcast > minHindcastPreci], na.rm = TRUE)
-& !is.na(frc))
-if (length(rain) > 0) {
-ecdfFrc <- ecdf(frc[rain])
-if (extrapolate == 'constant') {
-# This higher and lower index mean the extrapolation part
-higherIndex <- which(frc[rain] > max(hindcast, na.rm = TRUE))
-lowerIndex <- which(frc[rain] < min(hindcast, na.rm = TRUE))
-extrapolateIndex <- c(higherIndex, lowerIndex)
-non_extrapolateIndex <- setdiff(1:length(rain), extrapolateIndex)
-if (length(higherIndex) > 0) {
-maxHindcast <- max(hindcast, na.rm = TRUE)
-dif <- maxHindcast - max(obs, na.rm = TRUE)
-frc[rain[higherIndex]] <- frc[higherIndex] - dif
-}
-if (length(lowerIndex) > 0) {
-minHindcast <- min(hindcast, na.rm = TRUE)
-dif <- minHindcast - min(obs, nna.rm = TRUE)
-frc[rain[lowerIndex]] <- frc[lowerIndex] - dif
-}
-# Here the original function doesn't accout for the situation that extraploateIndex is 0
-# if it is 0, rain[-extraploateIndex] would be nothing
-# Above has been solved by using setdiff.
-frc[rain[non_extrapolateIndex]] <- quantile(obs[which(obs > prThreshold & !is.na(obs))],
-probs = ecdfHindcast(frc[rain[non_extrapolateIndex]]),
-na.rm = TRUE, type = 4)
-} else {
-frc[rain] <- quantile(obs[which(obs > prThreshold & !is.na(obs))],
-probs = ecdfHindcast(frc[rain]), na.rm = TRUE, type = 4)
-}
-}
-if (length(drizzle) > 0){
-# drizzle part is a seperate part. it use the ecdf of frc (larger than minHindcastPreci) to
-# biascorrect the original drizzle part
-frc[drizzle] <- quantile(frc[which(frc > min(hindcast[which(hindcast > minHindcastPreci)], na.rm = TRUE) &
-!is.na(frc))], probs = ecdfFrc(frc[drizzle]), na.rm = TRUE,
-type = 4)
-}
-frc[noRain] <- 0
-} else {
-# in this condition minHindcastPreci is the max of hindcast, so all hindcast <= minHindcastPreci
-# And frc distribution is used then.
-noRain <- which(frc <= minHindcastPreci & !is.na(frc))
-rain <- which(frc > minHindcastPreci & !is.na(frc))
-if (length(rain) > 0) {
-ecdfFrc <- ecdf(frc[rain])
-frc[rain] <- quantile(obs[which(obs > prThreshold & !is.na(obs))], probs = ecdfFrc(frc[rain]),
-na.rm = TRUE, type = 4)
-}
-frc[noRain]<-0
-}
-return(frc)
-}
-biasCorrect_core_gqm <- function(frc, hindcast, obs, prThreshold, minHindcastPreci) {
-if (any(obs > prThreshold)) {
-ind <- which(obs > prThreshold & !is.na(obs))
-obsGamma <- fitdistr(obs[ind],"gamma", lower = c(0, 0))
-ind <- which(hindcast > 0 & !is.na(hindcast))
-hindcastGamma <- fitdistr(hindcast[ind],"gamma", lower = c(0, 0))
-rain <- which(frc > minHindcastPreci & !is.na(frc))
-noRain <- which(frc <= minHindcastPreci & !is.na(frc))
-probF <- pgamma(frc[rain], hindcastGamma$estimate[1], rate = hindcastGamma$estimate[2])
-frc[rain] <- qgamma(probF,obsGamma$estimate[1], rate = obsGamma$estimate[2])
 frc[noRain] <- 0
 } else {
 warning('All the observations of this cell(station) are lower than the threshold,
@@ -510,3 +447,66 @@ devtools::check_win_devel()
 devtools::check_win_devel()
 devtools::build()
 devtools::build()
+devtools::check_win_devel()
+install.packages("sf")
+devtools::check_win_devel()
+install.packages("sf")
+install.packages("sf")
+devtools::check_win_devel()
+devtools::check_win_devel()
+devtools::check_win_devel()
+devtools::check_win_devel()
+devtools::build()
+devtools::build()
+devtools::check(remote = T, cran = T)
+devtools::document()
+devtools::check(remote = T, cran = T)
+devtools::check_win_devel()
+devtools::check_win_devel()
+install.packages("devtools")
+install.packages("devtools")
+install.packages("devtools")
+install.packages("devtools")
+install.packages("devtools")
+install.packages("devtools")
+install.packages("devtools")
+devtools::document()
+install.packages("cli")
+install.packages("cli")
+devtools::document()
+devtools::check(remote = T, cran = T)
+library(cli)
+devtools::document()
+library(devtools)
+devtools::document()
+library(rlang)
+devtools::document()
+devtools::check(remote = T, cran = T)
+devtools::build()
+?devtools
+devtools::build(binary = T)
+devtools::build()
+devtools::submit_cran()
+devtools::use_cran_comments()
+use_cran_comments()
+usethis::use_cran_comments()
+devtools::submit_cran()
+devtools::submit_cran()
+devtools::submit_cran()
+devtools::build()
+devtools::submit_cran()
+debug(devtools::build())
+debug(submit_cran)
+debug(devtools::submit_cran)
+devtools::submit_cran()
+devtools::submit_cran()
+r
+new_url
+new_url$query$submit == "1"
+new_url$query$submit
+new_url$query
+r$url
+httr::parse_url(r$url)
+devtools::submit_cran()
+undebug(devtools::submit_cran)
+devtools::submit_cran()

.Rproj.user/shared/notebooks/paths

@@ -1,7 +1,4 @@
-C:/hyfo/DESCRIPTION="E115FF50"
-C:/hyfo/R/getSpatialMap.R="360D9F5D"
-C:/hyfo/R/ncdf.R="6981B7D0"
-C:/hyfo/README.md="BBF5FB5B"
-C:/hyfo/man/getSpatialMap.Rd="B8BD6975"
-C:/hyfo/man/writeNcdf.Rd="665DA26C"
-C:/hyfo/vignettes/hyfo.Rmd="4D6D9459"
+/Users/yuanchaoxu/Documents/GitHub/hyfo/.travis.yml="3AC61E6F"
+/Users/yuanchaoxu/Documents/GitHub/hyfo/NAMESPACE="11200187"
+/Users/yuanchaoxu/Documents/GitHub/hyfo/NEWS="40156A70"
+/Users/yuanchaoxu/Documents/GitHub/hyfo/cran-comments.md="E91D33FC"

.travis.yml

@@ -36,8 +36,7 @@ apt_packages:
  - libproj0
 
 #r_binary_packages:
-# - rgdal
-# - rgeos
+# - sf
 # - data.table
 #r_packages:
 # - data.table

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 1.4.4
+Date: 2023-07-19 14:24:10 UTC
+SHA: 37791a34a0676a9a05cb6ee87291561f702e1bc7

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: hyfo
 Type: Package
 Title: Hydrology and Climate Forecasting
-Version: 1.4.3
-Date: 2020-8-26
+Version: 1.4.4
+Date: 2023-7-12
 Authors@R: person("Yuanchao", "Xu", email = "[email protected]",
  role = c("aut", "cre"))
 Description: Focuses on data processing and visualization in hydrology and
@@ -19,13 +19,12 @@ Imports:
  ggplot2 (>= 1.0.1),
  reshape2 (>= 1.4.1),
  zoo (>= 1.7-12),
- rgdal (>= 0.8-16),
+ sf (>= 1.0-12),
  plyr (>= 1.8.3),
  moments (>= 0.14),
  lmom (>= 2.5),
  maps(>= 2.3-9),
  maptools (>= 0.8-36),
- rgeos (>= 0.3-8),
  ncdf4 (>= 1.14.1),
  MASS (>= 7.3-39),
  methods,
@@ -39,4 +38,4 @@ LazyData: true
 URL: https://yuanchao-xu.github.io/hyfo/
 BugReports: https://github.com/Yuanchao-Xu/hyfo/issues
 Repository: CRAN
-RoxygenNote: 6.1.1
+RoxygenNote: 7.2.3

NAMESPACE

@@ -36,8 +36,7 @@ import(maps)
 import(maptools)
 import(ncdf4)
 import(plyr)
-import(rgdal)
-import(rgeos)
+import(sf)
 importFrom(MASS,fitdistr)
 importFrom(data.table,rbindlist)
 importFrom(grDevices,rainbow)
@@ -49,6 +48,7 @@ importFrom(methods,setMethod)
 importFrom(moments,kurtosis)
 importFrom(moments,skewness)
 importFrom(reshape2,melt)
+importFrom(sf,st_read)
 importFrom(stats,aggregate)
 importFrom(stats,coef)
 importFrom(stats,cor)

NEWS

@@ -69,6 +69,11 @@ Date: 2015-12-15
 NOTE:
 ====
 - for hyfo$Data part, when load and write using ncdf4, there will be very little differences compared to the original, which cannot be addressed. If you first load an ncdf file, then write it, then load it again. The data part may have very little difference, less than 10E-5.
+hyfo 1.4.4
+==========
+Date: 2023-07-12
+
+- change package from rgdal to sf due to retirement of rdgal
 
 
 

R/dataDocument.R

@@ -53,7 +53,7 @@
 
 
 #' testCat
-#' @format A catchment file generated by library rgdal.
+#' @format A catchment file generated by library sf.
 #' \describe{
 #' \item{class}{Formal class 'SpatialPolygonsDataFrame' [package "sp"] with 5 slots}
 #' ...

R/getSpatialMap.R

@@ -223,7 +223,7 @@ getSpatialMap <- function(dataset, method = NULL, member = 'mean', ...) {
 #' # More examples can be found in the user manual on https://yuanchao-xu.github.io/hyfo/
 #' 
 #' @export
-#' @import ggplot2 plyr maps maptools rgeos
+#' @import ggplot2 plyr maps maptools sf
 #' @importFrom stats median
 #' @importFrom reshape2 melt
 #' @references 
@@ -246,7 +246,7 @@ getSpatialMap <- function(dataset, method = NULL, member = 'mean', ...) {
 #' Objects. R package version 0.8-36. https://CRAN.R-project.org/package=maptools
 #' 
 #' \item Roger Bivand and Colin Rundel (2015). rgeos: Interface to Geometry Engine - Open Source (GEOS). R
-#' package version 0.3-11. https://CRAN.R-project.org/package=rgeos
+#' package version 0.3-11. https://CRAN.R-project.org/package=sf
 #' 
 #' }
 #' 

R/shp2cat.R

@@ -2,7 +2,7 @@
 #' @param filePath A string representing the path of the shape file.
 #' @return A catchment object can be used in \code{getSpatialMap()}.
 #' @export
-#' @details This function is based on the package \code{rgdal} and \code{sp}, and the output comes from the package 
+#' @details This function is based on the package \code{sf} and \code{sp}, and the output comes from the package 
 #' \code{sp}
 #' @examples
 #' #open internal file
@@ -11,13 +11,13 @@
 #' 
 #' # More examples can be found in the user manual on https://yuanchao-xu.github.io/hyfo/
 #' 
-#' @import rgdal
+#' @importFrom sf st_read
 #' @importFrom utils tail
 #' @references 
 #' 
 #' \itemize{
 #' \item Roger Bivand, Tim Keitt and Barry Rowlingson (2015). rgdal: Bindings for the Geospatial Data
-#' Abstraction Library. R package version 1.0-4. https://CRAN.R-project.org/package=rgdal
+#' Abstraction Library. R package version 1.0-4. https://CRAN.R-project.org/package=sf
 #' 
 #' \item R Core Team (2015). R: A language and environment for statistical computing. R Foundation for
 #' Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
@@ -46,6 +46,6 @@ shp2cat <- function(filePath) {
  }
 
  if (length(folderName) == 0) stop('No shape file found, make sure the shp file is selected.')
- catchment <- readOGR(folderName, catName1)
+ catchment <- st_read(folderName, catName1)
  return(catchment)
 }

cran-comments.md

@@ -0,0 +1,5 @@
+## R CMD check results
+
+0 errors | 0 warnings | 1 note
+
+* This is a new release.