version 0.1.4.9000

sp functions were moved to another package, sp2.

.Rbuildignore

@@ -1,3 +1,5 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^\.travis\.yml$
+^appveyor\.yml$
+^LICENSE\.md$

DESCRIPTION

@@ -1,35 +1,32 @@
 Package: Ipaper
 Type: Package
 Title: Paper writing tools
-Version: 0.1.3
+Version: 0.1.4.9000
 Authors@R: person("Dongdong", "Kong", email = "[email protected]",
   role = c("aut", "cre"))
 Description: Download papers batchly using DOIs from many database. And some practical functions.
-License: MIT + file LICENSE
+License: GPL-3
 LazyData: TRUE
 import: 
     RoxygenNote: 6.1.0
-Suggests: testthat,
+Suggests: 
+    testthat (>= 2.1.0),
     knitr,
     rmarkdown
-LinkingTo: 
-  Rcpp, RcppArmadillo
 Imports:
-    httr,
-    xml2,
+    httr, xml2, jsonlite, 
     magrittr,
     stringr, purrr, 
-    jsonlite, 
-    maptools,
-    sp,
-    rgdal,
+    lubridate, 
     data.table,
     openxlsx, readxl, 
-    plyr, 
     reshape2,
     graphics, methods,
-    Rcpp,
-    parallel,
-    doParallel
+    parallel, doParallel,
+    foreach, plyr
+Remotes:
+    kongdd/foreach,
+    kongdd/plyr
 VignetteBuilder: knitr
 RoxygenNote: 6.1.1
+Roxygen: list(markdown = TRUE)

Ipaper.Rproj

@@ -6,12 +6,14 @@ AlwaysSaveHistory: Default
 
 EnableCodeIndexing: Yes
 UseSpacesForTab: Yes
-NumSpacesForTab: 2
+NumSpacesForTab: 4
 Encoding: UTF-8
 
 RnwWeave: Sweave
 LaTeX: pdfLaTeX
 
+LineEndingConversion: Windows
+
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source

NAMESPACE

@@ -2,32 +2,32 @@
 
 export(InitCluster)
 export(Init_Check)
+export(add_dn)
 export(box_qtl)
-export(df2sp)
+export(chunk)
+export(contain)
 export(dir.show)
 export(download_aria2)
 export(download_httr)
 export(ensemble_mean)
-export(extractId)
 export(fprintf)
 export(getDOIs_endnote)
-export(getPointsMODISTile)
-export(get_grid)
 export(get_sbatch)
 export(getwd_clip)
 export(ggplot_legend)
 export(github)
-export(gridSaveToPoly)
+export(ifelse2)
 export(killCluster)
+export(listk)
 export(makeVIDEO)
 export(melt_list)
+export(merge_pdf)
+export(obj.size)
 export(pal)
 export(par_sbatch)
-export(prj84)
-export(rdist.earth)
 export(read_json.gee)
 export(read_jsons.gee)
-export(readxlsx_ToList)
+export(read_xlsx2list)
 export(runningId)
 export(setwd_clip)
 export(src_AMS)
@@ -46,26 +46,29 @@ export(which.na)
 export(which.notna)
 export(write_fig)
 export(write_fig2ps)
+export(write_list2xlsx)
 export(write_urls)
 export(write_webfile)
-export(writelist_ToXlsx)
 import(httr)
 import(magrittr)
 import(openxlsx)
+import(parallel)
 import(plyr)
 import(readxl)
 import(xml2)
-importFrom(Rcpp,sourceCpp)
 importFrom(data.table,as.data.table)
 importFrom(data.table,data.table)
 importFrom(data.table,fwrite)
 importFrom(data.table,is.data.table)
 importFrom(data.table,setkeyv)
 importFrom(doParallel,registerDoParallel)
+importFrom(ggplot2,ggplot_gtable)
 importFrom(graphics,rect)
 importFrom(jsonlite,fromJSON)
 importFrom(jsonlite,read_json)
-importFrom(maptools,readShapePoly)
+importFrom(lubridate,yday)
+importFrom(lubridate,year)
+importFrom(lubridate,ymd)
 importFrom(methods,as)
 importFrom(parallel,makeCluster)
 importFrom(parallel,mclapply)
@@ -75,18 +78,6 @@ importFrom(purrr,map)
 importFrom(purrr,reduce)
 importFrom(purrr,transpose)
 importFrom(reshape2,melt)
-importFrom(rgdal,project)
-importFrom(rgdal,writeOGR)
-importFrom(sp,"coordinates<-")
-importFrom(sp,"proj4string<-")
-importFrom(sp,CRS)
-importFrom(sp,GridTopology)
-importFrom(sp,SpatialPixelsDataFrame)
-importFrom(sp,SpatialPolygons)
-importFrom(sp,coordinates)
-importFrom(sp,over)
-importFrom(sp,proj4string)
 importFrom(stringr,str_extract)
 importFrom(utils,URLdecode)
 importFrom(utils,write.table)
-useDynLib(Ipaper, .registration = TRUE)

R/Ipaper-package.R

@@ -0,0 +1,24 @@
+#' @title Ipaper
+#' @name Ipaper
+#' @aliases Ipaper-package
+#' @docType package
+#' @keywords download paper DOI
+#' 
+#' @importFrom stringr str_extract
+#' @importFrom jsonlite fromJSON read_json
+#' @importFrom purrr is_empty map transpose
+#' @importFrom methods as
+#' @importFrom data.table data.table
+#' @importFrom graphics rect
+#' @import httr xml2 magrittr plyr
+#' 
+#' @keywords internal
+"_PACKAGE"
+
+# The following block is used by usethis to automatically manage
+# roxygen namespace tags. Modify with care!
+## usethis namespace: start
+## usethis namespace: end
+# ' @useDynLib Ipaper, .registration = TRUE
+# ' @importFrom Rcpp sourceCpp
+NULL

R/add_dn.R

@@ -0,0 +1,28 @@
+#' Add n-day flag
+#' 
+#' To aggregated data into n-day (e.g. 8-day, 16-day) like MODIS product, a 
+#' n-day flag is need.
+#' 
+#' @param d data.frame or data.table
+#' @param days Integer number or vector, can't have duplicated value.
+#' 
+#' @examples
+#' date = seq.Date(as.Date("2010-01-01"), as.Date("2010-12-31"), by = "day")
+#' d <- data.frame(date)
+#' dnew <- add_dn(d, days = c(8, 16))
+#' @importFrom lubridate ymd year yday
+#' @export
+add_dn <- function(d, days = 8){
+    if (class(d$date) != 'Date')
+        d$date %<>% ymd()
+
+    d %<>% plyr::mutate(d, year = year(date), doy = yday(date))
+
+    days <- floor(days)
+    for (i in seq_along(days)){
+        day <- days[i]
+        # d$d8  = ceiling(d$doy/8)
+        eval(parse(text = sprintf("d$d%d <- ceiling(d$doy/%d)", day, day)))
+    }
+    return(d)
+}

R/chunk.R

@@ -0,0 +1,2 @@
+#' @export
+chunk <- function(x,n) split(x, cut(seq_along(x), n, labels = FALSE))

R/contain.R

@@ -0,0 +1,13 @@
+#' contain
+#' find assigned pattern variable names
+#' @param d A data.frame vector, or list
+#' @param pattern string used to match `names(d)`
+#' 
+#' @examples
+#' df <- data.frame(year = 2010, day = 1:3, month = 1, site = "A")
+#' contain(df, "year|month|day")
+#' @rdname tools
+#' @export
+contain <- function(d, pattern = "NDVI|EVI") {
+    names(d) %>% .[grep(pattern, .)]
+}

R/excel.R

@@ -1,17 +1,17 @@
-#' @title writelist.xlsx
+#' write_list2xlsx
+#' 
 #' @description base function, write list x into fileName with each list in workbook,
 #' write shapefile dbf table into excel *.xlsx
-#' @details 
 #' 
-#' @param x List object to be saved, \code{x} should have names and can't be NULL.
+#' @param x List object to be saved, `x` should have names and can't be NULL.
 #' @param file xlsx file name
 #' @param .progress name of the progress bar to use, see create_progress_bar.
 #' @param rowNames a logical value indicating whether the row names are to 
 #' be written.
 #' 
 #' @import openxlsx
 #' @export
-writelist_ToXlsx <- function (x, file, .progress = "text", rowNames = FALSE)
+write_list2xlsx <- function (x, file, .progress = "text", rowNames = FALSE)
 {
     sheetNames <- names(x)
     if (is.null(sheetNames))
@@ -33,17 +33,17 @@ writelist_ToXlsx <- function (x, file, .progress = "text", rowNames = FALSE)
     saveWorkbook(wb, file, overwrite = TRUE)
 }
 
-#' readxlsx_ToList
+#' read_xlsx2list
 #' 
 #' If excel file hava many sheets, this function also works.
 #' 
 #' @param file xlsx or xls file path
-#' @param ... other parameters to \code{\link[readxl]{read_excel}}
+#' @param ... other parameters to [readxl::read_excel()]
 #' 
 #' @import openxlsx readxl
 #' @importFrom plyr llply
 #' @export
-readxlsx_ToList <- function(file, ...){
+read_xlsx2list <- function(file, ...){
   cat(sprintf("[---- Reading File: %s ----]\n", file))
   ## judge whether it's xls or xlsx
   #  if file is *.xls use readxl::read_excel

R/fprintf.R

@@ -0,0 +1,9 @@
+#' fprintf
+#' Print sprintf result into console, just like C style fprintf function
+#' @param fmt a character vector of format strings, each of up to 8192 bytes.
+#' @param ... other parameters will be passed to `sprintf`
+#' 
+#' @examples
+#' cat(fprintf("%s\n", "Hello phenofit!"))
+#' @export
+fprintf <- function(fmt, ...) cat(sprintf(fmt, ...))