From b1e9fd2a14b561f37a0c81bb5fa7bad41571501b Mon Sep 17 00:00:00 2001 From: Dongdong Kong Date: Wed, 15 May 2019 16:49:43 +0800 Subject: [PATCH] version 0.1.4.9000 sp functions were moved to another package, sp2. --- .Rbuildignore | 2 + DESCRIPTION | 27 +- Ipaper.Rproj | 4 +- LICENSE | 21 - LICENSE.md | 595 ++++++++++++++++++ NAMESPACE | 37 +- R/Ipaper-package.R | 24 + R/RcppExports.R | 7 - R/add_dn.R | 28 + R/chunk.R | 2 + R/contain.R | 13 + R/excel.R | 14 +- R/fprintf.R | 9 + R/getPointsMODISTile.R | 39 -- R/getwd_clip.R | 58 ++ R/ggplot_legend.R | 1 + R/ifelse2.R | 19 + R/listk.R | 33 + R/makeVIDEO.R | 19 + R/{list.R => melt_list.R} | 0 R/merge_pdf.R | 22 + R/obj.size.R | 12 + R/parallel_init.R | 12 +- R/runningId.R | 16 + R/spatial.R | 150 ----- R/src_FUN.R | 30 +- R/src_download.R | 19 +- R/temp/parallel_remote_functions.R | 6 +- {src => R/temp/src}/.gitignore | 0 {src => R/temp/src}/RcppExports.cpp | 0 {src => R/temp/src}/split_array.cpp | 0 R/zzz.R | 114 ---- README.md | 35 +- appveyor.yml | 52 ++ man/Init_Check.Rd | 8 +- man/Ipaper.Rd | 10 +- man/add_dn.Rd | 22 + man/df2sp.Rd | 20 - man/dir.show.Rd | 4 +- man/download_aria2.Rd | 14 +- man/download_httr.Rd | 2 +- man/extractId.Rd | 16 - man/fprintf.Rd | 24 +- man/getPointsMODISTile.Rd | 29 - man/get_grid.Rd | 28 - man/get_sbatch.Rd | 2 +- man/getwd_clip.Rd | 22 +- man/gridSaveToPoly.Rd | 17 - man/ifelse2.Rd | 22 + man/killCluster.Rd | 11 + man/listk.Rd | 24 +- man/makeVIDEO.Rd | 2 +- man/merge_pdf.Rd | 26 + man/obj.size.Rd | 19 + man/pal.Rd | 2 +- man/prj84.Rd | 16 - man/rdist.earth.Rd | 16 - man/read_gee.Rd | 2 +- man/{readxlsx_ToList.Rd => read_xlsx2list.Rd} | 10 +- man/runningId.Rd | 25 + man/setwd_clip.Rd | 11 - man/srcFUN.Rd | 38 +- man/tools.Rd | 22 + ...writelist_ToXlsx.Rd => write_list2xlsx.Rd} | 13 +- man/write_urls.Rd | 2 +- man/write_webfile.Rd | 2 +- tests/testthat.R | 4 + tests/testthat/test-add_dn.R | 11 + tests/testthat/test-ifelse2.R | 6 + tests/testthat/test-listk.R | 12 + vignettes/.gitignore | 2 + vignettes/doi_paper.Rmd | 43 ++ 72 files changed, 1312 insertions(+), 667 deletions(-) delete mode 100644 LICENSE create mode 100644 LICENSE.md create mode 100644 R/Ipaper-package.R delete mode 100644 R/RcppExports.R create mode 100644 R/add_dn.R create mode 100644 R/chunk.R create mode 100644 R/contain.R create mode 100644 R/fprintf.R delete mode 100644 R/getPointsMODISTile.R create mode 100644 R/getwd_clip.R create mode 100644 R/ifelse2.R create mode 100644 R/listk.R create mode 100644 R/makeVIDEO.R rename R/{list.R => melt_list.R} (100%) create mode 100644 R/merge_pdf.R create mode 100644 R/obj.size.R create mode 100644 R/runningId.R delete mode 100644 R/spatial.R rename {src => R/temp/src}/.gitignore (100%) rename {src => R/temp/src}/RcppExports.cpp (100%) rename {src => R/temp/src}/split_array.cpp (100%) delete mode 100644 R/zzz.R create mode 100644 appveyor.yml create mode 100644 man/add_dn.Rd delete mode 100644 man/df2sp.Rd delete mode 100644 man/extractId.Rd delete mode 100644 man/getPointsMODISTile.Rd delete mode 100644 man/get_grid.Rd delete mode 100644 man/gridSaveToPoly.Rd create mode 100644 man/ifelse2.Rd create mode 100644 man/killCluster.Rd create mode 100644 man/merge_pdf.Rd create mode 100644 man/obj.size.Rd delete mode 100644 man/prj84.Rd delete mode 100644 man/rdist.earth.Rd rename man/{readxlsx_ToList.Rd => read_xlsx2list.Rd} (55%) create mode 100644 man/runningId.Rd delete mode 100644 man/setwd_clip.Rd create mode 100644 man/tools.Rd rename man/{writelist_ToXlsx.Rd => write_list2xlsx.Rd} (76%) create mode 100644 tests/testthat.R create mode 100644 tests/testthat/test-add_dn.R create mode 100644 tests/testthat/test-ifelse2.R create mode 100644 tests/testthat/test-listk.R create mode 100644 vignettes/.gitignore create mode 100644 vignettes/doi_paper.Rmd diff --git a/.Rbuildignore b/.Rbuildignore index 112ad26..3f2e071 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,3 +1,5 @@ ^.*\.Rproj$ ^\.Rproj\.user$ ^\.travis\.yml$ +^appveyor\.yml$ +^LICENSE\.md$ diff --git a/DESCRIPTION b/DESCRIPTION index a26636d..f1b6fb4 100644 --- a/DESCRIPTION +++ b/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 = "kongdd.sysu@gmail.com", 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) diff --git a/Ipaper.Rproj b/Ipaper.Rproj index eaa6b81..b3d39a6 100644 --- a/Ipaper.Rproj +++ b/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 diff --git a/LICENSE b/LICENSE deleted file mode 100644 index 3b7f36c..0000000 --- a/LICENSE +++ /dev/null @@ -1,21 +0,0 @@ -MIT License - -Copyright (c) 2017 Dongdong Kong - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..e4d8cbb --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,595 @@ +GNU General Public License +========================== + +_Version 3, 29 June 2007_ +_Copyright 2007 Free Software Foundation, Inc. <>_ + +Everyone is permitted to copy and distribute verbatim copies of this license +document, but changing it is not allowed. + +## Preamble + +The GNU General Public License is a free, copyleft license for software and other +kinds of works. + +The licenses for most software and other practical works are designed to take away +your freedom to share and change the works. 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To “grant” such a patent license to a party means to make +such an agreement or commitment not to enforce a patent against the party. + +If you convey a covered work, knowingly relying on a patent license, and the +Corresponding Source of the work is not available for anyone to copy, free of charge +and under the terms of this License, through a publicly available network server or +other readily accessible means, then you must either **(1)** cause the Corresponding +Source to be so available, or **(2)** arrange to deprive yourself of the benefit of the +patent license for this particular work, or **(3)** arrange, in a manner consistent with +the requirements of this License, to extend the patent license to downstream +recipients. “Knowingly relying” means you have actual knowledge that, but +for the patent license, your conveying the covered work in a country, or your +recipient's use of the covered work in a country, would infringe one or more +identifiable patents in that country that you have reason to believe are valid. + +If, pursuant to or in connection with a single transaction or arrangement, you +convey, or propagate by procuring conveyance of, a covered work, and grant a patent +license to some of the parties receiving the covered work authorizing them to use, +propagate, modify or convey a specific copy of the covered work, then the patent +license you grant is automatically extended to all recipients of the covered work and +works based on it. + +A patent license is “discriminatory” if it does not include within the +scope of its coverage, prohibits the exercise of, or is conditioned on the +non-exercise of one or more of the rights that are specifically granted under this +License. You may not convey a covered work if you are a party to an arrangement with +a third party that is in the business of distributing software, under which you make +payment to the third party based on the extent of your activity of conveying the +work, and under which the third party grants, to any of the parties who would receive +the covered work from you, a discriminatory patent license **(a)** in connection with +copies of the covered work conveyed by you (or copies made from those copies), or **(b)** +primarily for and in connection with specific products or compilations that contain +the covered work, unless you entered into that arrangement, or that patent license +was granted, prior to 28 March 2007. + +Nothing in this License shall be construed as excluding or limiting any implied +license or other defenses to infringement that may otherwise be available to you +under applicable patent law. + +### 12. No Surrender of Others' Freedom + +If conditions are imposed on you (whether by court order, agreement or otherwise) +that contradict the conditions of this License, they do not excuse you from the +conditions of this License. If you cannot convey a covered work so as to satisfy +simultaneously your obligations under this License and any other pertinent +obligations, then as a consequence you may not convey it at all. For example, if you +agree to terms that obligate you to collect a royalty for further conveying from +those to whom you convey the Program, the only way you could satisfy both those terms +and this License would be to refrain entirely from conveying the Program. + +### 13. Use with the GNU Affero General Public License + +Notwithstanding any other provision of this License, you have permission to link or +combine any covered work with a work licensed under version 3 of the GNU Affero +General Public License into a single combined work, and to convey the resulting work. +The terms of this License will continue to apply to the part which is the covered +work, but the special requirements of the GNU Affero General Public License, section +13, concerning interaction through a network will apply to the combination as such. + +### 14. Revised Versions of this License + +The Free Software Foundation may publish revised and/or new versions of the GNU +General Public License from time to time. Such new versions will be similar in spirit +to the present version, but may differ in detail to address new problems or concerns. + +Each version is given a distinguishing version number. If the Program specifies that +a certain numbered version of the GNU General Public License “or any later +version” applies to it, you have the option of following the terms and +conditions either of that numbered version or of any later version published by the +Free Software Foundation. If the Program does not specify a version number of the GNU +General Public License, you may choose any version ever published by the Free +Software Foundation. + +If the Program specifies that a proxy can decide which future versions of the GNU +General Public License can be used, that proxy's public statement of acceptance of a +version permanently authorizes you to choose that version for the Program. + +Later license versions may give you additional or different permissions. However, no +additional obligations are imposed on any author or copyright holder as a result of +your choosing to follow a later version. + +### 15. Disclaimer of Warranty + +THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. +EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES +PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER +EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE +QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE +DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + +### 16. Limitation of Liability + +IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY +COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS +PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, +INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE +PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE +OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE +WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE +POSSIBILITY OF SUCH DAMAGES. + +### 17. Interpretation of Sections 15 and 16 + +If the disclaimer of warranty and limitation of liability provided above cannot be +given local legal effect according to their terms, reviewing courts shall apply local +law that most closely approximates an absolute waiver of all civil liability in +connection with the Program, unless a warranty or assumption of liability accompanies +a copy of the Program in return for a fee. + +_END OF TERMS AND CONDITIONS_ + +## How to Apply These Terms to Your New Programs + +If you develop a new program, and you want it to be of the greatest possible use to +the public, the best way to achieve this is to make it free software which everyone +can redistribute and change under these terms. + +To do so, attach the following notices to the program. It is safest to attach them +to the start of each source file to most effectively state the exclusion of warranty; +and each file should have at least the “copyright” line and a pointer to +where the full notice is found. + + + Copyright (C) 2019 Dongdong Kong + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + +If the program does terminal interaction, make it output a short notice like this +when it starts in an interactive mode: + + Ipaper Copyright (C) 2019 Dongdong Kong + This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type 'show c' for details. + +The hypothetical commands `show w` and `show c` should show the appropriate parts of +the General Public License. Of course, your program's commands might be different; +for a GUI interface, you would use an “about box”. + +You should also get your employer (if you work as a programmer) or school, if any, to +sign a “copyright disclaimer” for the program, if necessary. For more +information on this, and how to apply and follow the GNU GPL, see +<>. + +The GNU General Public License does not permit incorporating your program into +proprietary programs. If your program is a subroutine library, you may consider it +more useful to permit linking proprietary applications with the library. If this is +what you want to do, use the GNU Lesser General Public License instead of this +License. But first, please read +<>. diff --git a/NAMESPACE b/NAMESPACE index 4da01c9..ae6b2a5 100644 --- a/NAMESPACE +++ b/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) diff --git a/R/Ipaper-package.R b/R/Ipaper-package.R new file mode 100644 index 0000000..2c9c926 --- /dev/null +++ b/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 diff --git a/R/RcppExports.R b/R/RcppExports.R deleted file mode 100644 index d3e7a24..0000000 --- a/R/RcppExports.R +++ /dev/null @@ -1,7 +0,0 @@ -# Generated by using Rcpp::compileAttributes() -> do not edit by hand -# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393 - -split_array <- function(x) { - .Call(`_Ipaper_split_array`, x) -} - diff --git a/R/add_dn.R b/R/add_dn.R new file mode 100644 index 0000000..f4b8115 --- /dev/null +++ b/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) +} diff --git a/R/chunk.R b/R/chunk.R new file mode 100644 index 0000000..a189d23 --- /dev/null +++ b/R/chunk.R @@ -0,0 +1,2 @@ +#' @export +chunk <- function(x,n) split(x, cut(seq_along(x), n, labels = FALSE)) diff --git a/R/contain.R b/R/contain.R new file mode 100644 index 0000000..85179f3 --- /dev/null +++ b/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, .)] +} diff --git a/R/excel.R b/R/excel.R index 01e5825..eeb1660 100644 --- a/R/excel.R +++ b/R/excel.R @@ -1,9 +1,9 @@ -#' @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 @@ -11,7 +11,7 @@ #' #' @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 diff --git a/R/fprintf.R b/R/fprintf.R new file mode 100644 index 0000000..0b637ed --- /dev/null +++ b/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, ...)) diff --git a/R/getPointsMODISTile.R b/R/getPointsMODISTile.R deleted file mode 100644 index 55bcb30..0000000 --- a/R/getPointsMODISTile.R +++ /dev/null @@ -1,39 +0,0 @@ -#' Get points data from MODIS tiles -#' -#' @param coor 2-column matrix of coordinates (longitude, latitude) -#' @param cellsize 500m products, cellsize is regarded as 1/240; 1km product, -#' cellsize is regarded as 1/120. -#' -#' @return -#' \itemize{ -#' \item{h} MODIS tile horizontal id -#' \item{v} MODIS tile vertical id -#' \item{i} point horizontal position at the tile -#' \item{j} point vertical position at the tile -#' } -#' @references -#' https://landweb.modaps.eosdis.nasa.gov/cgi-bin/developer/tilemap.cgi -#' https://modis-land.gsfc.nasa.gov/MODLAND_grid.html -#' -#' @export -#' @importFrom data.table data.table -#' @importFrom rgdal project -getPointsMODISTile <- function(coor, cellsize = 1/240){ - scale <- 463.312716528 *cellsize*240 # meter; 1km: 926.625433055833 - nline <- 1/cellsize*10 # how many lines per tile? - - proj_sin <- "+proj=sinu +lon_0=0 +x_0=0 +y_0=0 +a=6371007.181 +b=6371007.181 +units=m +no_defs" - - # coor: coordinate matrix, (longitude, latitude) - sin_xy <- project(coor, proj_sin) - sin_ij <- sin_xy/scale - - h <- floor(sin_ij[, 1]/nline) + 18 - v <- 8 - floor(sin_ij[, 2]/nline) - # calculate the tile and its location - px <- cbind( ceiling(sin_ij[, 1] %% nline), # horizontal - ceiling(nline - sin_ij[, 2] %% nline)) %>% - set_colnames(sprintf("s%d_%s", ceiling(scale/1e2)*1e2, c("i", "j")))# vertical - - data.table(coor, h, v, px)#return -} diff --git a/R/getwd_clip.R b/R/getwd_clip.R new file mode 100644 index 0000000..d5e8be0 --- /dev/null +++ b/R/getwd_clip.R @@ -0,0 +1,58 @@ +# windowsFonts( +# Times = windowsFont("Times New Roman"), +# ST = windowsFont("宋体"), +# YH = windowsFont("Microsoft Yahei"), +# Arial = windowsFont("Arial")) + +#' pal +#' show colors in figure device +#' +#' @param col colors to be visualize. +#' @param border rect border for each color +#' +#' @export +pal <- function(col, border = "light gray") +{ + n <- length(col) + plot(0, 0, type="n", xlim = c(0, 1), ylim = c(0, 1), + axes = FALSE, xlab = "", ylab = "") + rect(0:(n-1)/n, 0, 1:n/n, 1, col = col, border = border) +} + +#' @title dir.show +#' @description open assign path in windows explorer, and default path is +#' current directory. This function is only designed for windows system. +#' +#' @param path the path you want to open +#' @export +dir.show <- function(path = getwd()){ + if (.Platform$OS.type == 'windows'){ + commandStr <- paste("Explorer /e, ", gsub("/", "\\\\", path)) + suppressWarnings(shell(commandStr)) + } +} + +#' GET or SET working directory +#' +#' @description +#' * `getwd_clip`: get directory path in clipboard, same as getwd function +#' * `setwd_clip`: set directory path in clipboard, same as setwd function +#' +#' @references +#' 1. https://stackoverflow.com/questions/10959521/how-to-write-to-clipboard-on-ubuntu-linux-in-r +#' @note Only works in windows +#' +#' @examples +#' getwd_clip() +#' @export +getwd_clip <- function(){ + if (.Platform$OS.type == 'windows') { + path <- suppressWarnings(gsub("\\\\", "/", readLines("clipboard"))) + writeLines(path, "clipboard", sep = "") + path#quickly return + } +} + +#' @rdname getwd_clip +#' @export +setwd_clip <- function() setwd(getwd_clip()) diff --git a/R/ggplot_legend.R b/R/ggplot_legend.R index 285bb13..8c6738f 100644 --- a/R/ggplot_legend.R +++ b/R/ggplot_legend.R @@ -1,3 +1,4 @@ +#' @importFrom ggplot2 ggplot_gtable #' @export ggplot_legend<-function(g){ tmp <- ggplot_gtable(ggplot_build(g)) diff --git a/R/ifelse2.R b/R/ifelse2.R new file mode 100644 index 0000000..727e8e8 --- /dev/null +++ b/R/ifelse2.R @@ -0,0 +1,19 @@ +#' ifelse2 +#' +#' ternary operator just like java `test ? yes : no` +#' +#' @param test an object which can be coerced to logical mode. +#' @param yes return values for true elements of test. +#' @param no return values for false elements of test. +#' +#' @examples +#' x <- ifelse2(TRUE, 1:4, 1:10) +#' +#' @export +ifelse2 <- function(test, yes, no){ + if (test){ + yes + } else{ + no + } +} diff --git a/R/listk.R b/R/listk.R new file mode 100644 index 0000000..ae72825 --- /dev/null +++ b/R/listk.R @@ -0,0 +1,33 @@ +#' listk +#' @param ... objects, possibly named. +#' +#' @examples +#' a = 1 +#' b = 1:2 +#' c = 1:3 +#' l1 <- listk(a, b, c) +#' l2 <- listk(a, b, c = 1:3) +#' l3 <- listk(a = 1, b = 1:2, c = 1:3) +#' l4 <- listk(1, 1:2, c) +#' @export +listk <- function(...){ + # get variable names from input expressions + cols <- as.list(substitute(list(...)))[-1] + vars <- names(cols) + Id_noname <- if (is.null(vars)) seq_along(cols) else which(vars == "") + + if (length(Id_noname) > 0) + vars[Id_noname] <- sapply(cols[Id_noname], deparse) + # ifelse(is.null(vars), Id_noname <- seq_along(cols), Id_noname <- which(vars == "")) + x <- setNames(list(...), vars) + return(x) +} + +# ' @param x A list object, with data.frame of element +# ' @rdname listk +# ' @export +list.cbind <- function(x) do.call(cbind.data.frame, x) %>% set_colnames(names(x)) + +# ' @rdname listk +# ' @export +list.rbind <- function(x) do.call(rbind.data.frame, x) %>% set_rownames(names(x))#%>% set_rownames(names(x)) diff --git a/R/makeVIDEO.R b/R/makeVIDEO.R new file mode 100644 index 0000000..6e2a0dc --- /dev/null +++ b/R/makeVIDEO.R @@ -0,0 +1,19 @@ +#' @title makeVIDEO +#' @description make video through ffmpeg +#' +#' @param file filename of output video +#' @param path The path of figures, i.e, pngs, to make video +#' @param pattern regular expression pattern to filter figures +#' @param mode must be one of "ultrafast", "slow", "veryslow" +#' +#' @export +makeVIDEO <- function(file = "ffmpeg_%d.avi", + path = ".", pattern = "*.png", + mode = c("ultrafast", "slow", "veryslow")){ + mode <- mode[1] + system(sprintf("(for %%i in (%s\\%s) do @echo file '%%i') > list.txt", + gsub("/", "\\\\", path), pattern)) + system(sprintf("ffmpeg -safe 0 -f concat -r 2 -i list.txt -c:v libx264 -preset %s -crf 0 %s", + mode, gsub("/", "\\\\", file) )) + file.remove("list.txt") #remove list.txt, return null +} diff --git a/R/list.R b/R/melt_list.R similarity index 100% rename from R/list.R rename to R/melt_list.R diff --git a/R/merge_pdf.R b/R/merge_pdf.R new file mode 100644 index 0000000..e10d3ce --- /dev/null +++ b/R/merge_pdf.R @@ -0,0 +1,22 @@ +#' merge_pdf +#' +#' rely on python pdfmerge package, `pip install pdfmerge` +#' +#' @param outfile String +#' @param indir Directory to search pdfs +#' @param pattern string used to match pdf filename +#' @param del Booolean. If true, after merge, original pdf files will be delete. +#' +#' @examples +#' \dontrun{ +#' merge_pdf("RPlot.pdf", indir = 'Figure', pattern = "*.pdf") +#' } +#' @export +merge_pdf <- function(outfile = "RPlot.pdf", indir = 'Figure', pattern = "*.pdf", del = FALSE){ + files <- dir(indir, pattern, full.names = TRUE) + cmd <- sprintf("pdfmerge -o %s %s", outfile, paste(files, collapse = " ")) + + system(cmd, wait = del) + # system(sprintf('pdfmerge -o %s %s', outfile, pattern) ) + if (del) file.remove(files) +} diff --git a/R/obj.size.R b/R/obj.size.R new file mode 100644 index 0000000..76e5243 --- /dev/null +++ b/R/obj.size.R @@ -0,0 +1,12 @@ +#' obj.size +#' +#' Get object size in `unit` +#' @param obj Object +#' @param unit "Kb", "Mb" or "Gb" +#' +#' @examples +#' obj.size(1:100) +#' @export +obj.size <- function(obj, unit = "Mb"){ + cat(format(object.size(obj), unit), "\n") +} diff --git a/R/parallel_init.R b/R/parallel_init.R index c593b49..95eed22 100644 --- a/R/parallel_init.R +++ b/R/parallel_init.R @@ -1,5 +1,15 @@ +#' killCluster +#' #' @export -killCluster <- function() system("taskkill /IM Rscript.exe -f") +killCluster <- function(){ + os = .Platform$OS.type + if (os == "windows") { + system("taskkill /IM Rscript.exe -f") + } else if (os == "unix"){ + system("pkill -f R") + # NULL + } +} #' @importFrom doParallel registerDoParallel #' @importFrom parallel makeCluster diff --git a/R/runningId.R b/R/runningId.R new file mode 100644 index 0000000..134939e --- /dev/null +++ b/R/runningId.R @@ -0,0 +1,16 @@ +#' print the running ID in the console +#' +#' @param i the running Id. +#' @param N The number of total iteration +#' @param step how long of print step. +#' @param prefix prefix string +#' +#' @examples +#' for (i in 1:10){ +#' runningId(i, prefix = "phenofit") +#' } +#' @export +runningId <- function(i, step = 1, N, prefix = "") { + perc <- ifelse(missing(N), "", sprintf(", %.1f%% ", i/N*100)) + if (mod(i, step) == 0) cat(sprintf("[%s] running%s %d ...\n", prefix, perc, i)) +} diff --git a/R/spatial.R b/R/spatial.R deleted file mode 100644 index 9a43a10..0000000 --- a/R/spatial.R +++ /dev/null @@ -1,150 +0,0 @@ -#' prj84 -#' Default Spatial object projection: WGS84. -#' @importFrom sp CRS -#' @export -prj84 <- CRS("+proj=longlat +ellps=WGS84 +datum=WGS84") -# CRS("+init=epsg:4326") - -#' df2sp -#' Convert dataframe data into SpatialPointsDataframe -#' -#' @param d A data.frame with coordinates information -#' @param formula ~longitude+latitude -#' @inheritParams get_grid -#' -#' @importFrom sp coordinates proj4string coordinates<- proj4string<- -#' @export -df2sp <- function (d, formula = ~lon + lat, prj){ - if (missing(prj)) prj <- prj84 - coordinates(d) <- formula - proj4string(d) <- prj - return(d) -} - -#' extractId -#' -#' @param sp A SpatialPointDataFrame with the station coordinates information -#' @param shpfile A character, shape file path. -#' @inheritParams df2sp -#' -#' @importFrom maptools readShapePoly -#' @importFrom sp SpatialPolygons over -#' @export -extractId <- function(sp, shpfile){ - # formula <- ~lon+lat - # sp <- df2sp(station, formula, prj84) - shp <- readShapePoly(shpfile, proj4string = prj84) - bound <- SpatialPolygons(shp@polygons, proj4string = prj84) - ## clipped station - clipId <- which(!is.na(over(sp, bound))) %>% as.numeric - - plot(shp, axes = T) - plot(sp[clipId, ], add = T) - clipId#return clipId -} - -#' get_grid -#' construct SpatialGridDataFrame -#' -#' @param range A numeric vector, [lat_min, lat_max, lon_min, lon_max] -#' @param cellsize A numeric, grid cell size. -#' @param midgrid A vector, [midgrid_long, midgrid_lat]. If midgrid = false, then -#' begin point and end point locate on grid lines; If true, then begin point and -#' end point in the middle of grid. -#' @param prj \code{\link[sp]{CRS-class}} Projection. -#' -#' @examples -#' range <- c(25, 40, 73, 105) # Tibetan Plateau -#' Grid <- get_grid(range, cellsize = 1/12, midgrid = TRUE) -#' @importFrom sp GridTopology SpatialPixelsDataFrame -#' @export -get_grid <- function(range, cellsize, midgrid = c(TRUE, TRUE), prj = prj84) { - lat_range <- range[1:2] - long_range <- range[3:4] - # lat_range <- c(25, 40); long_range <- c(73, 105) - - if (length(midgrid) == 1){ - midgrid <- rep(midgrid, 2) - }else if(length(midgrid) != 2){ - midgrid <- midgrid[1:2] - message("error: midgrid length should be 1 or 2!") - } - - offset <- c(long_range[1], lat_range[1]) + cellsize/2 * (midgrid) - dims <- {c(diff(long_range), diff(lat_range)) / cellsize + !midgrid} %>% - ceiling() - - grid <- GridTopology( - cellcentre.offset = offset, - cellsize = c(1, 1) * cellsize, cells.dim = dims) - #SpatialPixelsDataFrame, other than GirdDataframe. They have a big difference! - grid <- SpatialPixelsDataFrame(grid, data = data.frame(id = seq.int(1, prod(dims))), - proj4string = prj) - return(grid) -} - -#' rdist.earth -#' -#' @param x1 A position matrix [lat, lon], degree unit. -#' @param x2 A position matrix [lat, lon], degree unit. -#' @export -rdist.earth <- function (x1, x2 = NULL){ - R <- 6378.388 - # coslat1 <- cos(x1[, 2]) - # sinlat1 <- sin(x1[, 2]) - # coslon1 <- cos(x1[, 1]) - # sinlon1 <- sin(x1[, 1]) - coslat1 <- cos((x1[, 2] * pi)/180) - sinlat1 <- sin((x1[, 2] * pi)/180) - coslon1 <- cos((x1[, 1] * pi)/180) - sinlon1 <- sin((x1[, 1] * pi)/180) - - coslat2 <- cos((x2[, 2] * pi)/180) - sinlat2 <- sin((x2[, 2] * pi)/180) - coslon2 <- cos((x2[, 1] * pi)/180) - sinlon2 <- sin((x2[, 1] * pi)/180) - pp <- cbind(coslat1 * coslon1, coslat1 * sinlon1, sinlat1) %*% - t(cbind(coslat2 * coslon2, coslat2 * sinlon2, sinlat2)) - return(R * acos(ifelse(abs(pp) > 1, 1 * sign(pp), pp))) -} - -# #' get_nearGrids -# #' -# #' find nearest 3*3 grids of points -# #' -# #' with the help of RANN package to quickly select nearest 3*3 grids -# #' use line dist to replace sphere distance -# #' -# #' @param grid SpatialGridDataFrame object -# #' @param sp SpatialPointDataframe object -# #' @param ngrid how many nearest grids to be extracted? -# #' @return nearId nearest order -# #' -# #' @importFrom RANN nn2 -# #' @export -# get_nearGrids <- function(grid, station, ngrid = 3*3){ -# loc_grid <- coordinates(grid) -# loc_station <- coordinates(station) -# x <- nn2(loc_grid, loc_station, ngrid) -# res <- data.frame(stationId = rep(station@data$stationId, ngrid), -# nearId = rep(1:ngrid, rep(nrow(station), ngrid)), -# idx = as.numeric(x$nn.idx), -# dists = as.numeric(x$nn.dists) *6371 * pi/180) -# # rdist.earth(loc_grid[res$idx, ], loc_station) -# return(res) -# } - -#' gridSaveToPoly -#' -#' Write spatialPixelDataframe into polygon shpfile for the convenience of -#' checking in google earth. -#' -#' @param grid The spatialPixelDataframe or spatialGridDataframe object. -#' @param file The string of output shapefile name including path. -#' @importFrom rgdal writeOGR -#' @export -gridSaveToPoly <- function(grid, file){ - poly <- as(grid, "SpatialPolygonsDataFrame") - # writePolyShape(poly, file) #, can't write prj info - writeOGR(poly, dsn = file, layer = basename(file), driver = "ESRI Shapefile") -} diff --git a/R/src_FUN.R b/R/src_FUN.R index 707fe28..0bca5b4 100644 --- a/R/src_FUN.R +++ b/R/src_FUN.R @@ -6,33 +6,31 @@ src_URL <- function(url) url #' srcFUN function #' -#' \itemize{ -#' \item \code{src_URL} simplest srcFUN, just treat the input url as download link. -#' \item \code{src_wiley_I} wiley library. Journal like GRL, JGR, WRR, HP, +#' * `src_URL` simplest srcFUN, just treat the input url as download link. +#' * `src_wiley_I` wiley library. Journal like GRL, JGR, WRR, HP, #' all in the database. Compared with other srcFUNs, this one is quite #' complicated. It relies on previous web page identidy authentication. Hence, #' it can't download simply by pdf urls, likes other database. -#' \item \code{src_SciDirect.doi} access elsevier database trough doi. -#' \item \code{src_SciDirect.url} access elsevier database trough url. -#' \item \code{src_AMS} American Meteorological Society. -#' \item \code{src_Springer} Springer. -#' \item \code{src_SciReps} Scientific Reports. -#' \item \code{src_IOP} IOPscience database. -#' \item \code{src_hess} HESS. -#' \item \code{src_SciReps} Scientific Reports. -#' } +#' * `src_SciDirect.doi` access elsevier database trough doi. +#' * `src_SciDirect.url` access elsevier database trough url. +#' * `src_AMS` American Meteorological Society. +#' * `src_Springer` Springer. +#' * `src_SciReps` Scientific Reports. +#' * `src_IOP` IOPscience database. +#' * `src_hess` HESS. +#' * `src_SciReps` Scientific Reports. #' -#' If just src returned, you need to download with \code{\link{download_httr}} +#' If just src returned, you need to download with [download_httr()] #' #' @param doi Character, Digital Object Identifier, like #' "10.1175/JHM-D-15-0157.1", URLencoding format is also supported, i.e. #' "10.1175\%2FJHM-D-15-0157.1". -#' Based on doi, \code{srcFUN} find corresponding paper and download it. -#' @param DOIs Character vectors, multiple \code{doi}. +#' Based on doi, `srcFUN` find corresponding paper and download it. +#' @param DOIs Character vectors, multiple `doi`. #' @param outdir Output file directory #' @param .download If true, it will will download pdf directly, and return #' pdf src. If false, only pdf src returned, without downlaoding pdf. -#' @param ... other parameters pass to \code{\link[httr]{GET}} +#' @param ... other parameters pass to [httr::GET()] #' @rdname srcFUN #' @export src_wiley_I <- function(DOIs, outdir = "./", .download = TRUE, ...){ diff --git a/R/src_download.R b/R/src_download.R index fa951fb..c720edb 100644 --- a/R/src_download.R +++ b/R/src_download.R @@ -1,12 +1,3 @@ -# library(openxlsx) -# library(reshape2) -# library(plyr) - -# library(httr) -# library(xml2) -# library(magrittr) -# library(stringr) - # httpheader: used to cheat web server header <- "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" @@ -20,7 +11,7 @@ header <- "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, #' @param src download link #' @param outdir output directory #' @param file file name -#' @param ... other parameters to \code{\link[httr]{GET}} +#' @param ... other parameters to [httr::GET()] #' @export write_webfile <- function(src, outdir = "./", file = NULL, ...){ # extract pdf filename from src, and combine with outdir @@ -110,7 +101,7 @@ Init_Check <- function(doi, outdir){ #' download using aria2 #' -#' download papers batchly using aria2. \code{srcFUN} function is used +#' download papers batchly using aria2. `srcFUN` function is used #' to generate pdf download links. You can also construct src function personally #' to support more. #' @@ -121,13 +112,13 @@ Init_Check <- function(doi, outdir){ #' @param n maximum number of parallel downloads. We used aria2c to download #' papers batchly. In this function we set --max-concurrent-downloads, --split and #' --max-connection-per-server all equal to n. Detailed information about this -#' parameters could be find in aria2c document \url{https://aria2.github.io/manual/en/html/}. +#' parameters could be find in aria2c document . #' @param Rshell whether execute aria2c command in R shell. If false, it will save #' command string to clipboard, and then you can paste this command in cmd OR other #' shells which can execute aria2c command #' @param ... other parameter pass to srcFUN. #' -#' @author Dongdong Kong \url{kongdd@live.cn} +#' @author Dongdong Kong #' #' @examples #' # First, you need to get doi; @@ -156,7 +147,7 @@ download_aria2 <- function(DOIs, journal = '.', srcFUN = NULL, n = 8, Rshell = F # --header "%s" cmd <- sprintf('aria2c -x%d -s%d -j%d -k1M -c -i %s.txt -d %s', n, n, n, journal, journal) if (.Platform$OS.type == 'windows') writeLines(cmd, "clipboard") - if (Rshell) shell(cmd) + if (Rshell) system(cmd) } #' download using httr diff --git a/R/temp/parallel_remote_functions.R b/R/temp/parallel_remote_functions.R index fecdac6..c0130e3 100644 --- a/R/temp/parallel_remote_functions.R +++ b/R/temp/parallel_remote_functions.R @@ -99,10 +99,10 @@ selectHost <- function(cl){ #' #' @param client List object #' \itemize{ -#' \item \code{rshcmd} The command to be run on the master to launch a process +#' \item `rshcmd` The command to be run on the master to launch a process #' on another host. Defaults to ssh. -#' \item \code{user} The user name to be used when communicating with another host. -#' \item \code{host} Host ip or name +#' \item `user` The user name to be used when communicating with another host. +#' \item `host` Host ip or name #' } #' @export sysinfo <- function(client){ diff --git a/src/.gitignore b/R/temp/src/.gitignore similarity index 100% rename from src/.gitignore rename to R/temp/src/.gitignore diff --git a/src/RcppExports.cpp b/R/temp/src/RcppExports.cpp similarity index 100% rename from src/RcppExports.cpp rename to R/temp/src/RcppExports.cpp diff --git a/src/split_array.cpp b/R/temp/src/split_array.cpp similarity index 100% rename from src/split_array.cpp rename to R/temp/src/split_array.cpp diff --git a/R/zzz.R b/R/zzz.R deleted file mode 100644 index 0caa6ba..0000000 --- a/R/zzz.R +++ /dev/null @@ -1,114 +0,0 @@ -#' @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 -#' -#' @useDynLib Ipaper, .registration = TRUE -#' @importFrom Rcpp sourceCpp -NULL -# windowsFonts( -# Times = windowsFont("Times New Roman"), -# ST = windowsFont("宋体"), -# YH = windowsFont("Microsoft Yahei"), -# Arial = windowsFont("Arial")) - -#' pal -#' show colors in figure device -#' -#' @param col colors to be visualize. -#' @param border rect border for each color -#' -#' @export -pal <- function(col, border = "light gray") -{ - n <- length(col) - plot(0, 0, type="n", xlim = c(0, 1), ylim = c(0, 1), - axes = FALSE, xlab = "", ylab = "") - rect(0:(n-1)/n, 0, 1:n/n, 1, col = col, border = border) -} - -#' @title dir.show -#' @description open assign path in windows explorer, and default path is -#' current directory. This function is only designed for windows system. -#' -#' @param path the path you want to open -#' @export -dir.show <- function(path = getwd()){ - if (.Platform$OS.type == 'windows'){ - commandStr <- paste("Explorer /e, ", gsub("/", "\\\\", path)) - suppressWarnings(shell(commandStr)) - } -} - -#' getwd_clip -#' -#' get directory path in clipboard, same as getwd function -#' -#' @references -#' https://stackoverflow.com/questions/10959521/how-to-write-to-clipboard-on-ubuntu-linux-in-r -#' @export -getwd_clip <- function(){ - if (.Platform$OS.type == 'windows') { - path <- suppressWarnings(gsub("\\\\", "/", readLines("clipboard"))) - writeLines(path, "clipboard", sep = "") - path#quickly return - } -} - -#' @title setwd_clip -#' @description set directory path in clipboard, same as setwd function -#' @export -setwd_clip <- function() setwd(getwd_clip()) - -#' 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 ... values to be passed into fmt. Only logical, integer, real and -#' character vectors are supported, but some coercion will be done: see the -#' ‘Details’ section. Up to 100. -#' -#' @export -fprintf <- function(fmt, ...) cat(sprintf(fmt, ...)) - -#' print the running ID in the console -#' -#' @param i the running Id. -#' @param prefix prefix string -#' @param step how long of print step. -#' -#' @rdname fprintf -#' @export -runningId <- function(i, prefix = "", step = 1) { - if (mod(i, step) == 0) cat(sprintf("%s | running i=%5d ...\n", prefix, i)) -} - - -#' @title makeVIDEO -#' @description make video through ffmpeg -#' -#' @param file filename of output video -#' @param path The path of figures, i.e, pngs, to make video -#' @param pattern regular expression pattern to filter figures -#' @param mode must be one of "ultrafast", "slow", "veryslow" -#' -#' @export -makeVIDEO <- function(file = "ffmpeg_%d.avi", - path = ".", pattern = "*.png", - mode = c("ultrafast", "slow", "veryslow")){ - mode <- mode[1] - system(sprintf("(for %%i in (%s\\%s) do @echo file '%%i') > list.txt", - gsub("/", "\\\\", path), pattern)) - system(sprintf("ffmpeg -safe 0 -f concat -r 2 -i list.txt -c:v libx264 -preset %s -crf 0 %s", - mode, gsub("/", "\\\\", file) )) - file.remove("list.txt") #remove list.txt, return null -} diff --git a/README.md b/README.md index 3576088..035249d 100644 --- a/README.md +++ b/README.md @@ -1,36 +1,23 @@ # Ipaper + + [![Travis Build Status](https://travis-ci.org/kongdd/Ipaper.svg?branch=master)](https://travis-ci.org/kongdd/Ipaper) +[![AppVeyor Build +Status](https://ci.appveyor.com/api/projects/status/github/kongdd/rwiki?branch=master&svg=true)](https://ci.appveyor.com/project/kongdd/Ipaper) [![codecov](https://codecov.io/gh/kongdd/Ipaper/branch/master/graph/badge.svg)](https://codecov.io/gh/kongdd/Ipaper) +[![License](http://img.shields.io/badge/license-GPL%20%28%3E=%202%29-brightgreen.svg?style=flat)](http://www.gnu.org/licenses/gpl-2.0.html) +[![CRAN](http://www.r-pkg.org/badges/version/rwiki)](https://cran.r-project.org/package=rwiki) + -# Batch download paper with `aria2` and `httr`. ## Installation -```{r} -install.packages("devtools") +``` r devtools::install_github("kongdd/Ipaper") ``` -you also need to download [aria2](https://github.com/aria2/aria2/releases/tag/release-1.32.0), and add -aria2 path to your system environment variables. - -## Get doi - -If you want to download paper use that package, you need to get the corresponding DOI. First of all, you should be confirm that your IP have the right to download that paper. And if you want to batch download paper, I suggest you get the DOIs from [Web Of Science](http://login.webofknowledge.com/). -## Select suitable `srcFUN` according to paper database. -If this package have not yet, you can consider to extend the srcFUN, or contact me directly. +* Batch download paper with doi. -Their are two way, we provide to download paper. -- 1.[aria2](https://aria2.github.io/manual/en/html/), which is same like wget, but can download parallel. +* Base tools, e.g. `dir.show`, `runningId`, `subl` and `github` -- 2.[httr](https://cran.r-project.org/web/packages/httr/index.html) package by Hadley, which download files with the help of `curl`. +* Parallel functions, e.g. `InitCluster`, `killCluster`. -## Examples - -```{r} -# download_httr -download_httr("10.1175%2FJHM-D-15-0157.1", journal = '.', srcFUN = src_AMS) - -# download_aria2 -DOIs <- rep("10.1175%2FJHM-D-15-0157.1", 4) #test aria2 parallel download -download_aria2(DOIs, journal = "JHM", srcFUN = src_AMS, n = 4, Rshell = TRUE) -``` diff --git a/appveyor.yml b/appveyor.yml new file mode 100644 index 0000000..3a75e16 --- /dev/null +++ b/appveyor.yml @@ -0,0 +1,52 @@ +# DO NOT CHANGE the "init" and "install" sections below + +# Download script file from GitHub +init: + ps: | + $ErrorActionPreference = "Stop" + Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1" + Import-Module '..\appveyor-tool.ps1' + +install: + ps: Bootstrap + +cache: + - C:\RLibrary + +environment: + NOT_CRAN: true + # env vars that may need to be set, at least temporarily, from time to time + # see https://github.com/krlmlr/r-appveyor#readme for details + # USE_RTOOLS: true + # R_REMOTES_STANDALONE: true + +# Adapt as necessary starting from here + +build_script: + - travis-tool.sh install_deps + +test_script: + - travis-tool.sh run_tests + +on_failure: + - 7z a failure.zip *.Rcheck\* + - appveyor PushArtifact failure.zip + +artifacts: + - path: '*.Rcheck\**\*.log' + name: Logs + + - path: '*.Rcheck\**\*.out' + name: Logs + + - path: '*.Rcheck\**\*.fail' + name: Logs + + - path: '*.Rcheck\**\*.Rout' + name: Logs + + - path: '\*_*.tar.gz' + name: Bits + + - path: '\*_*.zip' + name: Bits diff --git a/man/Init_Check.Rd b/man/Init_Check.Rd index 620d93f..c1fc73b 100644 --- a/man/Init_Check.Rd +++ b/man/Init_Check.Rd @@ -7,9 +7,9 @@ Init_Check(doi, outdir) } \arguments{ -\item{doi}{Character, Digital Object Identifier, like -"10.1175/JHM-D-15-0157.1", URLencoding format is also supported, i.e. -"10.1175\%2FJHM-D-15-0157.1". +\item{doi}{Character, Digital Object Identifier, like +"10.1175/JHM-D-15-0157.1", URLencoding format is also supported, i.e. +"10.1175\%2FJHM-D-15-0157.1". Based on doi, \code{srcFUN} find corresponding paper and download it.} \item{outdir}{Output file directory} @@ -18,6 +18,6 @@ Based on doi, \code{srcFUN} find corresponding paper and download it.} URLdecode doi } \description{ -Check whether outdir exist, if not then will create it. If doi was URLencoded, +Check whether outdir exist, if not then will create it. If doi was URLencoded, then decode it. } diff --git a/man/Ipaper.Rd b/man/Ipaper.Rd index dcdcd86..48e8e86 100644 --- a/man/Ipaper.Rd +++ b/man/Ipaper.Rd @@ -1,13 +1,19 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/zzz.R +% Please edit documentation in R/Ipaper-package.R \docType{package} \name{Ipaper} \alias{Ipaper} +\alias{_PACKAGE} \alias{Ipaper-package} \title{Ipaper} \description{ -Ipaper +Download papers batchly using DOIs from many database. And some practical functions. +} +\author{ +\strong{Maintainer}: Dongdong Kong \email{kongdd.sysu@gmail.com} + } \keyword{DOI} \keyword{download} +\keyword{internal} \keyword{paper} diff --git a/man/add_dn.Rd b/man/add_dn.Rd new file mode 100644 index 0000000..68abadc --- /dev/null +++ b/man/add_dn.Rd @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/add_dn.R +\name{add_dn} +\alias{add_dn} +\title{Add n-day flag} +\usage{ +add_dn(d, days = 8) +} +\arguments{ +\item{d}{data.frame or data.table} + +\item{days}{Integer number or vector, can't have duplicated value.} +} +\description{ +To aggregated data into n-day (e.g. 8-day, 16-day) like MODIS product, a +n-day flag is need. +} +\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)) +} diff --git a/man/df2sp.Rd b/man/df2sp.Rd deleted file mode 100644 index 6b772d4..0000000 --- a/man/df2sp.Rd +++ /dev/null @@ -1,20 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/spatial.R -\name{df2sp} -\alias{df2sp} -\title{df2sp -Convert dataframe data into SpatialPointsDataframe} -\usage{ -df2sp(d, formula = ~lon + lat, prj) -} -\arguments{ -\item{d}{A data.frame with coordinates information} - -\item{formula}{~longitude+latitude} - -\item{prj}{\code{\link[sp]{CRS-class}} Projection.} -} -\description{ -df2sp -Convert dataframe data into SpatialPointsDataframe -} diff --git a/man/dir.show.Rd b/man/dir.show.Rd index 73b5234..9ce7856 100644 --- a/man/dir.show.Rd +++ b/man/dir.show.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/zzz.R +% Please edit documentation in R/getwd_clip.R \name{dir.show} \alias{dir.show} \title{dir.show} @@ -10,6 +10,6 @@ dir.show(path = getwd()) \item{path}{the path you want to open} } \description{ -open assign path in windows explorer, and default path is +open assign path in windows explorer, and default path is current directory. This function is only designed for windows system. } diff --git a/man/download_aria2.Rd b/man/download_aria2.Rd index ea1a5a3..cbeb3c0 100644 --- a/man/download_aria2.Rd +++ b/man/download_aria2.Rd @@ -12,23 +12,23 @@ download_aria2(DOIs, journal = ".", srcFUN = NULL, n = 8, \item{journal}{journal name, string used to make new directory to save papers} -\item{srcFUN}{function used to generate pdf download links according to DOIs. +\item{srcFUN}{function used to generate pdf download links according to DOIs. If srcFUN is null, then this function will treat input parameter DOIs as download urls.} -\item{n}{maximum number of parallel downloads. We used aria2c to download -papers batchly. In this function we set --max-concurrent-downloads, --split and +\item{n}{maximum number of parallel downloads. We used aria2c to download +papers batchly. In this function we set --max-concurrent-downloads, --split and --max-connection-per-server all equal to n. Detailed information about this parameters could be find in aria2c document \url{https://aria2.github.io/manual/en/html/}.} \item{Rshell}{whether execute aria2c command in R shell. If false, it will save -command string to clipboard, and then you can paste this command in cmd OR other +command string to clipboard, and then you can paste this command in cmd OR other shells which can execute aria2c command} \item{...}{other parameter pass to srcFUN.} } \description{ -download papers batchly using aria2. \code{srcFUN} function is used -to generate pdf download links. You can also construct src function personally +download papers batchly using aria2. \code{srcFUN} function is used +to generate pdf download links. You can also construct src function personally to support more. } \examples{ @@ -43,5 +43,5 @@ download_aria2(DOIs, journal = "JHM", srcFUN = src_AMS, n = 4, Rshell = TRUE) } } \author{ -Dongdong Kong \url{kongdd@live.cn} +Dongdong Kong \href{mailto:kongdd@live.cn}{kongdd@live.cn} } diff --git a/man/download_httr.Rd b/man/download_httr.Rd index 1e880c5..26a8b7e 100644 --- a/man/download_httr.Rd +++ b/man/download_httr.Rd @@ -11,7 +11,7 @@ download_httr(DOIs, journal = ".", srcFUN = NULL, ...) \item{journal}{journal name, string used to make new directory to save papers} -\item{srcFUN}{function used to generate pdf download links according to DOIs. +\item{srcFUN}{function used to generate pdf download links according to DOIs. If srcFUN is null, then this function will treat input parameter DOIs as download urls.} \item{...}{other parameter pass to srcFUN.} diff --git a/man/extractId.Rd b/man/extractId.Rd deleted file mode 100644 index a532070..0000000 --- a/man/extractId.Rd +++ /dev/null @@ -1,16 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/spatial.R -\name{extractId} -\alias{extractId} -\title{extractId} -\usage{ -extractId(sp, shpfile) -} -\arguments{ -\item{sp}{A SpatialPointDataFrame with the station coordinates information} - -\item{shpfile}{A character, shape file path.} -} -\description{ -extractId -} diff --git a/man/fprintf.Rd b/man/fprintf.Rd index 0b37567..fd8a278 100644 --- a/man/fprintf.Rd +++ b/man/fprintf.Rd @@ -1,31 +1,21 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/zzz.R +% Please edit documentation in R/fprintf.R \name{fprintf} \alias{fprintf} -\alias{runningId} \title{fprintf -print sprintf result into console just like C style fprintf function} +Print sprintf result into console, just like C style fprintf function} \usage{ fprintf(fmt, ...) - -runningId(i, prefix = "", step = 1) } \arguments{ \item{fmt}{a character vector of format strings, each of up to 8192 bytes.} -\item{...}{values to be passed into fmt. Only logical, integer, real and -character vectors are supported, but some coercion will be done: see the -‘Details’ section. Up to 100.} - -\item{i}{the running Id.} - -\item{prefix}{prefix string} - -\item{step}{how long of print step.} +\item{...}{other parameters will be passed to \code{sprintf}} } \description{ fprintf -print sprintf result into console just like C style fprintf function - -print the running ID in the console +Print sprintf result into console, just like C style fprintf function +} +\examples{ +cat(fprintf("\%s\\n", "Hello phenofit!")) } diff --git a/man/getPointsMODISTile.Rd b/man/getPointsMODISTile.Rd deleted file mode 100644 index 7accd23..0000000 --- a/man/getPointsMODISTile.Rd +++ /dev/null @@ -1,29 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/getPointsMODISTile.R -\name{getPointsMODISTile} -\alias{getPointsMODISTile} -\title{Get points data from MODIS tiles} -\usage{ -getPointsMODISTile(coor, cellsize = 1/240) -} -\arguments{ -\item{coor}{2-column matrix of coordinates (longitude, latitude)} - -\item{cellsize}{500m products, cellsize is regarded as 1/240; 1km product, -cellsize is regarded as 1/120.} -} -\value{ -\itemize{ -\item{h} MODIS tile horizontal id -\item{v} MODIS tile vertical id -\item{i} point horizontal position at the tile -\item{j} point vertical position at the tile -} -} -\description{ -Get points data from MODIS tiles -} -\references{ -https://landweb.modaps.eosdis.nasa.gov/cgi-bin/developer/tilemap.cgi -https://modis-land.gsfc.nasa.gov/MODLAND_grid.html -} diff --git a/man/get_grid.Rd b/man/get_grid.Rd deleted file mode 100644 index 579ea02..0000000 --- a/man/get_grid.Rd +++ /dev/null @@ -1,28 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/spatial.R -\name{get_grid} -\alias{get_grid} -\title{get_grid -construct SpatialGridDataFrame} -\usage{ -get_grid(range, cellsize, midgrid = c(TRUE, TRUE), prj = prj84) -} -\arguments{ -\item{range}{A numeric vector, [lat_min, lat_max, lon_min, lon_max]} - -\item{cellsize}{A numeric, grid cell size.} - -\item{midgrid}{A vector, [midgrid_long, midgrid_lat]. If midgrid = false, then -begin point and end point locate on grid lines; If true, then begin point and -end point in the middle of grid.} - -\item{prj}{\code{\link[sp]{CRS-class}} Projection.} -} -\description{ -get_grid -construct SpatialGridDataFrame -} -\examples{ -range <- c(25, 40, 73, 105) # Tibetan Plateau -Grid <- get_grid(range, cellsize = 1/12, midgrid = TRUE) -} diff --git a/man/get_sbatch.Rd b/man/get_sbatch.Rd index cc46b6b..3951c4d 100644 --- a/man/get_sbatch.Rd +++ b/man/get_sbatch.Rd @@ -10,7 +10,7 @@ get_sbatch(indir = ".", pattern = "result.*.RDS", outfile = NULL, \arguments{ \item{indir}{directory to search rda files} -\item{pattern}{an optional regular expression. Only file names which match +\item{pattern}{an optional regular expression. Only file names which match the regular expression will be returned.} \item{outfile}{If Save = T, output rda file name.} diff --git a/man/getwd_clip.Rd b/man/getwd_clip.Rd index 7038ab5..6223cd3 100644 --- a/man/getwd_clip.Rd +++ b/man/getwd_clip.Rd @@ -1,14 +1,28 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/zzz.R +% Please edit documentation in R/getwd_clip.R \name{getwd_clip} \alias{getwd_clip} -\title{getwd_clip} +\alias{setwd_clip} +\title{GET or SET working directory} \usage{ getwd_clip() + +setwd_clip() } \description{ -get directory path in clipboard, same as getwd function +\itemize{ +\item \code{getwd_clip}: get directory path in clipboard, same as getwd function +\item \code{setwd_clip}: set directory path in clipboard, same as setwd function +} +} +\note{ +Only works in windows +} +\examples{ +getwd_clip() } \references{ -https://stackoverflow.com/questions/10959521/how-to-write-to-clipboard-on-ubuntu-linux-in-r +\enumerate{ +\item https://stackoverflow.com/questions/10959521/how-to-write-to-clipboard-on-ubuntu-linux-in-r +} } diff --git a/man/gridSaveToPoly.Rd b/man/gridSaveToPoly.Rd deleted file mode 100644 index 93c9b14..0000000 --- a/man/gridSaveToPoly.Rd +++ /dev/null @@ -1,17 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/spatial.R -\name{gridSaveToPoly} -\alias{gridSaveToPoly} -\title{gridSaveToPoly} -\usage{ -gridSaveToPoly(grid, file) -} -\arguments{ -\item{grid}{The spatialPixelDataframe or spatialGridDataframe object.} - -\item{file}{The string of output shapefile name including path.} -} -\description{ -Write spatialPixelDataframe into polygon shpfile for the convenience of -checking in google earth. -} diff --git a/man/ifelse2.Rd b/man/ifelse2.Rd new file mode 100644 index 0000000..401c338 --- /dev/null +++ b/man/ifelse2.Rd @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/ifelse2.R +\name{ifelse2} +\alias{ifelse2} +\title{ifelse2} +\usage{ +ifelse2(test, yes, no) +} +\arguments{ +\item{test}{an object which can be coerced to logical mode.} + +\item{yes}{return values for true elements of test.} + +\item{no}{return values for false elements of test.} +} +\description{ +ternary operator just like java \code{test ? yes : no} +} +\examples{ +x <- ifelse2(TRUE, 1:4, 1:10) + +} diff --git a/man/killCluster.Rd b/man/killCluster.Rd new file mode 100644 index 0000000..6803f0a --- /dev/null +++ b/man/killCluster.Rd @@ -0,0 +1,11 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/parallel_init.R +\name{killCluster} +\alias{killCluster} +\title{killCluster} +\usage{ +killCluster() +} +\description{ +killCluster +} diff --git a/man/listk.Rd b/man/listk.Rd index c9b8436..7233356 100644 --- a/man/listk.Rd +++ b/man/listk.Rd @@ -1,15 +1,20 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/list.R -\name{melt_list} +% Please edit documentation in R/listk.R, R/melt_list.R +\name{listk} +\alias{listk} \alias{melt_list} -\title{melt_list} +\title{listk} \usage{ +listk(...) + melt_list(list, var.name, na.rm = TRUE, ...) } \arguments{ +\item{...}{objects, possibly named.} + \item{list}{A list object, with the same colnames data.frame in every element.} -\item{var.name}{vector of id variables. Can be integer (variable position) +\item{var.name}{vector of id variables. Can be integer (variable position) or string (variable name). If blank, will use all non-measured variables.} \item{na.rm}{Boolean} @@ -17,5 +22,16 @@ or string (variable name). If blank, will use all non-measured variables.} \item{...}{other parameters to melt} } \description{ +listk + melt_list } +\examples{ +a = 1 +b = 1:2 +c = 1:3 +l1 <- listk(a, b, c) +l2 <- listk(a, b, c = 1:3) +l3 <- listk(a = 1, b = 1:2, c = 1:3) +l4 <- listk(1, 1:2, c) +} diff --git a/man/makeVIDEO.Rd b/man/makeVIDEO.Rd index 6de2130..1099489 100644 --- a/man/makeVIDEO.Rd +++ b/man/makeVIDEO.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/zzz.R +% Please edit documentation in R/makeVIDEO.R \name{makeVIDEO} \alias{makeVIDEO} \title{makeVIDEO} diff --git a/man/merge_pdf.Rd b/man/merge_pdf.Rd new file mode 100644 index 0000000..f77f88b --- /dev/null +++ b/man/merge_pdf.Rd @@ -0,0 +1,26 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/merge_pdf.R +\name{merge_pdf} +\alias{merge_pdf} +\title{merge_pdf} +\usage{ +merge_pdf(outfile = "RPlot.pdf", indir = "Figure", pattern = "*.pdf", + del = FALSE) +} +\arguments{ +\item{outfile}{String} + +\item{indir}{Directory to search pdfs} + +\item{pattern}{string used to match pdf filename} + +\item{del}{Booolean. If true, after merge, original pdf files will be delete.} +} +\description{ +rely on python pdfmerge package, \code{pip install pdfmerge} +} +\examples{ +\dontrun{ +merge_pdf("RPlot.pdf", indir = 'Figure', pattern = "*.pdf") +} +} diff --git a/man/obj.size.Rd b/man/obj.size.Rd new file mode 100644 index 0000000..f1a850f --- /dev/null +++ b/man/obj.size.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/obj.size.R +\name{obj.size} +\alias{obj.size} +\title{obj.size} +\usage{ +obj.size(obj, unit = "Mb") +} +\arguments{ +\item{obj}{Object} + +\item{unit}{"Kb", "Mb" or "Gb"} +} +\description{ +Get object size in \code{unit} +} +\examples{ +obj.size(1:100) +} diff --git a/man/pal.Rd b/man/pal.Rd index 20a82ba..b220c68 100644 --- a/man/pal.Rd +++ b/man/pal.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/zzz.R +% Please edit documentation in R/getwd_clip.R \name{pal} \alias{pal} \title{pal diff --git a/man/prj84.Rd b/man/prj84.Rd deleted file mode 100644 index 0eff01f..0000000 --- a/man/prj84.Rd +++ /dev/null @@ -1,16 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/spatial.R -\docType{data} -\name{prj84} -\alias{prj84} -\title{prj84 -Default Spatial object projection: WGS84.} -\format{An object of class \code{CRS} of length 1.} -\usage{ -prj84 -} -\description{ -prj84 -Default Spatial object projection: WGS84. -} -\keyword{datasets} diff --git a/man/rdist.earth.Rd b/man/rdist.earth.Rd deleted file mode 100644 index d6c48b1..0000000 --- a/man/rdist.earth.Rd +++ /dev/null @@ -1,16 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/spatial.R -\name{rdist.earth} -\alias{rdist.earth} -\title{rdist.earth} -\usage{ -rdist.earth(x1, x2 = NULL) -} -\arguments{ -\item{x1}{A position matrix [lat, lon], degree unit.} - -\item{x2}{A position matrix [lat, lon], degree unit.} -} -\description{ -rdist.earth -} diff --git a/man/read_gee.Rd b/man/read_gee.Rd index e2f0ec8..5117d4f 100644 --- a/man/read_gee.Rd +++ b/man/read_gee.Rd @@ -13,7 +13,7 @@ read_json.gee(file, baseprob = c("site", "date"), is_buffer) \arguments{ \item{indir}{Input directory which contains the target json files} -\item{pattern}{an optional regular expression. Only file names which match +\item{pattern}{an optional regular expression. Only file names which match the regular expression will be returned.} \item{baseprob}{the properties name of input point.} diff --git a/man/readxlsx_ToList.Rd b/man/read_xlsx2list.Rd similarity index 55% rename from man/readxlsx_ToList.Rd rename to man/read_xlsx2list.Rd index b549761..562af5c 100644 --- a/man/readxlsx_ToList.Rd +++ b/man/read_xlsx2list.Rd @@ -1,15 +1,15 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/excel.R -\name{readxlsx_ToList} -\alias{readxlsx_ToList} -\title{readxlsx_ToList} +\name{read_xlsx2list} +\alias{read_xlsx2list} +\title{read_xlsx2list} \usage{ -readxlsx_ToList(file, ...) +read_xlsx2list(file, ...) } \arguments{ \item{file}{xlsx or xls file path} -\item{...}{other parameters to \code{\link[readxl]{read_excel}}} +\item{...}{other parameters to \code{\link[readxl:read_excel]{readxl::read_excel()}}} } \description{ If excel file hava many sheets, this function also works. diff --git a/man/runningId.Rd b/man/runningId.Rd new file mode 100644 index 0000000..454551d --- /dev/null +++ b/man/runningId.Rd @@ -0,0 +1,25 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/runningId.R +\name{runningId} +\alias{runningId} +\title{print the running ID in the console} +\usage{ +runningId(i, step = 1, N, prefix = "") +} +\arguments{ +\item{i}{the running Id.} + +\item{step}{how long of print step.} + +\item{N}{The number of total iteration} + +\item{prefix}{prefix string} +} +\description{ +print the running ID in the console +} +\examples{ +for (i in 1:10){ + runningId(i, prefix = "phenofit") +} +} diff --git a/man/setwd_clip.Rd b/man/setwd_clip.Rd deleted file mode 100644 index 9d3a8a4..0000000 --- a/man/setwd_clip.Rd +++ /dev/null @@ -1,11 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/zzz.R -\name{setwd_clip} -\alias{setwd_clip} -\title{setwd_clip} -\usage{ -setwd_clip() -} -\description{ -set directory path in clipboard, same as setwd function -} diff --git a/man/srcFUN.Rd b/man/srcFUN.Rd index 635afe1..ba7fe26 100644 --- a/man/srcFUN.Rd +++ b/man/srcFUN.Rd @@ -37,35 +37,35 @@ src_hess(doi) \item{outdir}{Output file directory} -\item{.download}{If true, it will will download pdf directly, and return +\item{.download}{If true, it will will download pdf directly, and return pdf src. If false, only pdf src returned, without downlaoding pdf.} -\item{...}{other parameters pass to \code{\link[httr]{GET}}} +\item{...}{other parameters pass to \code{\link[httr:GET]{httr::GET()}}} \item{urls}{pdf urls} -\item{doi}{Character, Digital Object Identifier, like -"10.1175/JHM-D-15-0157.1", URLencoding format is also supported, i.e. -"10.1175\%2FJHM-D-15-0157.1". +\item{doi}{Character, Digital Object Identifier, like +"10.1175/JHM-D-15-0157.1", URLencoding format is also supported, i.e. +"10.1175\%2FJHM-D-15-0157.1". Based on doi, \code{srcFUN} find corresponding paper and download it.} } \description{ \itemize{ - \item \code{src_URL} simplest srcFUN, just treat the input url as download link. - \item \code{src_wiley_I} wiley library. Journal like GRL, JGR, WRR, HP, - all in the database. Compared with other srcFUNs, this one is quite - complicated. It relies on previous web page identidy authentication. Hence, - it can't download simply by pdf urls, likes other database. - \item \code{src_SciDirect.doi} access elsevier database trough doi. - \item \code{src_SciDirect.url} access elsevier database trough url. - \item \code{src_AMS} American Meteorological Society. - \item \code{src_Springer} Springer. - \item \code{src_SciReps} Scientific Reports. - \item \code{src_IOP} IOPscience database. - \item \code{src_hess} HESS. - \item \code{src_SciReps} Scientific Reports. +\item \code{src_URL} simplest srcFUN, just treat the input url as download link. +\item \code{src_wiley_I} wiley library. Journal like GRL, JGR, WRR, HP, +all in the database. Compared with other srcFUNs, this one is quite +complicated. It relies on previous web page identidy authentication. Hence, +it can't download simply by pdf urls, likes other database. +\item \code{src_SciDirect.doi} access elsevier database trough doi. +\item \code{src_SciDirect.url} access elsevier database trough url. +\item \code{src_AMS} American Meteorological Society. +\item \code{src_Springer} Springer. +\item \code{src_SciReps} Scientific Reports. +\item \code{src_IOP} IOPscience database. +\item \code{src_hess} HESS. +\item \code{src_SciReps} Scientific Reports. } } \details{ -If just src returned, you need to download with \code{\link{download_httr}} +If just src returned, you need to download with \code{\link[=download_httr]{download_httr()}} } diff --git a/man/tools.Rd b/man/tools.Rd new file mode 100644 index 0000000..fd9a642 --- /dev/null +++ b/man/tools.Rd @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/contain.R +\name{contain} +\alias{contain} +\title{contain +find assigned pattern variable names} +\usage{ +contain(d, pattern = "NDVI|EVI") +} +\arguments{ +\item{d}{A data.frame vector, or list} + +\item{pattern}{string used to match \code{names(d)}} +} +\description{ +contain +find assigned pattern variable names +} +\examples{ +df <- data.frame(year = 2010, day = 1:3, month = 1, site = "A") +contain(df, "year|month|day") +} diff --git a/man/writelist_ToXlsx.Rd b/man/write_list2xlsx.Rd similarity index 76% rename from man/writelist_ToXlsx.Rd rename to man/write_list2xlsx.Rd index 7b8360a..34fbffb 100644 --- a/man/writelist_ToXlsx.Rd +++ b/man/write_list2xlsx.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/excel.R -\name{writelist_ToXlsx} -\alias{writelist_ToXlsx} -\title{writelist.xlsx} +\name{write_list2xlsx} +\alias{write_list2xlsx} +\title{write_list2xlsx} \usage{ -writelist_ToXlsx(x, file, .progress = "text", rowNames = FALSE) +write_list2xlsx(x, file, .progress = "text", rowNames = FALSE) } \arguments{ \item{x}{List object to be saved, \code{x} should have names and can't be NULL.} @@ -13,13 +13,10 @@ writelist_ToXlsx(x, file, .progress = "text", rowNames = FALSE) \item{.progress}{name of the progress bar to use, see create_progress_bar.} -\item{rowNames}{a logical value indicating whether the row names are to +\item{rowNames}{a logical value indicating whether the row names are to be written.} } \description{ base function, write list x into fileName with each list in workbook, write shapefile dbf table into excel *.xlsx } -\details{ - -} diff --git a/man/write_urls.Rd b/man/write_urls.Rd index 97e78e2..f44f3ab 100644 --- a/man/write_urls.Rd +++ b/man/write_urls.Rd @@ -12,6 +12,6 @@ write_urls(urls, file) \item{file}{urls are written into file.} } \description{ -write character vectors of urls into text file, in order to the use of +write character vectors of urls into text file, in order to the use of subsequent aria2 download } diff --git a/man/write_webfile.Rd b/man/write_webfile.Rd index 9690cec..0af0c22 100644 --- a/man/write_webfile.Rd +++ b/man/write_webfile.Rd @@ -13,7 +13,7 @@ write_webfile(src, outdir = "./", file = NULL, ...) \item{file}{file name} -\item{...}{other parameters to \code{\link[httr]{GET}}} +\item{...}{other parameters to \code{\link[httr:GET]{httr::GET()}}} } \description{ download web file through web link src diff --git a/tests/testthat.R b/tests/testthat.R new file mode 100644 index 0000000..087fadd --- /dev/null +++ b/tests/testthat.R @@ -0,0 +1,4 @@ +library(testthat) +library(Ipaper) + +test_check("Ipaper") diff --git a/tests/testthat/test-add_dn.R b/tests/testthat/test-add_dn.R new file mode 100644 index 0000000..1d2f2d4 --- /dev/null +++ b/tests/testthat/test-add_dn.R @@ -0,0 +1,11 @@ +context("test-add_dn") + +test_that("add_dn works", { + date = seq.Date(as.Date("2010-01-01"), as.Date("2010-12-31"), by = "day") + d <- data.frame(date) + days <- c(8, 16) + dnew <- add_dn(d, days) + + # check colnames of \code{days} + expect_true(all(is.element(paste0("d", days), colnames(dnew)))) +}) diff --git a/tests/testthat/test-ifelse2.R b/tests/testthat/test-ifelse2.R new file mode 100644 index 0000000..677d3d6 --- /dev/null +++ b/tests/testthat/test-ifelse2.R @@ -0,0 +1,6 @@ +context("ifelse2") + +test_that("ifelse2 works", { + expect_equal(1:4, ifelse2(TRUE, 1:4, 1:10)) + expect_equal(1:10, ifelse2(FALSE, 1:4, 1:10)) +}) diff --git a/tests/testthat/test-listk.R b/tests/testthat/test-listk.R new file mode 100644 index 0000000..f8370bf --- /dev/null +++ b/tests/testthat/test-listk.R @@ -0,0 +1,12 @@ +test_that("multiplication works", { + a = 1 + b = 1:2 + c = 1:3 + l1 <- listk(a, b, c) + l2 <- listk(a, b, c = 1:3) + l3 <- listk(a = 1, b = 1:2, c = 1:3) + l4 <- listk(1, 1:2, c) + expect_equal(l1, l2) + expect_equal(l1, l3) + expect_equal(names(l4), c("1", "1:2", "c")) +}) diff --git a/vignettes/.gitignore b/vignettes/.gitignore new file mode 100644 index 0000000..097b241 --- /dev/null +++ b/vignettes/.gitignore @@ -0,0 +1,2 @@ +*.html +*.R diff --git a/vignettes/doi_paper.Rmd b/vignettes/doi_paper.Rmd new file mode 100644 index 0000000..c8dc9b1 --- /dev/null +++ b/vignettes/doi_paper.Rmd @@ -0,0 +1,43 @@ +--- +title: "doi_paper" +output: rmarkdown::html_vignette +vignette: > + %\VignetteIndexEntry{doi_paper} + %\VignetteEngine{knitr::rmarkdown} + %\VignetteEncoding{UTF-8} +--- + +```{r, include = FALSE} +knitr::opts_chunk$set( + collapse = TRUE, + comment = "#>" +) +``` + +# Batch download paper with `aria2` and `httr`. + +you need to download [aria2](https://github.com/aria2/aria2/releases/tag/release-1.32.0), and add +aria2 path to your system environment variables. + +## Get doi + +If you want to download paper use that package, you need to get the corresponding DOI. First of all, you should be confirm that your IP have the right to download that paper. And if you want to batch download paper, I suggest you get the DOIs from [Web Of Science](http://login.webofknowledge.com/). + +## Select suitable `srcFUN` according to paper database. +If this package have not yet, you can consider to extend the srcFUN, or contact me directly. + +Their are two way, we provide to download paper. +- 1.[aria2](https://aria2.github.io/manual/en/html/), which is same like wget, but can download parallel. + +- 2.[httr](https://cran.r-project.org/web/packages/httr/index.html) package by Hadley, which download files with the help of `curl`. + +## Examples + +```{r} +library(Ipaper) +# download_httr +download_httr("10.1175%2FJHM-D-15-0157.1", journal = '.', srcFUN = src_AMS) +# download_aria2 +DOIs <- rep("10.1175%2FJHM-D-15-0157.1", 4) #test aria2 parallel download +download_aria2(DOIs, journal = "JHM", srcFUN = src_AMS, n = 4, Rshell = TRUE) +```