├── .gitignore
├── NAMESPACE
├── R
    ├── ospkgs.R
    ├── ro_key_check.R
    ├── ro_search.r
    ├── ro_sources.r
    └── ropensci_helpers.R
├── README-NOT.md
├── README.md
└── data
    └── rosources.rda


/.gitignore:
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1 | .DS_Store
2 | .Rhistory
3 | R/testing.R


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/NAMESPACE:
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1 | export(rosources)
2 | import(RCurl)
3 | import(RJSONIO)
4 | import(ggplot2)
5 | import(stringr)
6 | import(rplos)
7 | import(rmendeley)


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/R/ospkgs.R:
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 1 | # FOR NOW, I just source the functions commented below here and then use ospkgs
 2 | # source("/Users/ScottMac/treeBASE/R/treebase.R")
 3 | # source("/Users/ScottMac/rbhl/R/namesearch.R")
 4 | # source("/Users/ScottMac/rplos/R/searchplos.R")
 5 | # source("/Users/ScottMac/rgbif/R/taxoncount.R")
 6 | # source("/Users/ScottMac/rbold/R/getsampleids.R")
 7 | 
 8 | # ospkgs.R
 9 | 
10 | ospkgs <- function(species = NA)
11 | # Args:
12 | #   species: species name (character)
13 | # Examples:
14 | #   ospkgs(species = "Andrena")
15 | {
16 |   treeBASE_out <- suppressMessages(
17 |     search_treebase(paste('"', species, '"', sep = ""), by="taxon"))
18 |   rplos_out <- searchplos(species, 'everything', 999)
19 |   rgbif_out <- taxoncount(species)
20 |   rbhl_out <- namesearch(species, "json")
21 |   rbold_out <- getsampleids(species)
22 |   outlist <- list(treeBASE = c(length(treeBASE_out), "phylotrees"))
23 |   outlist$rplos <- c(as.numeric(rplos_out[[1]]), "papers")
24 |   outlist$rgbif <- c(rgbif_out, "records")
25 |   outlist$rbhl <- c(length(rbhl_out[,2]), "records")
26 |   outlist$rbold <- c(length(rbold_out), "records")
27 |   df <- ldply(outlist)
28 |   names(df) <- c("Package", "Number", "Datatype")
29 |   return(df)
30 | }


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/R/ro_key_check.R:
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 1 | #' Checks for missing API keys
 2 | #'
 3 | #'@param key <what param does>
 4 | #'@param error_types <what param does>
 5 | #'@keywords
 6 | #'@seealso
 7 | #'@return
 8 | #'@alias
 9 | #'@export
10 | #'@examples \dontrun{
11 | #'
12 | #'}
13 | ropensci_key<-function(key = NULL)
14 | {
15 | 	if(is.null(key)) {
16 | 		stop("You need to specify a key to look for", call.=FALSE)
17 | 	}
18 | x <- try(getOption(key),silent=T)
19 | if(is.null(x))
20 | 	{
21 | 		message <- paste("Missing API key for package",key,"\n","?ropensci_key for more information on storing keys")
22 | 		stop(message)
23 | 	}
24 | 	invisible()
25 | }


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/R/ro_search.r:
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 1 | #'A simple search across existing packages
 2 | #'
 3 | #'<longer description>
 4 | #'@param query = NULL <what param does>
 5 | #'@keywords
 6 | #'@seealso
 7 | #'@return
 8 | #'@alias
 9 | #'@export
10 | #'@examples \dontrun{
11 | #'
12 | #'}
13 | ro_search <- function(query = NULL) {
14 | if(!is.null(query)) {
15 | 	stop("You did not include a query term", call.= FALSE)
16 |  }
17 | # source_list=ro_sources() 
18 | # # load packages
19 | # search rPLOS
20 | # search RMendeley
21 | # search rDryad (tricky because there is no API based search method)
22 | # concat the results and return it.
23 | }


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/R/ro_sources.r:
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 1 | #'Package to list current ropensci sources 
 2 | #'
 3 | #'@param sources Reads data stored in data folder
 4 | #'@param  verbose = TRUE Default is complete listing
 5 | #'@keywords
 6 | #'@seealso
 7 | #'@return data frame
 8 | #'@alias
 9 | #'@export
10 | #'@examples \dontrun{
11 | #'
12 | #'}
13 | ro_sources <- function(sources='..data/rosources.rda', verbose = TRUE, working = NULL) {
14 | load(sources)	
15 | if(!is.null(working)) {
16 | 	sources = subset(sources, working == TRUE)
17 | }
18 | return(rosources)	
19 | }
20 | 
21 | # Generating package data
22 | # data_source = c("Dryad", "Mendeley", "PLOS")
23 | # package_name = c("rDryad", "RMendeley", "rPLOS")
24 | # working = c(TRUE, TRUE, TRUE)
25 | # sources=data.frame(data_source, package_name, working)
26 | # save(sources, file="../data/rosources.rda")
27 | 


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/R/ropensci_helpers.R:
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https://raw.githubusercontent.com/ropensci-archive/rOpenSci/3fbd5fe80ee885fa9d7c39d732c34afa57a1c86d/R/ropensci_helpers.R


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/README-NOT.md:
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1 | # rOpenSci
2 | 
3 | [![Project Status: Abandoned](https://www.repostatus.org/badges/latest/abandoned.svg)](https://www.repostatus.org/#abandoned)
4 | 
5 | This package has been archived. The former README is now in [README-NOT.md](README-NOT.md).
6 | 


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/README.md:
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1 | # rOpenSci
2 | 
3 | [![Project Status: Abandoned](https://www.repostatus.org/badges/latest/abandoned.svg)](https://www.repostatus.org/#abandoned)
4 | 
5 | This repository has been archived. The former README is now in [README-NOT.md](README-NOT.md).
6 | 


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/data/rosources.rda:
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https://raw.githubusercontent.com/ropensci-archive/rOpenSci/3fbd5fe80ee885fa9d7c39d732c34afa57a1c86d/data/rosources.rda


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