add package infrastructure

.Rbuildignore

@@ -1,3 +1,6 @@
+.git
+.gitignore
 inst/api
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^\.travis\.yml$

.travis.yml

@@ -0,0 +1,24 @@
+# Sample .travis.yml for R projects from https://github.com/craigcitro/r-travis
+
+language: c
+
+before_install:
+  - curl -OL http://raw.github.com/craigcitro/r-travis/master/scripts/travis-tool.sh
+  - chmod 755 ./travis-tool.sh
+  - ./travis-tool.sh bootstrap
+
+install:
+  - ./travis-tool.sh install_deps
+
+script: ./travis-tool.sh run_tests
+
+after_failure:
+  - ./travis-tool.sh dump_logs
+
+env:
+  - WARNINGS_ARE_ERRORS=1
+
+notifications:
+  email:
+    on_success: change
+    on_failure: change

DESCRIPTION

@@ -4,12 +4,14 @@ Title: R Interface to FishBASE
 Version: 2.0.0
 License: CC0
 Authors@R: c(person("Carl", "Boettiger", role = c("aut"), email = "cboettig@ropensci.org"),
-             person("Scott", "Chamberlain", role = c("cre", "aut")), email = "scott@ropensci.org")
+             person("Scott", "Chamberlain", role = c("cre", "aut"), email = "scott@ropensci.org"))
 URL: https://github.com/ropensci/rfishbase
 BugReports: https://github.com/ropensci/rfishbase/issues
 Depends:
     R (>= 3.0)
 Imports:
-    httr
+    httr,
+    tidyr,
+    stringr
 Suggests:
     testthat

NAMESPACE

@@ -0,0 +1,6 @@
+# Generated by roxygen2 (4.1.0): do not edit by hand
+
+export(species_table)
+import(httr)
+import(stringr)
+import(tidyr)

R/fishbase.R

@@ -1,133 +1,9 @@
-SERVER = "http://server.carlboettiger.info:4567"
-
-## Provide wrapper to work with species lists.
-#' @param species_list Takes a vector of scientific names (each element as "genus species").
-#'   if only one name is given in an element (no space), assumes it is the genus and returns
-#'   all species matching that genus.
-#' @param verbose should the function give warnings?
-#' @return a data.frame with rows for species and columns for the fields returned by the query (FishBase 'species' table)
-#' @examples
-#' \donttest{
-#' 
-#' species_table(c("Oreochromis niloticus", "Bolbometopon muricatum")) 
-#' # There are 5 species in this genus, so returns 5 rows:
-#' species_table("Labroides") 
-#' }
-#' @export
-species_table <- function(species_list, verbose = TRUE, .limit = 50, .server = SERVER){
-  # Just wraps an lapply around the "per_species" function and combines the resulting data.frames.
-  # .limit limits the number of returns in a single API call.  As we are usually matching species, we expect
-  # only one hit per call anyway so limit may as well be 1.  If we are matching genus only, we can hit
-  # several species and limit should justifiably be higher. 
-  do.call("rbind", lapply(species_list, per_species, verbose = verbose, limit = .limit, server = .server))
-}
-
-
-
-#' @import httr stringr
-per_species <- function(species, verbose = TRUE, limit = 10, server = SERVER){
-
-  ## parse scientific name (FIXME function should also do checks.)
-  s <- parse_name(species)
-
-  ## Make the API call for the species requested
-  args <- list(species = s$species, genus = s$genus, limit = limit)
-  resp <- GET(paste0(server, "/species"), query = args)
-
-  ## check response for http errors
-  stop_for_status(resp)
-
-  ## Parse the http response
-  out <- content(resp)
-
-  ## Check for errors or other issues
-  error_checks(out, verbose = verbose)
-
-  ## Combine into data.frame and tidy
-  tidy_species_table(out$data)
-}
-
-
-
-
-## Family query is 2 api calls, one to look up FamCode. 1 call for subFamily
-## Higher taxonomy: less relevant?
-
-
-
-
-error_checks <- function(resp, verbose = TRUE){
-  ## check for errors in the API query
-  if(!is.null(out$error) && verbose) 
-    stop(out$error)
-
-  ## Comment if returns are incomplete.
-  if(verbose && out$count > out$returned)
-    warning(paste("Retruning first", out$returned, "matches out of", out$count, "matches.",
-                  "\n Increase limit or refine query for more results"))
-
-}
-
-
-## Metadata used by tidy_species_table
-#meta <- system.file("metadata", "species.csv", package="rfishbase")
-meta <- 'inst/metadata/species.csv'
-species_meta <- read.csv(meta)
-row.names(species_meta) <- species_meta$field
-
-
-#' @import tidyr
-tidy_species_table <- function(data) {
-  L <- lapply(data, null_to_NA)
-  df <- do.call(rbind.data.frame, L)
-  # Convert columns to the appropriate class
-  for(n in names(df)){
-    class <- as.character(species_meta[[n, "class"]])
-    if(class=="Date")
-      df[,n] <- as.Date(as.character(df[,n]))
-    else if(class=="logical")
-      df[,n] <- as(as.numeric(df[,n]), class)
-    else 
-      df[,n] <- as(as.character(df[,n]), class)
-  }
-  ## Drop useless columns. Once reference table implemented, we may want to return those numbers. Same for expert ids.
-  df <- df[,species_meta$keep]
-  ## Rename columns (pick names to indicate units on numeric values?)
-
-  ## Arrange columns
-
-  df
-}
-
-# simple helper function
-null_to_NA <- function(x) {
-  x[sapply(x, is.null)] <- NA
-  return(x)
-}
-
-# resp <- GET("http://server.carlboettiger.info:4567/species/?genus=Labroides")
-# data <- content(resp)$data
-# tidy_species_table(data)
-
-# -1 is TRUE, 0 is FALSE
-
-
-
-# parse scientific name.   FIXME stupid function, should do more check & error handling
-parse_name <- function(x){
-  x <- str_split(x, " ")[[1]]
-  switch(length(x), 
-         list(genus = x[1]),
-         list(genus = x[1], species = x[2]))
-}
-
-
-#' 
-#' @import httr
-get_id <- function(genus, species, server = SERVER){  
-  resp <- GET(paste0(server, "/species", "/?genus=", genus, "&species=", species, "&fields=speciesrefno,speccode"))
-  sapply(content(resp)$data, `[[`, "speciesrefno")
-}
-
-
+#' @name rfishbase-package
+#' @aliases rfishbase
+#' @docType package
+#' @title The new R interface to Fishbase, v2.0
+#' @author Carl Boettiger \email{carl@@ropensci.org}
+#' @author Scott Chamberlain \email{scott@@ropensci.org}
+#' @keywords package
+NULL
 

R/heartbeat.R

@@ -0,0 +1,4 @@
+# Check that server is responding
+
+heartbeat <- function(server = SERVER)
+  GET(paste0(server, "/heartbeat"))

R/species_table.R

@@ -0,0 +1,137 @@
+SERVER = "http://server.carlboettiger.info:4567"
+
+#' species_table
+#' 
+#' Provide wrapper to work with species lists.
+#' @param species_list Takes a vector of scientific names (each element as "genus species").
+#'   if only one name is given in an element (no space), assumes it is the genus and returns
+#'   all species matching that genus.
+#' @param verbose should the function give warnings?
+#' @param limit The maximum number of matches from a single API call.  (Applicable only when
+#'  querying at genus level, typically only one #' record will match the scientific name and
+#'  will try all names given.)  Thus the default is almost always fine. 
+#' @param server URL of the FishBase API server.
+#' @return a data.frame with rows for species and columns for the fields returned by the query (FishBase 'species' table)
+#' @details 
+#' The Species table is the heart of FishBase. This function provides a convenient way to 
+#' query, tidy, and assemble data from that table given an entire list of species.
+#' For details, see: http://www.fishbase.org/manual/english/fishbasethe_species_table.htm
+#' 
+#' Species scientific names are defined according to fishbase taxonomy and nomenclature.
+#' 
+#' @examples
+#' \donttest{
+#' 
+#' species_table(c("Oreochromis niloticus", "Bolbometopon muricatum")) 
+#' # There are 5 species in this genus, so returns 5 rows:
+#' species_table("Labroides") 
+#' }
+#' @import httr stringr tidyr
+#' @export
+species_table <- function(species_list, verbose = TRUE, limit = 50, server = SERVER){
+  # Just wraps an lapply around the "per_species" function and combines the resulting data.frames.
+  # .limit limits the number of returns in a single API call.  As we are usually matching species, we expect
+  # only one hit per call anyway so limit may as well be 1.  If we are matching genus only, we can hit
+  # several species and limit should justifiably be higher. 
+  do.call("rbind", lapply(species_list, per_species, verbose = verbose, limit = limit, server = server))
+}
+
+
+
+per_species <- function(species, verbose = TRUE, limit = 10, server = SERVER){
+
+  ## parse scientific name (FIXME function should also do checks.)
+  s <- parse_name(species)
+
+  ## Make the API call for the species requested
+  args <- list(species = s$species, genus = s$genus, limit = limit)
+  resp <- GET(paste0(server, "/species"), query = args)
+
+  ## check response for http errors
+  stop_for_status(resp)
+
+  ## Parse the http response
+  parsed <- content(resp)
+
+  ## Check for errors or other issues
+  error_checks(parsed, verbose = verbose)
+
+  ## Combine into data.frame and tidy
+  tidy_species_table(parsed$data)
+}
+
+
+
+
+## Family query is 2 api calls, one to look up FamCode. 1 call for subFamily
+## Higher taxonomy: less relevant?
+
+
+
+
+error_checks <- function(parsed, verbose = TRUE){
+  ## check for errors in the API query
+  if(!is.null(parsed$error) && verbose) 
+    stop(parsed$error)
+
+  ## Comment if returns are incomplete.
+  if(verbose && parsed$count > parsed$returned)
+    warning(paste("Retruning first", parsed$returned, "matches parsed of", parsed$count, "matches.",
+                  "\n Increase limit or refine query for more results"))
+
+}
+
+
+## Metadata used by tidy_species_table
+meta <- system.file("metadata", "species.csv", package="rfishbase")
+species_meta <- read.csv(meta)
+row.names(species_meta) <- species_meta$field
+
+
+## helper routine for tidying species data
+tidy_species_table <- function(data) {
+  L <- lapply(data, null_to_NA)
+  df <- do.call(rbind.data.frame, L)
+  # Convert columns to the appropriate class
+  for(n in names(df)){
+    class <- as.character(species_meta[[n, "class"]])
+    if(class=="Date")
+      df[,n] <- as.Date(as.character(df[,n]))
+    else if(class=="logical")
+      df[,n] <- as(as.numeric(df[,n]), class)
+    else 
+      df[,n] <- as(as.character(df[,n]), class)
+  }
+  ## Drop useless columns. Once reference table implemented, we may want to return those numbers. Same for expert ids.
+  df <- df[,species_meta$keep]
+  ## Rename columns (pick names to indicate units on numeric values?)
+
+  ## Arrange columns
+
+  df
+}
+
+# simple helper function
+null_to_NA <- function(x) {
+  x[sapply(x, is.null)] <- NA
+  return(x)
+}
+
+# resp <- GET("http://server.carlboettiger.info:4567/species/?genus=Labroides")
+# data <- content(resp)$data
+# tidy_species_table(data)
+
+# -1 is TRUE, 0 is FALSE
+
+
+
+# parse scientific name.   FIXME stupid function, should do more check & error handling
+parse_name <- function(x){
+  x <- str_split(x, " ")[[1]]
+  switch(length(x), 
+         list(genus = x[1]),
+         list(genus = x[1], species = x[2]))
+}
+
+
+

man/rfishbase-package.Rd

@@ -0,0 +1,17 @@
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/fishbase.R
+\docType{package}
+\name{rfishbase-package}
+\alias{rfishbase}
+\alias{rfishbase-package}
+\title{The new R interface to Fishbase, v2.0}
+\description{
+The new R interface to Fishbase, v2.0
+}
+\author{
+Carl Boettiger \email{carl@ropensci.org}
+
+Scott Chamberlain \email{scott@ropensci.org}
+}
+\keyword{package}
+