CRAN Release 1.2.0

.Rbuildignore

@@ -3,3 +3,5 @@ README.md
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^cran-comments\.md$
+codecov.yml
+^data-raw$

.travis.yml

@@ -1,27 +1,42 @@
 # .travis.yml for ices-tools packages
 
-warnings_are_errors: false
-
-os:
-  - linux
-
+# Header
 language: r
-r:
-  - oldrel
-  - release
-  - devel
-
 sudo: false
+cache: packages
+warnings_are_errors: false
+
+# matrix: 3x Linux, 1x OS X
+matrix:
+  include:
+  - r: release
+  - r: oldrel
+  - r: devel
+  - os: osx
+    osx_image: beta-xcode6.1
+    disable_homebrew: true
+    r: release
+    latex: false
+
+# notifications
+notifications:
+  email:
+    on_success: change
+    on_failure: change
 
 repos:
   CRAN: https://cloud.r-project.org
 
+# r_packages
 r_packages:
+  - icesVocab
+  - testthat
   - rmarkdown
 
-cache: packages
+# r_github_packages
+r_github_packages:
+  - jimhester/covr
 
-notifications:
-  email:
-    on_success: change
-    on_failure: change
+# after_success
+after_success:
+  - Rscript -e 'covr::codecov()'

DESCRIPTION

@@ -1,14 +1,14 @@
 Package: icesDatras
-Version: 1.0-0
-Date: 2016-08-04
+Version: 1.2-0
+Date: 2017-01-10
 Title: DATRAS Trawl Database Web Services
 Authors@R: c(person("Colin", "Millar", role=c("aut","cre"), email="colin.millar@ices.dk"),
-             person("Einar", "Hjorleifsson", role="aut"))
-Suggests: knitr
-Imports: RCurl,
-         XML,
-         utils
-Description: Functions that access the web services of the ICES (International
+             person("Scott", "Large", role="aut"),
+             person("Arni", "Magnusson", role="aut"))
+Imports: utils
+Suggests: icesVocab,
+          testthat
+Description: R interface to access the web services of the ICES (International
              Council for the Exploration of the Sea) DATRAS trawl survey
              database <https://datras.ices.dk/WebServices/Webservices.aspx>.
 License: GPL (>= 2)

NAMESPACE

@@ -1,14 +1,17 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(print,datrasoverview)
+export(checkSurveyOK)
+export(checkSurveyYearOK)
+export(checkSurveyYearQuarterOK)
 export(getCAdata)
+export(getCatchWgt)
+export(getDATRAS)
 export(getDatrasDataOverview)
 export(getHHdata)
 export(getHLdata)
 export(getSurveyList)
 export(getSurveyYearList)
 export(getSurveyYearQuarterList)
-importFrom(RCurl,basicTextGatherer)
-importFrom(RCurl,curlPerform)
-importFrom(XML,xmlParse)
-importFrom(XML,xmlToDataFrame)
 importFrom(utils,capture.output)
+importFrom(utils,download.file)

NEWS

@@ -1,3 +1,48 @@
+--------------------------------------------------------------------------------
+icesDatras 1.2-0 (2016-12-xx)
+--------------------------------------------------------------------------------
+o
+
+
+--------------------------------------------------------------------------------
+icesDatras 1.1-1 (2016-09-14)
+--------------------------------------------------------------------------------
+o Improved XML parsing, exploiting structure of data and that we can
+  delete XML nodes once read.
+
+o Added function to extract catch weigthts by species and haul.
+
+
+
+--------------------------------------------------------------------------------
+icesDatras 1.1-0 (2016-08-17)
+--------------------------------------------------------------------------------
+o New argument 'surveys' in function getDatrasDataOverview() allows faster
+  overviews for one or few surveys.
+
+o Improved XML parsing, so both leading and trailing white space is removed.
+
+o Improved XML parsing, so -9 and "" is converted to NA.
+
+o Improved XML parsing, so data frame columns are automatically coerced to the
+  appropriate storage mode (character, numeric, integer).
+
+
+
+
+--------------------------------------------------------------------------------
+icesDatras 1.0-3 (2016-08-09)
+--------------------------------------------------------------------------------
+o Fixed bug where code assumed stringsAsFactors = FALSE by default.
+
+o Remove trailing white space from HHdata table entries.
+
+o Added function getDATRAS() from retired package rICES to extract multiple
+  years and quarters.
+
+
+
+
 --------------------------------------------------------------------------------
 icesDatras 1.0-0 (2016-08-04)
 --------------------------------------------------------------------------------

R/checkInputs.R

@@ -1,5 +1,25 @@
-#' @importFrom utils capture.output
+#' Check that a survey name is in the database
+#'
+#' Checks a survey name against a list of all survey names in the DATRAS database.
+#' If the name is not matched it puts up a message showing the available survey names.
+#'
+#' @param survey the survey acronym, e.g. NS-IBTS.
+#'
+#' @return logical.
+#'
+#' @seealso
+#' \code{\link{checkSurveyYearOK}} and \code{\link{getSurveyYearQuarterList}}
+#'  also perform checks against the DATRAS database.
+#'
+#' \code{\link{icesDatras-package}} gives an overview of the package.
+#'
+#' @examples
+#' checkSurveyOK(survey = "ROCKALL")
+#' checkSurveyOK(survey = "NOTALL")
+#'
+#' @export
 
+#' @importFrom utils capture.output
 checkSurveyOK <- function(survey) {
   # check survey name against available surveys
   available_surveys <- getSurveyList()
@@ -13,9 +33,33 @@ checkSurveyOK <- function(survey) {
   }
 }
 
+
+#' Check that a survey and year combination is in the database
+#'
+#' Checks a year and/or survey name against a list of all survey year combinations in the DATRAS database.
+#' If the combination is not matched it puts up a message showing the available options.
+#'
+#' @param survey the survey acronym, e.g. NS-IBTS.
+#' @param year the year of the survey, e.g. 2010.
+#' @param checksurvey logical, should the survey name also be checked.
+#'
+#' @return logical.
+#'
+#' @seealso
+#' \code{\link{checkSurveyOK}} and \code{\link{checkSurveyYearQuarterOK}}
+#'  also perform checks against the DATRAS database.
+#'
+#' \code{\link{icesDatras-package}} gives an overview of the package.
+#'
+#' @examples
+#' checkSurveyYearOK(survey = "ROCKALL", 2015)
+#' checkSurveyYearOK(survey = "ROCKALL", 2000)
+#' checkSurveyYearOK(survey = "NOTALL", 2000)
+#'
+#' @export
+
 checkSurveyYearOK <- function(survey, year, checksurvey = TRUE) {
   # check year against available years for a given survey
-
   if (checksurvey) {
     # check survey name
     if (!checkSurveyOK(survey)) return(FALSE)
@@ -31,16 +75,47 @@ checkSurveyYearOK <- function(survey, year, checksurvey = TRUE) {
   }
 }
 
+
+#' Check that a survey, year and quarter combination is in the database
+#'
+#' Checks a quarter and/or year and/or survey name against a list of all survey year quarter
+#' combinations in the DATRAS database.
+#' If the combination is not matched it puts up a message showing the available options.
+#'
+#' @param survey the survey acronym, e.g. NS-IBTS.
+#' @param year the year of the survey, e.g. 2010.
+#' @param quarter the quarter of the year the survey took place, i.e. 1, 2, 3 or 4.
+#' @param checksurvey logical, should the survey name also be checked.
+#' @param checkyear logical, should the year also be checked.
+#'
+#' @return logical.
+#'
+#' @seealso
+#' \code{\link{checkSurveyOK}} and \code{\link{checkSurveyYearOK}}
+#'  also perform checks against the DATRAS database.
+#'
+#' \code{\link{icesDatras-package}} gives an overview of the package.
+#'
+#' @examples
+#' checkSurveyYearQuarterOK(survey = "ROCKALL", 2015, 3)
+#' checkSurveyYearQuarterOK(survey = "ROCKALL", 2015, 1)
+#' checkSurveyYearQuarterOK(survey = "ROCKALL", 2000, 1)
+#' checkSurveyYearQuarterOK(survey = "NOTALL", 2000, 1)
+#'
+#' # be careful of unexpected results with checksurvey and checkyear!
+#' checkSurveyYearQuarterOK(survey = "NOTALL", 2000, 1, checksurvey=FALSE)
+#'
+#' @export
+
 checkSurveyYearQuarterOK <- function(survey, year, quarter, checksurvey = TRUE, checkyear = TRUE) {
   # check year against available years for a given survey
-
   if (checksurvey) {
     # check survey name
     if (!checkSurveyOK(survey)) return(FALSE)
   }
 
   if (checkyear) {
-    # check survey name
+    # check survey year
     if (!checkSurveyYearOK(survey, year, checksurvey = FALSE)) return(FALSE)
   }
 

R/getCAdata.R

@@ -1,36 +1,30 @@
-#' Age based data
+#' Get Age-Based Data
 #'
-#' Returns age-based information such as sex, maturity, and age counts per length of sampled species.
+#' Get age-based data such as sex, maturity, and age counts per length of sampled species.
 #'
-#' @param survey the survey accronym e.g. NS-IBTS, BITS.
-#' @param year the numeric year of the survey, e.g. 2010.
+#' @param survey the survey acronym, e.g. NS-IBTS.
+#' @param year the year of the survey, e.g. 2010.
 #' @param quarter the quarter of the year the survey took place, i.e. 1, 2, 3 or 4.
 #'
-#'
-#' @return A data.frame.
+#' @return A data frame.
 #'
 #' @seealso
-#' \code{\link{getSurveyList}} returns the acronyms for available surveys.
-#'
-#' \code{\link{getSurveyYearList}} returns the years available for a given survey.
+#' \code{\link{getDATRAS}} supports querying many years and quarters in one function call.
 #'
-#' \code{\link{getSurveyYearQuarterList}} returns the quarters available for a given survey and year.
+#' \code{\link{getHHdata}} and \code{\link{getHLdata}} get haul data and
+#' length-based data.
 #'
 #' \code{\link{icesDatras-package}} gives an overview of the package.
 #'
 #' @author Colin Millar.
 #'
 #' @examples
-#' # read age data
-#' cadata <- getCAdata(survey = "BTS", year = 2015, quarter = 3)
+#' cadata <- getCAdata(survey = "ROCKALL", year = 2002, quarter = 3)
 #' str(cadata)
 #'
-#'
 #' @export
 
 getCAdata <- function(survey, year, quarter) {
-  # Returns age-based information such as sex, maturity, and age counts per length of sampled species.
-
   # check survey name
   if (!checkSurveyOK(survey)) return(FALSE)
 
@@ -40,16 +34,13 @@ getCAdata <- function(survey, year, quarter) {
   # check quarter
   if (!checkSurveyYearQuarterOK(survey, year, quarter, checksurvey = FALSE, checkyear = FALSE)) return(FALSE)
 
-  # read and parse XML from api
+  # read url and parse to data frame
   url <-
     sprintf(
       "https://datras.ices.dk/WebServices/DATRASWebService.asmx/getCAdata?survey=%s&year=%i&quarter=%i",
       survey, year, quarter)
-  out <- curlDatras(url = url)
+  out <- readDatras(url)
   out <- parseDatras(out)
 
-  # return
   out
 }
-
-