Merge pull request #16 from karlropkins/main

logo update
atmoschem · Jul 12, 2024 · eec5757 · eec5757
2 parents 87ffe00 + 0a09e1a
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diff --git a/.Rproj.user/shared/notebooks/paths b/.Rproj.user/shared/notebooks/paths
@@ -1,6 +1,7 @@
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/ITS/projects/IPSOS/_______________latest/dts/banes/_techNote_IPSOSDefra_DTTrend_BANES_working_04.Rmd="EF13DF93"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/ITS/projects/Leeds_CPRPC/_working/climate_rough_01.Rmd="59DA471D"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/ITS/projects/NERC_TRANSISTION/events/Clean Air Networks Conference/naei estimate.Rmd="1BB48545"
+C:/Users/trakradmin/OneDrive - University of Leeds/Documents/ITS/students/___studentPaper_AirQualityEvidence/coding/batch.coding.001.build.archives_v1.R="0F0B4BEB"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/_isolateContribution&breakPointAnalysis_KR_20230824.R="F18B98A3"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/_projects/_paper_01_IntroToRespeciate/MS Access Versions/speciate_5.2_0/test.R="FCE2E494"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/_projects/_print error/_codeNote_PrintError.Rmd="ED822FAC"
@@ -28,6 +29,7 @@ C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/rsp.build.R="5A264727"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/rsp.cluster.R="B197B439"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/rsp.cor.R="DE099ED6"
+C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/rsp.eu.R="F043375D"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/rsp.find.R="E59DFEFA"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/rsp.id.R="91880E8A"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/rsp.info.R="FD1BAD48"

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,15 +1,17 @@
 Package: respeciate
 Title: Speciation profiles for gases and aerosols
-Version: 0.3.1
-Date: 2024-06-12
-Description: Access to the air pollutant emission profiles in US EPA SPECIATE (v5.2) and EU JRC
-          SPECIEUROPE archives. More details in Simon et al (2010) doi:10.5094/APR.2010.026 and
-          Pernigotti et al (2016) doi:10.1016/j.apr.2015.10.007, respectively.
+Version: 0.3.2
+Date: 2024-07-09
+Description: Access to the air pollutant emission profiles in US EPA SPECIATE (v5.2) and
+         EU JRC SPECIEUROPE archives. More details in Simon et al (2010)
+         doi:10.5094/APR.2010.026 and Pernigotti et al (2016)
+         doi:10.1016/j.apr.2015.10.007, respectively.
 Type: Package
-Authors@R: c( person(given = "Sergio", family = "Ibarra-Espinosa", role = c("aut", "cre"), email
-          = "sergio.ibarra@usp.br", comment = c(ORCID = "0000-0002-3162-1905")), person(given =
-          "Karl", family = "Ropkins", role = c("aut"), email = "k.ropkins@its.leeds.ac.uk",
-          comment = c(ORCID = "0000-0002-0294-6997")) )
+Authors@R: c( person(given = "Sergio", family = "Ibarra-Espinosa", role = c("aut",
+         "cre"), email = "sergio.ibarra@usp.br", comment = c(ORCID =
+         "0000-0002-3162-1905")), person(given = "Karl", family = "Ropkins", role =
+         c("aut"), email = "k.ropkins@its.leeds.ac.uk", comment = c(ORCID =
+         "0000-0002-0294-6997")) )
 License: MIT + file LICENSE
 URL: https://github.com/atmoschem/respeciate
 BugReports: https://github.com/atmoschem/respeciate/issues

diff --git a/NAMESPACE b/NAMESPACE
@@ -25,6 +25,9 @@ export(rsp_dcast)
 export(rsp_dcast_profile)
 export(rsp_dcast_species)
 export(rsp_distance_profile)
+export(rsp_eu)
+export(rsp_eu_pm10)
+export(rsp_eu_pm2.5)
 export(rsp_find_profile)
 export(rsp_find_species)
 export(rsp_id_btex)

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,10 @@
 # Release Notes Version 0.3
 
+* [0.3.2] 
+    * released 2024-07-09 
+    * added rsp_eu shortcut for SPECIEUROPE profiles 
+
+
 * [0.3.1] 
     * released 2024-06-12 
     * added standard plot output handler for rsp_ and pls_ plots 

diff --git a/R/rsp.R b/R/rsp.R
@@ -125,7 +125,7 @@
 #           we could base this on ..rsp_[whatever]_meta and .rsp_eu2us
 #           unexported functions. .rsp_eu2us was used to handle eu data
 #           when we were defaulting to us structure (early code from 0.3.1,
-#           now superceded)...
+#           now superseded)...
 
 
 

diff --git a/R/rsp.eu.R b/R/rsp.eu.R
@@ -0,0 +1,67 @@
+#' @name rsp.eu
+#' @title Quick access to common SPECIAEUROPE subsets.
+#' @aliases rsp_eu rsp_eu_pm10 rsp_eu_pm2.5
+
+#' @description \code{\link{rsp_eu}} and \code{rsp_eu_} functions are
+#' quick access wrappers to commonly requested SPECIEUROPE subsets.
+
+#' @return \code{rsp_eu} and \code{rsp_eu_}functions typically return
+#' a \code{respeciate} \code{data.frame} of the requested profiles:
+#'
+#' \code{rsp_eu()} returns all profiles in the local version of
+#' \code{\link{SPECIEUROPE}}
+#'
+#' \code{rsp_eu_pm10} returns all SPECIEUROPE profiles classified as
+#' PM10 (using \code{Particle.Size=="PM10"}), \code{rsp_eu_pm10} for PM2.5
+#' and so on...
+#'
+#' @seealso \code{\link{SPECIEUROPE}}
+
+
+#############################
+#NOTES
+############################
+
+# might not be keeping these
+
+
+###########################
+# functions
+###########################
+
+# work in progress
+
+# get all of SPEIEUROPE
+#     not a big job at moment...
+#          < 300 profiles
+
+#' @rdname rsp.eu
+#' @export
+
+rsp_eu <- function(){
+  rsp(rsp_find_profile(source="eu"))
+}
+
+#subsets
+
+# SPECIEUROPE Particle.Size
+# "PM10"  "TSP"   "PM2.5" "PMraw" "PM50"  "PM1"   "PM"
+#      currently only doing pm10 and pm2,5
+
+#' @rdname rsp.eu
+#' @export
+
+rsp_eu_pm10 <- function(){
+  rsp(rsp_find_profile("pm10", by="particle.size",
+                       source="eu", partial=FALSE))
+}
+
+#' @rdname rsp.eu
+#' @export
+
+rsp_eu_pm2.5 <- function(){
+  rsp(rsp_find_profile("pm2.5", by="particle.size",
+                       source="eu", partial=FALSE))
+}
+
+
diff --git a/R/rsp.us.R b/R/rsp.us.R
@@ -25,6 +25,7 @@
 #' \code{rsp_us_other} returns all profiles classified as other in SPECIATE
 #' (\code{PROFILE_TYPE == 'OTHER'}).
 #'
+#' @seealso \code{\link{SPECIATE}}
 
 
 #############################
@@ -36,20 +37,25 @@
 # SPECIATE profile types
 # GAS, OTHER, PM, PM-AE6, PM-AE8, PM-CR1, PM-Simplified
 
+# started similar for SPECIEUROPE in rsp.eu.R
 
 ##########################
 # to do / think about ...
 #########################
 
-# any others worth doing???
-#     others from SPECIATE (as rsp_us_... ???)
-#     anything similar in SPECIEUROPE (as rsp_eu_... ???)
 
-# feels like ther should be a quicker way of doing this...
+# feels like there should be a quicker way of doing this...
 #    maybe try going SPECIATE directly instead of using rsp_profile_info???
 #       BUT might not be much a speed saving...
 
-# rsp() or rsp_profile() ????
+# comparing rsp.us and rsp.eu code
+#     function nomenclature
+#         rsp() or rsp_profile() ????
+#         rsp_profile_info() or rsp_find_profile() ???
+#     rsp_eu for all SPECIEUROPE but not rsp_us for all SPECIATE
+#         reason SPECIATE is both PM and gas profiles; not sure mixing wise ...
+#                SPECIEUROPE is only PM
+#                     (although different size fractions...)
 
 
 #' @rdname rsp.us

diff --git a/R/xxx.R b/R/xxx.R
@@ -392,7 +392,7 @@ utils::globalVariables(c("SPECIATE", "SPECIEUROPE", ".SD", "ans", "control",
   profiles.eu <- profiles.eu[!duplicated(profiles.eu$Id),]
   profiles.eu <- profiles.eu[c("Id", "Name", "Original.Name", "Country",
                                "Place", "Test.Year", "Profile.Type",
-                               "Latitude", "Longitude")]
+                               "Particle.Size", "Latitude", "Longitude")]
   profiles.eu$Keywords <- profiles.eu$Name
   profiles.eu$.profile.id <- paste("EU:", profiles.eu$Id, sep="")
   profiles.eu$.profile <- profiles.eu$Name

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diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
 pkgdown: 2.0.9
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-07-09T07:19Z
+last_built: 2024-07-12T16:43Z
 
diff --git a/docs/reference/SPECIATE.html b/docs/reference/SPECIATE.html
diff --git a/docs/reference/SPECIEUROPE.html b/docs/reference/SPECIEUROPE.html
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diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/docs/reference/respeciate-package.html b/docs/reference/respeciate-package.html
diff --git a/docs/reference/respeciate.generics.html b/docs/reference/respeciate.generics.html
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