Merge pull request #14 from karlropkins/main

respeciate (specieurope addtion)

.Rproj.user/shared/notebooks/paths

@@ -5,36 +5,41 @@ C:/Users/trakradmin/OneDrive - University of Leeds/Documents/_isolateContributio
 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/_slides_02_CRC/r code 2/_marylebone_CRC_Slides_04.Rmd="5042A905"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/_projects/_slides_02_CRC/r code/_marylebone_CRC_Slides_04.Rmd="25A452C7"
+C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/_projects/diagnostic ratios/_codeNote_DiagnosticRatios_202406.Rmd="D00DD16B"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/_projects/marylebone03/_marylebone_analysis_pls_01.Rmd="F2B723A3"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/_projects/marylebone03/_marylebone_initial_observations_01.Rmd="E72195E5"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/_projects/marylebone03/_marylebone_metals_03.Rmd="D2C38DFE"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/_projects/match01/_match_notes_01.Rmd="A446C96C"
+C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/data/specieurope/auto_update_specieurope/_codeNote_autoUpdateSpecieurope_202406.Rmd="3B5FC5B7"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/.Rbuildignore="BAFF788D"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/.Rproj.user/shared/notebooks/paths="DB89FCB7"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/.github/workflows/R-CMD-check.yml="33EF2D32"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/.gitignore="2CB231D9"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/DESCRIPTION="8BA937B7"
-C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/NAMESPACE="DBDDE80C"
+C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/NAMESPACE="F0FEEA54"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/NEWS.md="F6ED8BF4"
+C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/SPECIATE.R="E322F17B"
+C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/SPECIEUROPE.R="1AE009A4"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/respeciate-package.R="A43C9569"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/respeciate.generics.R="54ECE8F1"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/rsp.R="787EA0C5"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/rsp.average.R="67ED42C3"
 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.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"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/rsp.match.R="7AE83929"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/rsp.pad.R="FEC8C57D"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/rsp.plot.R="80B907E9"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/rsp.pls.R="430E71B2"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/rsp.pls.plot.R="07565C15"
-C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/rsp.q.R="2721C15F"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/rsp.rescale.R="2C292C00"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/rsp.reshape.R="94C8EF32"
-C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/rsp.x.R="4DA91187"
-C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/sysdata.R="82103C52"
+C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/rsp.us.R="36FA3EE9"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/xxx.R="3415FF44"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/README.Rmd="887EDA27"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/README.md="D46A00DB"
+C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/man/SPECIATE.Rd="5BBCE9FA"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/man/respeciate.generics.Rd="2897F12C"

DESCRIPTION

@@ -1,19 +1,20 @@
 Package: respeciate
 Title: Speciation profiles for gases and aerosols
-Version: 0.3.0
-Date: 2024-05-17
-Description: Access to the US.EPA Speciate (v5.2) tool, to generate speciation profiles for
-          gases and particles. More details in Simon et al (2010) <doi:10.5094/APR.2010.026>.
+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.
 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
 LazyData: yes
 Depends: R (>= 3.5.0)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Encoding: UTF-8
 Imports: data.table, lattice, latticeExtra

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(as.respeciate,default)
+S3method(merge,respeciate)
 S3method(plot,respeciate)
 S3method(plot,rsp_pls)
 S3method(print,respeciate)
@@ -17,6 +18,7 @@ export(pls_report)
 export(pls_test)
 export(rsp)
 export(rsp_average_profile)
+export(rsp_build_simx)
 export(rsp_build_x)
 export(rsp_cor_species)
 export(rsp_dcast)
@@ -25,29 +27,30 @@ export(rsp_dcast_species)
 export(rsp_distance_profile)
 export(rsp_find_profile)
 export(rsp_find_species)
+export(rsp_id_btex)
+export(rsp_id_copy)
+export(rsp_id_nalkane)
+export(rsp_id_pah16)
 export(rsp_info)
 export(rsp_match_profile)
 export(rsp_melt_wide)
 export(rsp_pad)
 export(rsp_plot_profile)
 export(rsp_plot_species)
-export(rsp_pls_profile)
+export(rsp_pls_x)
 export(rsp_profile)
 export(rsp_profile_info)
-export(rsp_q_gas)
-export(rsp_q_other)
-export(rsp_q_pm)
-export(rsp_q_pm.ae6)
-export(rsp_q_pm.ae8)
-export(rsp_q_pm.cr1)
-export(rsp_q_pm.simplified)
 export(rsp_rescale)
 export(rsp_rescale_profile)
 export(rsp_rescale_species)
 export(rsp_species_info)
-export(rsp_x_btex)
-export(rsp_x_copy)
-export(rsp_x_nalkane)
+export(rsp_us_gas)
+export(rsp_us_other)
+export(rsp_us_pm)
+export(rsp_us_pm.ae6)
+export(rsp_us_pm.ae8)
+export(rsp_us_pm.cr1)
+export(rsp_us_pm.simplified)
 importFrom(data.table,":=")
 importFrom(grDevices,as.graphicsAnnot)
 importFrom(grDevices,cm.colors)

NEWS.md

@@ -1,5 +1,21 @@
 # Release Notes Version 0.3
 
+* [0.3.1] 
+    * released 2024-06-12 
+    * added standard plot output handler for rsp_ and pls_ plots 
+    * added SPECIEUROPE data set; and renamed sysdata SPECIATE for 
+    consistency 
+    * added source argument to rsp(), 'us', 'eu', 'all' for extraction 
+    from SPECIATE, SPECIEUROPE or both; also added same to rsp_find_... 
+    functions  
+    * various function updates to handle SPECIEUROPE profiles  
+    * renamed rsp_q_... functions rsp_us_... because SPECIATE only 
+    * renamed rsp_x_... functions rsp_id_... (request after rsp_x objects 
+    added) 
+    * various fixes; some typos in docs; rsp_plot_species id 
+    tracking when species is factor  
+
+
 * [0.3.0] 
     * released 2024-05-17 
     * code and documentation refresh...  

R/sysdata.R → R/SPECIATE.R

@@ -1,13 +1,13 @@
 ############################################
-#' @title sysdata
+#' @title SPECIATE
 ############################################
 #'
-#' @name sysdata
-#' @description the re(SPECIATE) sysdata, a local versions of SPECIATE,
-#' the EPA's repository of organic gas and particulate matter (PM) speciation
+#' @name SPECIATE
+#' @description the SPECIATE data set is a local version of the EPA's
+#' SPECIATE repository of organic gas and particulate matter (PM) speciation
 #' profiles of air pollution sources.
 #'
-#' @format A (long) list, containing:
+#' @format A ( 13  long) 'list' object
 #' \describe{
 #'   \item{PROFILES}{The main \code{data.frame} of profile-specific meta-data,
 #'   with one row per profile, key term \code{PROFILE_CODE}.}
@@ -24,19 +24,10 @@
 #'   source meta-data, one row per reference, key term \code{REF_Code}.}
 #'   \item{And others}{Currently not documented.}
 #' }
-
-##################################
-##################################
-## IMPORTANT
-##################################
-##################################
-
-# this documentation needs doing
-
 #' @source https://www.epa.gov/air-emissions-modeling/speciate
 #' @references
 #' Simon, H., Beck, L., Bhave, P.V., Divita, F., Hsu, Y., Luecken, D.,
 #' Mobley, J.D., Pouliot, G.A., Reff, A., Sarwar, G. and Strum, M., 2010.
 #' The development and uses of EPA SPECIATE database.
 #' Atmospheric Pollution Research, 1(4), pp.196-206.
-"sysdata"
+"SPECIATE"

R/SPECIEUROPE.R

@@ -0,0 +1,21 @@
+############################################
+#' @title SPECIEUROPE
+############################################
+#'
+#' @name SPECIEUROPE
+#'
+#' @description The SPECIEUROPE data set is a local version of the European
+#' Commission (EC) Joint Research Centre JRC's repository of particulate matter
+#' (PM) speciation profiles of European air pollutant sources.
+#'
+#' @format A ( 3  long) 'list' object
+#' \describe{
+#'   \item{source}{The main SPECIEUROPE data set as of 2024/05/26.}
+#'   \item{ref}{The source citation, to be used whenever this data is used.}
+#'   \item{website}{The SPECIEUROPE project website}
+#' }
+#' @source https://source-apportionment.jrc.ec.europa.eu/
+#' @references Pernigotti, D., Belis, C.A., Spano, L., 2016. SPECIEUROPE: The
+#' European data base for PM source profiles. Atmospheric Pollution Research,
+#' 7(2), pp.307-314. DOI: https://doi.org/10.1016/j.apr.2015.10.007
+"SPECIEUROPE"