diff --git a/.Rproj.user/shared/notebooks/paths b/.Rproj.user/shared/notebooks/paths index 41ecd77..81d2417 100644 --- 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 index 33e4ff4..06d5dd7 100644 --- 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 index 6d81883..991eb1b 100644 --- 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 index 9b5f2f6..2552a8e 100644 --- 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 index c2ec6fb..8799474 100644 --- 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 new file mode 100644 index 0000000..db722c0 --- /dev/null +++ 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 index 6a93d07..12a8c9b 100644 --- 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 index 7b1ff48..eedd10d 100644 --- 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 diff --git a/docs/404.html b/docs/404.html index ea7fb52..a46c478 100644 --- a/docs/404.html +++ b/docs/404.html @@ -39,7 +39,7 @@ respeciate - 0.3.1 + 0.3.2 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index f89d36b..207aa94 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -17,7 +17,7 @@ respeciate - 0.3.1 + 0.3.2 diff --git a/docs/apple-touch-icon-114x114.png b/docs/apple-touch-icon-114x114.png new file mode 100644 index 0000000..ef59741 Binary files /dev/null and b/docs/apple-touch-icon-114x114.png differ diff --git a/docs/apple-touch-icon-120x120.png b/docs/apple-touch-icon-120x120.png index eb44e2d..de15b01 100644 Binary files a/docs/apple-touch-icon-120x120.png and b/docs/apple-touch-icon-120x120.png differ diff --git a/docs/apple-touch-icon-144x144.png b/docs/apple-touch-icon-144x144.png new file mode 100644 index 0000000..7f4755d Binary files /dev/null and b/docs/apple-touch-icon-144x144.png differ diff --git a/docs/apple-touch-icon-152x152.png b/docs/apple-touch-icon-152x152.png index e2936e2..22f4ec1 100644 Binary files a/docs/apple-touch-icon-152x152.png and b/docs/apple-touch-icon-152x152.png differ diff --git a/docs/apple-touch-icon-57x57.png b/docs/apple-touch-icon-57x57.png new file mode 100644 index 0000000..6839422 Binary files /dev/null and b/docs/apple-touch-icon-57x57.png differ diff --git a/docs/apple-touch-icon-60x60.png b/docs/apple-touch-icon-60x60.png index dcab541..7abab20 100644 Binary files a/docs/apple-touch-icon-60x60.png and b/docs/apple-touch-icon-60x60.png differ diff --git a/docs/apple-touch-icon-72x72.png b/docs/apple-touch-icon-72x72.png new file mode 100644 index 0000000..7817444 Binary files /dev/null and b/docs/apple-touch-icon-72x72.png differ diff --git a/docs/apple-touch-icon-76x76.png b/docs/apple-touch-icon-76x76.png index f9935ef..1c83e85 100644 Binary files a/docs/apple-touch-icon-76x76.png and b/docs/apple-touch-icon-76x76.png differ diff --git a/docs/authors.html b/docs/authors.html index 49e861d..17f8ab2 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ respeciate - 0.3.1 + 0.3.2 @@ -67,13 +67,13 @@

Citation

Ibarra-Espinosa S, Ropkins K (2024). respeciate: Speciation profiles for gases and aerosols. -R package version 0.3.1, https://github.com/atmoschem/respeciate. +R package version 0.3.2, https://github.com/atmoschem/respeciate. 

@Manual{,
   title = {respeciate: Speciation profiles for gases and aerosols},
   author = {Sergio Ibarra-Espinosa and Karl Ropkins},
   year = {2024},
-  note = {R package version 0.3.1},
+  note = {R package version 0.3.2},
   url = {https://github.com/atmoschem/respeciate},
 }
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Changelog

Release Notes Version 0.3

-
diff --git a/docs/reference/SPECIEUROPE.html b/docs/reference/SPECIEUROPE.html index 40c161f..5aef20b 100644 --- a/docs/reference/SPECIEUROPE.html +++ b/docs/reference/SPECIEUROPE.html @@ -19,7 +19,7 @@ respeciate - 0.3.1 + 0.3.2 diff --git a/docs/reference/figures/logo.png b/docs/reference/figures/logo.png index bf53f88..1851211 100644 Binary files a/docs/reference/figures/logo.png and b/docs/reference/figures/logo.png differ diff --git a/docs/reference/index.html b/docs/reference/index.html index abbc313..ebf1b45 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ respeciate - 0.3.1 + 0.3.2 @@ -70,6 +70,10 @@

All functions rsp_cor_species()

Species correlations

+ +

rsp_eu() rsp_eu_pm10() rsp_eu_pm2.5()

+ +

Quick access to common SPECIAEUROPE subsets.

rsp_find_profile() rsp_profile_info() rsp_find_species() rsp_species_info()

diff --git a/docs/reference/respeciate-package.html b/docs/reference/respeciate-package.html index a2e8e6d..2388c9c 100644 --- a/docs/reference/respeciate-package.html +++ b/docs/reference/respeciate-package.html @@ -18,7 +18,7 @@ respeciate - 0.3.1 + 0.3.2 diff --git a/docs/reference/respeciate.generics.html b/docs/reference/respeciate.generics.html index 6ae7056..bafc6d1 100644 --- a/docs/reference/respeciate.generics.html +++ b/docs/reference/respeciate.generics.html @@ -17,7 +17,7 @@ respeciate - 0.3.1 + 0.3.2 diff --git a/docs/reference/rsp.average.html b/docs/reference/rsp.average.html index 0989bf4..51a9d84 100644 --- a/docs/reference/rsp.average.html +++ b/docs/reference/rsp.average.html @@ -19,7 +19,7 @@ respeciate - 0.3.1 + 0.3.2 diff --git a/docs/reference/rsp.build.html b/docs/reference/rsp.build.html index 602639d..9b6482c 100644 --- a/docs/reference/rsp.build.html +++ b/docs/reference/rsp.build.html @@ -18,7 +18,7 @@ respeciate - 0.3.1 + 0.3.2 diff --git a/docs/reference/rsp.cluster.html b/docs/reference/rsp.cluster.html index 70cc9cb..7fde220 100644 --- a/docs/reference/rsp.cluster.html +++ b/docs/reference/rsp.cluster.html @@ -20,7 +20,7 @@ respeciate - 0.3.1 + 0.3.2 diff --git a/docs/reference/rsp.cor.html b/docs/reference/rsp.cor.html index d20ae5f..926691d 100644 --- a/docs/reference/rsp.cor.html +++ b/docs/reference/rsp.cor.html @@ -20,7 +20,7 @@ respeciate - 0.3.1 + 0.3.2 diff --git a/docs/reference/rsp.eu.html b/docs/reference/rsp.eu.html new file mode 100644 index 0000000..a6d3c41 --- /dev/null +++ b/docs/reference/rsp.eu.html @@ -0,0 +1,112 @@ + +Quick access to common SPECIAEUROPE subsets. — rsp.eu • respeciate + + +
+
+ + + +
+
+
+

Quick access to common SPECIAEUROPE subsets.

+ Source: R/rsp.eu.R + +
+ +
+

rsp_eu and rsp_eu_ functions are +quick access wrappers to commonly requested SPECIEUROPE subsets.

+
+ +
+ 
rsp_eu()
+
+rsp_eu_pm10()
+
+rsp_eu_pm2.5()
+
+ +
+

Value

+ + +

rsp_eu and rsp_eu_functions typically return +a respeciate

+

+

data.frame of the requested profiles:

+ + +

rsp_eu() returns all profiles in the local version of +SPECIEUROPE

+ + + +

rsp_eu_pm10 returns all SPECIEUROPE profiles classified as +PM10 (using Particle.Size=="PM10"), rsp_eu_pm10 for PM2.5 +and so on...

+
+
+

See also

+

SPECIEUROPE

+
+ +
+ +
+ + +
+

Developed by Sergio Ibarra-Espinosa, Karl Ropkins.

+
+ +
+

Site built with pkgdown 2.0.9.

+
+ +
+ + + + + + + + diff --git a/docs/reference/rsp.find.html b/docs/reference/rsp.find.html index f91ae7c..0b840ab 100644 --- a/docs/reference/rsp.find.html +++ b/docs/reference/rsp.find.html @@ -22,7 +22,7 @@ respeciate - 0.3.1 + 0.3.2 diff --git a/docs/reference/rsp.html b/docs/reference/rsp.html index 662da66..ea30c43 100644 --- a/docs/reference/rsp.html +++ b/docs/reference/rsp.html @@ -17,7 +17,7 @@ respeciate - 0.3.1 + 0.3.2 diff --git a/docs/reference/rsp.id.html b/docs/reference/rsp.id.html index 7fec3e4..8aee442 100644 --- a/docs/reference/rsp.id.html +++ b/docs/reference/rsp.id.html @@ -30,7 +30,7 @@ respeciate - 0.3.1 + 0.3.2 diff --git a/docs/reference/rsp.info.html b/docs/reference/rsp.info.html index 837949d..46cd35e 100644 --- a/docs/reference/rsp.info.html +++ b/docs/reference/rsp.info.html @@ -20,7 +20,7 @@ respeciate - 0.3.1 + 0.3.2 diff --git a/docs/reference/rsp.match.html b/docs/reference/rsp.match.html index 8a769f0..4b29552 100644 --- a/docs/reference/rsp.match.html +++ b/docs/reference/rsp.match.html @@ -20,7 +20,7 @@ respeciate - 0.3.1 + 0.3.2 diff --git a/docs/reference/rsp.pad.html b/docs/reference/rsp.pad.html index da8e281..c733d2d 100644 --- a/docs/reference/rsp.pad.html +++ b/docs/reference/rsp.pad.html @@ -19,7 +19,7 @@ respeciate - 0.3.1 + 0.3.2 diff --git a/docs/reference/rsp.plot.html b/docs/reference/rsp.plot.html index dfd09af..6e205cd 100644 --- a/docs/reference/rsp.plot.html +++ b/docs/reference/rsp.plot.html @@ -19,7 +19,7 @@ respeciate - 0.3.1 + 0.3.2 diff --git a/docs/reference/rsp.pls.html b/docs/reference/rsp.pls.html index 9bb95df..f16fc0f 100644 --- a/docs/reference/rsp.pls.html +++ b/docs/reference/rsp.pls.html @@ -29,7 +29,7 @@ respeciate - 0.3.1 + 0.3.2 diff --git a/docs/reference/rsp.pls.plot.html b/docs/reference/rsp.pls.plot.html index d815ab7..a050e54 100644 --- a/docs/reference/rsp.pls.plot.html +++ b/docs/reference/rsp.pls.plot.html @@ -19,7 +19,7 @@ respeciate - 0.3.1 + 0.3.2 diff --git a/docs/reference/rsp.rescale.html b/docs/reference/rsp.rescale.html index 32abb81..2b33145 100644 --- a/docs/reference/rsp.rescale.html +++ b/docs/reference/rsp.rescale.html @@ -21,7 +21,7 @@ respeciate - 0.3.1 + 0.3.2 diff --git a/docs/reference/rsp.reshape.html b/docs/reference/rsp.reshape.html index 27ba7d3..f5d7e6c 100644 --- a/docs/reference/rsp.reshape.html +++ b/docs/reference/rsp.reshape.html @@ -24,7 +24,7 @@ respeciate - 0.3.1 + 0.3.2 diff --git a/docs/reference/rsp.us.html b/docs/reference/rsp.us.html index bff7fc9..a7b1389 100644 --- a/docs/reference/rsp.us.html +++ b/docs/reference/rsp.us.html @@ -18,7 +18,7 @@ respeciate - 0.3.1 + 0.3.2 @@ -100,6 +100,10 @@

Value

rsp_us_other returns all profiles classified as other in SPECIATE (PROFILE_TYPE == 'OTHER').

+
+

See also

+

SPECIATE

+