rsp_match_profile update

.Rproj.user/shared/notebooks/paths

@@ -1,17 +1,17 @@
-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"
-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/marylebone01/_template_match_notes_03.Rmd="0E46D0BD"
 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/_projects/match04/_match_notes_04.Rmd="86D39C7D"
+C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/_working/_rsp_match/_codeNote_rsp_match.Rmd="2C6D68F7"
 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"
@@ -28,6 +28,7 @@ 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.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.combine.R="B14AB6C9"
 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"
@@ -45,4 +46,7 @@ C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test
 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-package.Rd="C6302B15"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/man/respeciate.generics.Rd="2897F12C"
+C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/man/rsp.match.Rd="ED3F1B42"
+C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/man/rsp.plot.Rd="4A9AA108"

DESCRIPTION

@@ -1,22 +1,20 @@
 Package: respeciate
 Title: Speciation profiles for gases and aerosols
-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.
+Version: 0.3.5
+Date: 2025-02-19
+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: 7.3.1
+RoxygenNote: 7.3.2
 Encoding: UTF-8
 Imports: data.table, lattice, latticeExtra

NAMESPACE

@@ -23,7 +23,9 @@ export(rsp_build_x)
 export(rsp_cor_species)
 export(rsp_dcast)
 export(rsp_dcast_profile)
+export(rsp_dcast_profile_id)
 export(rsp_dcast_species)
+export(rsp_dcast_species_id)
 export(rsp_distance_profile)
 export(rsp_eu)
 export(rsp_eu_pm10)
@@ -35,9 +37,11 @@ export(rsp_id_copy)
 export(rsp_id_nalkane)
 export(rsp_id_pah16)
 export(rsp_info)
+export(rsp_lbind)
 export(rsp_match_profile)
 export(rsp_melt_wide)
 export(rsp_pad)
+export(rsp_plot_match)
 export(rsp_plot_profile)
 export(rsp_plot_species)
 export(rsp_pls_x)

NEWS.md

@@ -1,9 +1,24 @@
 # Release Notes Version 0.3
 
+* [0.3.5] 
+    * released 2025-02-19 
+    * rebuild rsp_match_profile using data.table 
+    * added rsp_plot_match (rsp_match_profile plot) output... 
+
+* [0.3.4] 
+    * released 2024-08-06 
+    * expended rsp_dcast to handle species, species.id, profile, 
+    profile.id, and track all in all rsp_dcasts... 
+
+* [0.3.3] 
+    * released 2024-07-13 
+    * added draft rsp_lbind 
+
+
 * [0.3.2] 
     * released 2024-07-09 
     * added rsp_eu shortcut for SPECIEUROPE profiles 
-
+    * updated logo; now SPECIATE + SPECIEUROPE
 
 * [0.3.1] 
     * released 2024-06-12 

R/SPECIEUROPE.R

@@ -12,7 +12,7 @@
 #' \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}
+#'   \item{website}{The SPECIEUROPE project website link}
 #' }
 #' @source https://source-apportionment.jrc.ec.europa.eu/
 #' @references Pernigotti, D., Belis, C.A., Spano, L., 2016. SPECIEUROPE: The

R/respeciate-package.R

@@ -1,2 +1,5 @@
 #' @keywords internal
+#' @name respeciate-package
+#' @aliases respeciate
 "_PACKAGE"
+NULL

R/respeciate.generics.R

@@ -210,14 +210,14 @@ print.respeciate <-
 
 
     rsp.rep <- "respeciate"
-    if(class(.x)[1] == "rsp_sw"){
+    if(class(.x)[1] %in% c("rsp_sw", "rsp_siw")){
       rsp.rep <- paste(rsp.rep, " (wide/species)", sep="")
       .x <- rsp_melt_wide(.x, pad=FALSE, drop.nas = TRUE)
       #####################################
       #should we loose this if we start testing if missing below...
       .x$.species.id <- .x$.species
     }
-    if(class(.x)[1] == "rsp_pw"){
+    if(class(.x)[1] %in%c("rsp_pw", "rsp_piw")){
       rsp.rep <- paste(rsp.rep, " (wide/profile)", sep="")
       .x <- rsp_melt_wide(.x, pad=FALSE, drop.nas = TRUE)
       #.x$PROFILE_NAME <- .x$PROFILE_CODE
@@ -743,6 +743,53 @@ merge.respeciate <-
 
 
 
+
+##################################
+# subset
+##################################
+
+# local subset for respeciate objects...
+# allowing function pass
+
+# example, would like this to work...
+# subset(rsp_eu(), rsp_id_pah16)
+
+# #' @rdname respeciate.generics
+# #' @method subset respeciate
+# #' @export
+
+################################
+# think about
+################################
+
+# wanted to do like above but subset.data.table not exported...
+# and currently not working...
+# maybe have a look at data.table subset and work up from that???
+
+#
+### example
+## to do...
+
+# subset.respeciate <-
+#   function(x, subset, ...){
+#    #setup
+#    .cls <- class(x)
+#    x <- data.table::as.data.table(x)
+#    s <- try(eval(substitute(subset), x, parent.frame()),
+#             silent=TRUE)
+#    if(class(s)[1]=="function"){
+#      subset <- s(x)
+#    } else {
+#      subset <- s
+#    }
+#    subset(x, subset, ...)
+#    out <- as.data.frame(x)
+#    class(out) <- .cls
+#    out
+#  }
+
+
+
 ################################
 # not sure about this
 ################################

R/rsp.build.R

@@ -15,8 +15,8 @@
 #' of these will need to be assigned.
 #' @param species_name,species_id (\code{character}) The names of the columns
 #' in \code{x} containing species name and identifiers, respectively. If not
-#' already named according to \code{respeciate} conventions, at least one of these will
-#' need to be assigned.
+#' already named according to \code{respeciate} conventions, at least one of
+#' these will need to be assigned.
 #' @param value (\code{character}) The name of the column in \code{x}
 #' containing measurement values. If not already named according to \code{respeciate}
 #' conventions, this will need to be assigned.
@@ -102,6 +102,13 @@
 #               to retain the data type history
 #               and drop back to tibble rather than data.frame....
 
+# wondering if .profile and .profile.id are wrong for rsp_x ??? 
+#     maybe they should be .sample and .sample.id 
+#     but need special handler method 
+#         for example: 
+#             rsp_x-to-rsp code at start of most functions 
+#             then a rsp-to-rsp_x at end (before all outputs if start code used... 
+
 
 #' @rdname rsp.build
 #' @export

R/rsp.combine.R

@@ -0,0 +1,123 @@
+#' @name rsp.combine
+#' @title combining respeciate profiles
+#' @aliases rsp_lbind
+
+#' @description Functions to combining respeciate data sets.
+
+#' @description \code{rsp_lbind} binds two or more \code{respeciate}-like
+#' objects. The default option is to stack the supplied data sets (e.g.
+#' \code{respeciate}, \code{data.frame}, etc) like \code{rbindlist}
+#' in \code{data.table} (or row_bind in dplyr). This matches columns by name
+#' before stacking the supplied data sets.
+
+#' @param ...  (various) This function is intended to be quite flexible. All
+#' supplied arguments are tested and handled as follows: \code{respeciate}-like
+#' objects are passed to \code{data.table::rbindlist} as a list to rbind using
+#' \code{data.table} methods; Any other arguments that are valid
+#' \code{rbindlist} arguments are passed on 'as is'; And, anything else is
+#' (hopefully) ignored.
+
+#' @return \code{rsp_lbind} attempts to return a single stacked version of the
+#' supplied data sets. If it is successful, the (stacked) data set is typically
+#' returned as a \code{respeciate} object or a \code{data.frame} with a warning
+#' if it is missing columns \code{respeciate} expects.
+
+## #' @note
+## TO DO: want a statement here about why we are not going with a rbind method
+## basically, it is a pain...
+##     ... if any of the data sets is a data.frame, and
+##          you get rbind.data.frame/default
+##     is some online discussion of its behaviour
+
+## #' @seealso [link to data.table::rbindlist if we can do that...]
+## not sure I am loading package
+
+#' @references
+#'   Dowle M, Srinivasan A (2023). data.table: Extension of `data.frame`.
+#'   R package version 1.14.8, \url{https://CRAN.R-project.org/package=data.table}.
+
+##########################################
+# general NOTES
+##########################################
+
+# not loading all of data.table, see xxx.r...
+
+######################
+#rsp_lbind
+######################
+
+#' @rdname rsp.combine
+#' @export
+
+#issues
+############################
+
+# not finished
+
+# bits of documentation to complete
+#    links to data.table::rbindlist need to be added
+#         in text and see also
+# error messages need tidying
+# currently not handling the class quite right
+#       ok for standard respeciate object,
+#             probably not for rsp_x
+#             definitely not for wides...
+#             stack, but probably breaks respeciate rules for
+#                  data.frame, etc without expected respeciate names .... ?
+#       (see notes in function)
+
+#think about...
+#############################
+
+# might need option to force object class
+# option(s) to make errors/warning silent ????
+# could we extend lbind to do cbind as well as rbind ????
+#       could we extend lbind to do merge as well ???
+
+rsp_lbind <- function(...){
+
+  # setup
+  #####################################
+  .args <- list(...)
+
+  # ... handling 1: the data.sets
+  #####################################
+  # based on method in rsp() method v 0.3
+  # allows data.frames, respeciate objects, etc
+  .rsp <- lapply(.args, function(.rsp){
+    if(is.data.frame(.rsp)){ .rsp }})
+
+  #might want to think about respeciate handling ???
+  #  if for example something is wide ???? or rsp_x ????
+
+  # rbindlist
+  ###################################
+  # currently using loa-like approach...
+  #    allowing only extra args formally declared in rbindlist
+  .refs <- names(formals(data.table::rbindlist))
+  .lbind <- modifyList(list(l=.rsp, fill=TRUE),
+                       .args[names(.args) %in% .refs])
+  .bound.dt <- do.call(data.table::rbindlist, .lbind)
+  if(nrow(.bound.dt)==0){
+    stop("RSP> Nothing to list and rbind...",
+         call. = FALSE)
+  }
+
+  # output
+  ###########################
+
+  # should this try to force class to that of first data set in call ???
+  #     might make most sense ???
+
+  .rsp <- try(as.respeciate(.bound.dt), silent=TRUE)
+  if(class(.rsp)[1]=="try-error"){
+    warning("RSP> not obvious respeciate; returning as data.frame...",
+            call. = FALSE)
+    as.data.frame(.bound.dt)
+  } else {
+    .rsp
+  }
+}
+
+
+