Merge pull request #8 from karlropkins/main

respeciate updates discussed yesterday

.Rproj.user/shared/notebooks/paths

@@ -1,7 +1,32 @@
+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/_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/marylebone02/_marylebone_metals_03.Rmd="63CDB89D"
+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/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/NEWS.md="F6ED8BF4"
+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/sp.001.R="0357CDCE"
+C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/sp.R="58F2A9BE"
+C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/sp.average.R="0A1E36E4"
+C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/sp.cluster.R="49C0F861"
+C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/sp.cor.R="3F1DA8E5"
+C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/sp.info.R="D0E7AC03"
+C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/sp.match.R="4326C1C3"
+C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/sp.pad.R="4962C940"
+C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/sp.pls.R="EACFE9A4"
+C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/sp.rescale.R="D668C5B2"
+C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/sp.reshape.R="CC655C60"
 C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/speciate.R="6C6E673A"
+C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/spq.R="3AD9ACC8"
+C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/R/spx.R="CA18044A"
+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/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/spec.Rd="8472593F"

DESCRIPTION

@@ -1,18 +1,19 @@
 Package: respeciate
 Title: Speciation profiles for gases and aerosols
-Version: 0.2.1
-Date: 2023-06-21
-Description: Acess to the US.EPA Speciate (v5.2) tool, to generate speciation for gases and particles.
-           More details in Simon et al (2010) <doi:10.5094/APR.2010.026>.
+Version: 0.2.3
+Date: 2023-09-23
+Description: Acess 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>.
 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
 Encoding: UTF-8
+Imports: data.table

NAMESPACE

@@ -2,13 +2,80 @@
 
 S3method(plot,respeciate)
 S3method(print,respeciate)
-S3method(print,respeciate.ref)
-S3method(print,respeciate.spcs)
+S3method(summary,respeciate)
 export(find_code)
+export(pls_fit_parent)
+export(pls_plot)
+export(pls_plot_profile)
+export(pls_plot_species)
+export(pls_refit_species)
+export(pls_report)
+export(sp_average_profile)
+export(sp_dcast)
+export(sp_dcast_profile)
+export(sp_dcast_species)
 export(sp_find_profile)
 export(sp_find_species)
+export(sp_info)
+export(sp_match_profile)
+export(sp_melt_wide)
+export(sp_pad)
+export(sp_pls_profile)
 export(sp_profile)
+export(sp_profile_distance)
+export(sp_profile_info)
+export(sp_rescale)
+export(sp_rescale_profile)
+export(sp_rescale_species)
+export(sp_species_cor)
+export(sp_species_info)
 export(spec)
+export(spq_gas)
+export(spq_other)
+export(spq_pm)
+export(spq_pm.ae6)
+export(spq_pm.ae8)
+export(spq_pm.cr1)
+export(spq_pm.simplified)
+export(spx_btex)
+export(spx_copy)
+export(spx_n_alkane)
+import(data.table)
+importFrom(grDevices,as.graphicsAnnot)
+importFrom(grDevices,cm.colors)
+importFrom(grDevices,colorRampPalette)
+importFrom(grDevices,dev.flush)
+importFrom(grDevices,dev.hold)
+importFrom(grDevices,heat.colors)
+importFrom(graphics,abline)
 importFrom(graphics,axis)
 importFrom(graphics,barplot)
+importFrom(graphics,grid)
+importFrom(graphics,legend)
+importFrom(graphics,lines)
+importFrom(graphics,mtext)
 importFrom(graphics,par)
+importFrom(graphics,plot.new)
+importFrom(graphics,plot.window)
+importFrom(graphics,points)
+importFrom(graphics,polygon)
+importFrom(graphics,rect)
+importFrom(graphics,text)
+importFrom(graphics,title)
+importFrom(stats,AIC)
+importFrom(stats,as.formula)
+importFrom(stats,coefficients)
+importFrom(stats,cophenetic)
+importFrom(stats,cor)
+importFrom(stats,cutree)
+importFrom(stats,dist)
+importFrom(stats,formula)
+importFrom(stats,hclust)
+importFrom(stats,heatmap)
+importFrom(stats,lm)
+importFrom(stats,nls)
+importFrom(stats,nls.control)
+importFrom(stats,predict)
+importFrom(stats,sd)
+importFrom(utils,head)
+importFrom(utils,modifyList)

NEWS.md

@@ -1,26 +1,43 @@
-NEWS
-===========
+# Version 0.0 - Release Notes
 
-### respeciate 0.2.1 (Release date: 2023-06-21)
+* [0.2.3] 
+    * released 2023-09-26 
+    * added functions: sp_rescale_species, sp_dcast, sp_dcast_species 
+    sp_pad, sp_pls_profile 
+    * added draft spq_ quick profile build  functions 
+    * added pls_ functions for sp_pls_profile outputs
+    * sp_profile update: references not included by default 
+    * sp_match: changed n to matches; added min.n (so more consistent 
+    with other functions); now averages x
+    * sp_species_cor: added heatmap and key list options 
 
-- updated sysdata (now using SPECIATE 5.2)
-- added sp\_find\_species 
-- extended sp\_find\_profile; now allows by='species_name'
-- simplified plot.respeciate
+* [0.2.2] 
+    * released 2023-08-24 
+    * now imports data.table; moving to data.table methods for speed 
+    * changed news format because build_news missing previous md text 
+    * added functions: sp_rescale_profile, sp_dcast_profile, sp_species_cor, 
+    sp_profile_dist, sp_match_profile, sp_melt_wide
+    * reduced object classes
+
+* [0.2.1] 
+    * released 2023-06-21 
+    * updated sysdata (now using SPECIATE 5.2)
+    * added sp_find_species 
+    * extended sp_find_profile; now searches by species_name
+    * simplified plot.respeciate
 
+* [0.2.0] 
+    * released 2021-05-26 
+    * Karl Ropkins joined
+    * moved your sysdata.rda to the package data folder
+    * reset lazy.data to TRUE  
+    * added an object class
+    * added sp_find_profile (find_code but making object class)
+    * added sp_profile (spec but making object class)
+    * added crude print and plot methods for object classes
+    * updated date and version
+    * The new code is in R:speciate.0.2.r
 
-### respeciate 0.2.0 (Release date: 2021-05-26)
-
-- Karl Ropkins joined
-- moved your sysdata.rda to the package data folder
-- reset lazy.data to TRUE  
-- added an object class
-- added sp\_find\_profile (find\_code but making object class)
-- added sp\_profile (spec but making object class)
-- added crude print and plot methods for object classes
-- updated date and version
-- The new code is in R/speciate.0.2.r
-
-### respeciate 0.1.0 (Release date: 2020-12-20)
-
-- Create respeciate
+* [0.1.0] 
+    * released 2020-12-20  
+    * Created respeciate