Merge pull request #13 from karlropkins/main

version 0.3...

.Rproj.user/shared/notebooks/paths

@@ -1,7 +1,10 @@
 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/_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/_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/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"
@@ -15,22 +18,23 @@ C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test
 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.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.plot.R="561F2EAC"
-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/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.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/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"
+C:/Users/trakradmin/OneDrive - University of Leeds/Documents/pkg/respeciate/test/respeciate/man/respeciate.generics.Rd="2897F12C"

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: respeciate
 Title: Speciation profiles for gases and aerosols
-Version: 0.2.7
-Date: 2024-02-17
-Description: Acess to the US.EPA Speciate (v5.2) tool, to generate speciation profiles for
+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>.
 Type: Package
 Authors@R: c( person(given = "Sergio", family = "Ibarra-Espinosa", role = c("aut", "cre"),

NAMESPACE

@@ -1,10 +1,12 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(as.respeciate,default)
 S3method(plot,respeciate)
+S3method(plot,rsp_pls)
 S3method(print,respeciate)
 S3method(print,rsp_pls)
 S3method(summary,respeciate)
-export(find_code)
+export(as.respeciate)
 export(pls_fit_species)
 export(pls_plot)
 export(pls_plot_profile)
@@ -13,39 +15,39 @@ export(pls_rebuild)
 export(pls_refit_species)
 export(pls_report)
 export(pls_test)
-export(sp_average_profile)
-export(sp_build_rsp_x)
-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_plot_profile)
-export(sp_plot_species)
-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)
+export(rsp)
+export(rsp_average_profile)
+export(rsp_build_x)
+export(rsp_cor_species)
+export(rsp_dcast)
+export(rsp_dcast_profile)
+export(rsp_dcast_species)
+export(rsp_distance_profile)
+export(rsp_find_profile)
+export(rsp_find_species)
+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_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)
 importFrom(data.table,":=")
 importFrom(grDevices,as.graphicsAnnot)
 importFrom(grDevices,cm.colors)
@@ -92,6 +94,7 @@ importFrom(stats,formula)
 importFrom(stats,hclust)
 importFrom(stats,heatmap)
 importFrom(stats,lm)
+importFrom(stats,na.omit)
 importFrom(stats,nls)
 importFrom(stats,nls.control)
 importFrom(stats,predict)

NEWS.md

@@ -1,11 +1,26 @@
-# Version 0.0 - Release Notes
+# Release Notes Version 0.3
+
+* [0.3.0] 
+    * released 2024-05-17 
+    * code and documentation refresh...  
+    * added as.respeciate method; replacing related unexported code 
+    * sp_profile, sp_build_rsp_x updates; both now use as.respeciate 
+    * sp_profile to rsp_profile; sp_dcast/melt to rsp_dcast/melt; both as 
+    part of object class rebuild 
+    * sp_pad to rsp_pad; sp_rescale to rsp_rescale; class rebuild 
+    * sp_match_profile to rsp_match_profile; class rebuild   
+    * sp_cor to rsp_cor; sp_distance to rsp_dist; class rebuild 
+    * rsp_plots now track factors 
+    * pls_plots updated for object class
+
+# Release Notes Version 0.2
 
 * [0.2.7] 
     * released 2024-02-17
     * sp_plot_species update; species order forced, added reset.x 
     * sp_match_profile update; fit methods for pd and sid (Belis) 
     * sp_match_profile update; added sid variations 
-    * pls_plot patch; forcing profile order   
+    * pls_plot patch; forcing profile order 1  
 
 * [0.2.6] 
     * released 2023-12-01
@@ -68,6 +83,8 @@
     * updated date and version
     * The new code is in R:speciate.0.2.r
 
+# Release Notes Version 0.1
+
 * [0.1.0] 
     * released 2020-12-20  
     * Created respeciate