********************** Windows PowerShell transcript start Start time: 20211108062637 Username: CDMOTOOLS\dramage RunAs User: CDMOTOOLS\dramage Machine: CDMOTOOLS (Microsoft Windows NT 10.0.14393.0) Host Application: powershell.exe -ExecutionPolicy Bypass -Command & .\NERRS_run_reserves_2021.ps1 Process ID: 3576 PSVersion: 5.1.14393.3866 PSEdition: Desktop PSCompatibleVersions: 1.0, 2.0, 3.0, 4.0, 5.0, 5.1.14393.3866 BuildVersion: 10.0.14393.3866 CLRVersion: 4.0.30319.42000 WSManStackVersion: 3.0 PSRemotingProtocolVersion: 2.3 SerializationVersion: 1.1.0.1 ********************** Transcript started, output file is C:\NERRS\CDMO_Automation_2021\01_process_log.txt Directory: C:\NERRS\CDMO_Automation_2021 Mode LastWriteTime Length Name ---- ------------- ------ ---- d----- 11/8/2021 6:26 AM 01_Reserve_working_files Directory: C:\NERRS\CDMO_Automation_2021\01_Reserve_working_files Mode LastWriteTime Length Name ---- ------------- ------ ---- d----- 11/8/2021 6:26 AM all_logs Directory: C:\NERRS\CDMO_Automation_2021 Mode LastWriteTime Length Name ---- ------------- ------ ---- d----- 11/8/2021 6:26 AM 01_Zipped_distrib_files d----- 11/8/2021 6:26 AM 01_last_years_extracted_files d----- 11/8/2021 6:26 AM 01_National_Report Directory: C:\NERRS\CDMO_Automation_2021\01_National_Report Mode LastWriteTime Length Name ---- ------------- ------ ---- d----- 11/8/2021 6:26 AM handoff_files R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > dest_dir_root = c('C:/NERRS/CDMO_Automation_2021/01_last_years_extracted_files') > old_zip_dir = c('C:/NERRS/CDMO_V2_2020/01_Reserve_distrib_files') > getwd() [1] "C:/NERRS/CDMO_Automation_2021" > source('./00_Additional_Materials/R/copy_zipped_report_files.R') > closeAllConnections() > ******************************************************** * Processing reserve 'ace' * *** Using updated spreadsheet: C:\NERRS\CDMO_Automation_2021\00_Annual_Update\Updated_reserve_var_sheets\Reserve_Level_Plotting_Variables_ace_2020.xlsx *** R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > target_year = c(2020) > year_range = c(2000,2020) > source('R/01_Load_Wrangle_Run.R') Loading required package: broom Loading required package: janitor Attaching package: 'janitor' The following objects are masked from 'package:stats': chisq.test, fisher.test Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: openxlsx Loading required package: readxl Loading required package: EnvStats Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default Loading required package: ggthemes Loading required package: RColorBrewer Loading required package: sf Linking to GEOS 3.9.1, GDAL 3.2.1, PROJ 7.2.1 Loading required package: ggmap Loading required package: ggplot2 Google's Terms of Service: https://cloud.google.com/maps-platform/terms/. Please cite ggmap if you use it! See citation("ggmap") for details. Loading required package: flextable Loading required package: officer Attaching package: 'officer' The following object is masked from 'package:readxl': read_xlsx Loading required package: SWMPr Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: SWMPrExtension Loading required package: devtools Loading required package: usethis There were 50 or more warnings (use warnings() to see the first 50) > closeAllConnections() > R call succeeded for ace ------------ * * Completed reserve 'ace' ******************************************************** ******************************************************** * Processing reserve 'apa' * *** Using updated spreadsheet: C:\NERRS\CDMO_Automation_2021\00_Annual_Update\Updated_reserve_var_sheets\Reserve_Level_Plotting_Variables_apa_2020.xlsx *** R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > target_year = c(2020) > year_range = c(2000,2020) > source('R/01_Load_Wrangle_Run.R') Loading required package: broom Loading required package: janitor Attaching package: 'janitor' The following objects are masked from 'package:stats': chisq.test, fisher.test Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: openxlsx Loading required package: readxl Loading required package: EnvStats Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default Loading required package: ggthemes Loading required package: RColorBrewer Loading required package: sf Linking to GEOS 3.9.1, GDAL 3.2.1, PROJ 7.2.1 Loading required package: ggmap Loading required package: ggplot2 Google's Terms of Service: https://cloud.google.com/maps-platform/terms/. Please cite ggmap if you use it! See citation("ggmap") for details. Loading required package: flextable Loading required package: officer Attaching package: 'officer' The following object is masked from 'package:readxl': read_xlsx Loading required package: SWMPr Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: SWMPrExtension Loading required package: devtools Loading required package: usethis There were 50 or more warnings (use warnings() to see the first 50) > closeAllConnections() > R call succeeded for apa ------------ * * Completed reserve 'apa' ******************************************************** ******************************************************** * Processing reserve 'cbm' * *** Using updated spreadsheet: C:\NERRS\CDMO_Automation_2021\00_Annual_Update\Updated_reserve_var_sheets\Reserve_Level_Plotting_Variables_cbm_2020.xlsx *** R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > target_year = c(2020) > year_range = c(2000,2020) > source('R/01_Load_Wrangle_Run.R') Loading required package: broom Loading required package: janitor Attaching package: 'janitor' The following objects are masked from 'package:stats': chisq.test, fisher.test Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: openxlsx Loading required package: readxl Loading required package: EnvStats Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default Loading required package: ggthemes Loading required package: RColorBrewer Loading required package: sf Linking to GEOS 3.9.1, GDAL 3.2.1, PROJ 7.2.1 Loading required package: ggmap Loading required package: ggplot2 Google's Terms of Service: https://cloud.google.com/maps-platform/terms/. Please cite ggmap if you use it! See citation("ggmap") for details. Loading required package: flextable Loading required package: officer Attaching package: 'officer' The following object is masked from 'package:readxl': read_xlsx Loading required package: SWMPr Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: SWMPrExtension Loading required package: devtools Loading required package: usethis There were 50 or more warnings (use warnings() to see the first 50) > closeAllConnections() > R call succeeded for cbm ------------ * * Completed reserve 'cbm' ******************************************************** ******************************************************** * Processing reserve 'cbv' * *** Using updated spreadsheet: C:\NERRS\CDMO_Automation_2021\00_Annual_Update\Updated_reserve_var_sheets\Reserve_Level_Plotting_Variables_cbv_2020.xlsx *** R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > target_year = c(2020) > year_range = c(2000,2020) > source('R/01_Load_Wrangle_Run.R') Loading required package: broom Loading required package: janitor Attaching package: 'janitor' The following objects are masked from 'package:stats': chisq.test, fisher.test Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: openxlsx Loading required package: readxl Loading required package: EnvStats Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default Loading required package: ggthemes Loading required package: RColorBrewer Loading required package: sf Linking to GEOS 3.9.1, GDAL 3.2.1, PROJ 7.2.1 Loading required package: ggmap Loading required package: ggplot2 Google's Terms of Service: https://cloud.google.com/maps-platform/terms/. Please cite ggmap if you use it! See citation("ggmap") for details. Loading required package: flextable Loading required package: officer Attaching package: 'officer' The following object is masked from 'package:readxl': read_xlsx Loading required package: SWMPr Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: SWMPrExtension Loading required package: devtools Loading required package: usethis There were 50 or more warnings (use warnings() to see the first 50) > closeAllConnections() > R call succeeded for cbv ------------ * * Completed reserve 'cbv' ******************************************************** ******************************************************** * Processing reserve 'del' * *** Using updated spreadsheet: C:\NERRS\CDMO_Automation_2021\00_Annual_Update\Updated_reserve_var_sheets\Reserve_Level_Plotting_Variables_del_2020.xlsx *** R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > target_year = c(2020) > year_range = c(2000,2020) > source('R/01_Load_Wrangle_Run.R') Loading required package: broom Loading required package: janitor Attaching package: 'janitor' The following objects are masked from 'package:stats': chisq.test, fisher.test Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: openxlsx Loading required package: readxl Loading required package: EnvStats Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default Loading required package: ggthemes Loading required package: RColorBrewer Loading required package: sf Linking to GEOS 3.9.1, GDAL 3.2.1, PROJ 7.2.1 Loading required package: ggmap Loading required package: ggplot2 Google's Terms of Service: https://cloud.google.com/maps-platform/terms/. Please cite ggmap if you use it! See citation("ggmap") for details. Loading required package: flextable Loading required package: officer Attaching package: 'officer' The following object is masked from 'package:readxl': read_xlsx Loading required package: SWMPr Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: SWMPrExtension Loading required package: devtools Loading required package: usethis There were 50 or more warnings (use warnings() to see the first 50) > closeAllConnections() > R call succeeded for del ------------ * * Completed reserve 'del' ******************************************************** ******************************************************** * Processing reserve 'elk' * *** Using updated spreadsheet: C:\NERRS\CDMO_Automation_2021\00_Annual_Update\Updated_reserve_var_sheets\Reserve_Level_Plotting_Variables_elk_2020.xlsx *** R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > target_year = c(2020) > year_range = c(2000,2020) > source('R/01_Load_Wrangle_Run.R') Loading required package: broom Loading required package: janitor Attaching package: 'janitor' The following objects are masked from 'package:stats': chisq.test, fisher.test Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: openxlsx Loading required package: readxl Loading required package: EnvStats Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default Loading required package: ggthemes Loading required package: RColorBrewer Loading required package: sf Linking to GEOS 3.9.1, GDAL 3.2.1, PROJ 7.2.1 Loading required package: ggmap Loading required package: ggplot2 Google's Terms of Service: https://cloud.google.com/maps-platform/terms/. Please cite ggmap if you use it! See citation("ggmap") for details. Loading required package: flextable Loading required package: officer Attaching package: 'officer' The following object is masked from 'package:readxl': read_xlsx Loading required package: SWMPr Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: SWMPrExtension Loading required package: devtools Loading required package: usethis There were 50 or more warnings (use warnings() to see the first 50) > closeAllConnections() > R call succeeded for elk ------------ * * Completed reserve 'elk' ******************************************************** ******************************************************** * Processing reserve 'gnd' * *** Using updated spreadsheet: C:\NERRS\CDMO_Automation_2021\00_Annual_Update\Updated_reserve_var_sheets\Reserve_Level_Plotting_Variables_gnd_2020.xlsx *** R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > target_year = c(2020) > year_range = c(2000,2020) > source('R/01_Load_Wrangle_Run.R') Loading required package: broom Loading required package: janitor Attaching package: 'janitor' The following objects are masked from 'package:stats': chisq.test, fisher.test Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: openxlsx Loading required package: readxl Loading required package: EnvStats Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default Loading required package: ggthemes Loading required package: RColorBrewer Loading required package: sf Linking to GEOS 3.9.1, GDAL 3.2.1, PROJ 7.2.1 Loading required package: ggmap Loading required package: ggplot2 Google's Terms of Service: https://cloud.google.com/maps-platform/terms/. Please cite ggmap if you use it! See citation("ggmap") for details. Loading required package: flextable Loading required package: officer Attaching package: 'officer' The following object is masked from 'package:readxl': read_xlsx Loading required package: SWMPr Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: SWMPrExtension Loading required package: devtools Loading required package: usethis There were 50 or more warnings (use warnings() to see the first 50) > closeAllConnections() > R call succeeded for gnd ------------ * * Completed reserve 'gnd' ******************************************************** ******************************************************** * Processing reserve 'grb' * *** Using updated spreadsheet: C:\NERRS\CDMO_Automation_2021\00_Annual_Update\Updated_reserve_var_sheets\Reserve_Level_Plotting_Variables_grb_2020.xlsx *** R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > target_year = c(2020) > year_range = c(2000,2020) > source('R/01_Load_Wrangle_Run.R') Loading required package: broom Loading required package: janitor Attaching package: 'janitor' The following objects are masked from 'package:stats': chisq.test, fisher.test Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: openxlsx Loading required package: readxl Loading required package: EnvStats Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default Loading required package: ggthemes Loading required package: RColorBrewer Loading required package: sf Linking to GEOS 3.9.1, GDAL 3.2.1, PROJ 7.2.1 Loading required package: ggmap Loading required package: ggplot2 Google's Terms of Service: https://cloud.google.com/maps-platform/terms/. Please cite ggmap if you use it! See citation("ggmap") for details. Loading required package: flextable Loading required package: officer Attaching package: 'officer' The following object is masked from 'package:readxl': read_xlsx Loading required package: SWMPr Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: SWMPrExtension Loading required package: devtools Loading required package: usethis There were 50 or more warnings (use warnings() to see the first 50) > closeAllConnections() > R call succeeded for grb ------------ * * Completed reserve 'grb' ******************************************************** ******************************************************** * Processing reserve 'gtm' * *** Using updated spreadsheet: C:\NERRS\CDMO_Automation_2021\00_Annual_Update\Updated_reserve_var_sheets\Reserve_Level_Plotting_Variables_gtm_2020.xlsx *** R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > target_year = c(2020) > year_range = c(2000,2020) > source('R/01_Load_Wrangle_Run.R') Loading required package: broom Loading required package: janitor Attaching package: 'janitor' The following objects are masked from 'package:stats': chisq.test, fisher.test Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: openxlsx Loading required package: readxl Loading required package: EnvStats Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default Loading required package: ggthemes Loading required package: RColorBrewer Loading required package: sf Linking to GEOS 3.9.1, GDAL 3.2.1, PROJ 7.2.1 Loading required package: ggmap Loading required package: ggplot2 Google's Terms of Service: https://cloud.google.com/maps-platform/terms/. Please cite ggmap if you use it! See citation("ggmap") for details. Loading required package: flextable Loading required package: officer Attaching package: 'officer' The following object is masked from 'package:readxl': read_xlsx Loading required package: SWMPr Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: SWMPrExtension Loading required package: devtools Loading required package: usethis There were 50 or more warnings (use warnings() to see the first 50) > closeAllConnections() > R call succeeded for gtm ------------ * * Completed reserve 'gtm' ******************************************************** ******************************************************** * Processing reserve 'hee' * *** No hee reserve-specific files from previous year *** *** Using updated spreadsheet: C:\NERRS\CDMO_Automation_2021\00_Annual_Update\Updated_reserve_var_sheets\Reserve_Level_Plotting_Variables_hee_2020.xlsx *** R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > target_year = c(2020) > year_range = c(2000,2020) > source('R/01_Load_Wrangle_Run.R') Loading required package: broom Loading required package: janitor Attaching package: 'janitor' The following objects are masked from 'package:stats': chisq.test, fisher.test Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: openxlsx Loading required package: readxl Loading required package: EnvStats Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default Loading required package: ggthemes Loading required package: RColorBrewer Loading required package: sf Linking to GEOS 3.9.1, GDAL 3.2.1, PROJ 7.2.1 Loading required package: ggmap Loading required package: ggplot2 Google's Terms of Service: https://cloud.google.com/maps-platform/terms/. Please cite ggmap if you use it! See citation("ggmap") for details. Loading required package: flextable Loading required package: officer Attaching package: 'officer' The following object is masked from 'package:readxl': read_xlsx Loading required package: SWMPr Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: SWMPrExtension Loading required package: devtools Loading required package: usethis There were 50 or more warnings (use warnings() to see the first 50) > closeAllConnections() > R call succeeded for hee ------------ * * Completed reserve 'hee' ******************************************************** ******************************************************** * Processing reserve 'hud' * *** Using updated spreadsheet: C:\NERRS\CDMO_Automation_2021\00_Annual_Update\Updated_reserve_var_sheets\Reserve_Level_Plotting_Variables_hud_2020.xlsx *** R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > target_year = c(2020) > year_range = c(2000,2020) > source('R/01_Load_Wrangle_Run.R') Loading required package: broom Loading required package: janitor Attaching package: 'janitor' The following objects are masked from 'package:stats': chisq.test, fisher.test Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: openxlsx Loading required package: readxl Loading required package: EnvStats Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default Loading required package: ggthemes Loading required package: RColorBrewer Loading required package: sf Linking to GEOS 3.9.1, GDAL 3.2.1, PROJ 7.2.1 Loading required package: ggmap Loading required package: ggplot2 Google's Terms of Service: https://cloud.google.com/maps-platform/terms/. Please cite ggmap if you use it! See citation("ggmap") for details. Loading required package: flextable Loading required package: officer Attaching package: 'officer' The following object is masked from 'package:readxl': read_xlsx Loading required package: SWMPr Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: SWMPrExtension Loading required package: devtools Loading required package: usethis R call succeeded for hud ------------ No handoff folder created * * Completed reserve 'hud' ******************************************************** ******************************************************** * Processing reserve 'jac' * *** Using updated spreadsheet: C:\NERRS\CDMO_Automation_2021\00_Annual_Update\Updated_reserve_var_sheets\Reserve_Level_Plotting_Variables_jac_2020.xlsx *** R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > target_year = c(2020) > year_range = c(2000,2020) > source('R/01_Load_Wrangle_Run.R') Loading required package: broom Loading required package: janitor Attaching package: 'janitor' The following objects are masked from 'package:stats': chisq.test, fisher.test Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: openxlsx Loading required package: readxl Loading required package: EnvStats Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default Loading required package: ggthemes Loading required package: RColorBrewer Loading required package: sf Linking to GEOS 3.9.1, GDAL 3.2.1, PROJ 7.2.1 Loading required package: ggmap Loading required package: ggplot2 Google's Terms of Service: https://cloud.google.com/maps-platform/terms/. Please cite ggmap if you use it! See citation("ggmap") for details. Loading required package: flextable Loading required package: officer Attaching package: 'officer' The following object is masked from 'package:readxl': read_xlsx Loading required package: SWMPr Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: SWMPrExtension Loading required package: devtools Loading required package: usethis There were 50 or more warnings (use warnings() to see the first 50) > closeAllConnections() > R call succeeded for jac ------------ * * Completed reserve 'jac' ******************************************************** ******************************************************** * Processing reserve 'job' * *** Using updated spreadsheet: C:\NERRS\CDMO_Automation_2021\00_Annual_Update\Updated_reserve_var_sheets\Reserve_Level_Plotting_Variables_job_2020.xlsx *** R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > target_year = c(2020) > year_range = c(2000,2020) > source('R/01_Load_Wrangle_Run.R') Loading required package: broom Loading required package: janitor Attaching package: 'janitor' The following objects are masked from 'package:stats': chisq.test, fisher.test Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: openxlsx Loading required package: readxl Loading required package: EnvStats Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default Loading required package: ggthemes Loading required package: RColorBrewer Loading required package: sf Linking to GEOS 3.9.1, GDAL 3.2.1, PROJ 7.2.1 Loading required package: ggmap Loading required package: ggplot2 Google's Terms of Service: https://cloud.google.com/maps-platform/terms/. Please cite ggmap if you use it! See citation("ggmap") for details. Loading required package: flextable Loading required package: officer Attaching package: 'officer' The following object is masked from 'package:readxl': read_xlsx Loading required package: SWMPr Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: SWMPrExtension Loading required package: devtools Loading required package: usethis There were 50 or more warnings (use warnings() to see the first 50) > closeAllConnections() > R call succeeded for job ------------ * * Completed reserve 'job' ******************************************************** ******************************************************** * Processing reserve 'kac' * *** Using updated spreadsheet: C:\NERRS\CDMO_Automation_2021\00_Annual_Update\Updated_reserve_var_sheets\Reserve_Level_Plotting_Variables_kac_2020.xlsx *** R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > target_year = c(2020) > year_range = c(2000,2020) > source('R/01_Load_Wrangle_Run.R') Loading required package: broom Loading required package: janitor Attaching package: 'janitor' The following objects are masked from 'package:stats': chisq.test, fisher.test Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: openxlsx Loading required package: readxl Loading required package: EnvStats Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default Loading required package: ggthemes Loading required package: RColorBrewer Loading required package: sf Linking to GEOS 3.9.1, GDAL 3.2.1, PROJ 7.2.1 Loading required package: ggmap Loading required package: ggplot2 Google's Terms of Service: https://cloud.google.com/maps-platform/terms/. Please cite ggmap if you use it! See citation("ggmap") for details. Loading required package: flextable Loading required package: officer Attaching package: 'officer' The following object is masked from 'package:readxl': read_xlsx Loading required package: SWMPr Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: SWMPrExtension Loading required package: devtools Loading required package: usethis There were 50 or more warnings (use warnings() to see the first 50) > closeAllConnections() > R call succeeded for kac ------------ * * Completed reserve 'kac' ******************************************************** ******************************************************** * Processing reserve 'lks' * *** Using updated spreadsheet: C:\NERRS\CDMO_Automation_2021\00_Annual_Update\Updated_reserve_var_sheets\Reserve_Level_Plotting_Variables_lks_2020.xlsx *** R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > target_year = c(2020) > year_range = c(2000,2020) > source('R/01_Load_Wrangle_Run.R') Loading required package: broom Loading required package: janitor Attaching package: 'janitor' The following objects are masked from 'package:stats': chisq.test, fisher.test Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: openxlsx Loading required package: readxl Loading required package: EnvStats Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default Loading required package: ggthemes Loading required package: RColorBrewer Loading required package: sf Linking to GEOS 3.9.1, GDAL 3.2.1, PROJ 7.2.1 Loading required package: ggmap Loading required package: ggplot2 Google's Terms of Service: https://cloud.google.com/maps-platform/terms/. Please cite ggmap if you use it! See citation("ggmap") for details. Loading required package: flextable Loading required package: officer Attaching package: 'officer' The following object is masked from 'package:readxl': read_xlsx Loading required package: SWMPr Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: SWMPrExtension Loading required package: devtools Loading required package: usethis There were 50 or more warnings (use warnings() to see the first 50) > closeAllConnections() > R call succeeded for lks ------------ * * Completed reserve 'lks' ******************************************************** ******************************************************** * Processing reserve 'mar' * *** Using updated spreadsheet: C:\NERRS\CDMO_Automation_2021\00_Annual_Update\Updated_reserve_var_sheets\Reserve_Level_Plotting_Variables_mar_2020.xlsx *** R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > target_year = c(2020) > year_range = c(2000,2020) > source('R/01_Load_Wrangle_Run.R') Loading required package: broom Loading required package: janitor Attaching package: 'janitor' The following objects are masked from 'package:stats': chisq.test, fisher.test Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: openxlsx Loading required package: readxl Loading required package: EnvStats Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default Loading required package: ggthemes Loading required package: RColorBrewer Loading required package: sf Linking to GEOS 3.9.1, GDAL 3.2.1, PROJ 7.2.1 Loading required package: ggmap Loading required package: ggplot2 Google's Terms of Service: https://cloud.google.com/maps-platform/terms/. Please cite ggmap if you use it! See citation("ggmap") for details. Loading required package: flextable Loading required package: officer Attaching package: 'officer' The following object is masked from 'package:readxl': read_xlsx Loading required package: SWMPr Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: SWMPrExtension Loading required package: devtools Loading required package: usethis R call succeeded for mar ------------ No handoff folder created * * Completed reserve 'mar' ******************************************************** ******************************************************** * Processing reserve 'nar' * *** Using updated spreadsheet: C:\NERRS\CDMO_Automation_2021\00_Annual_Update\Updated_reserve_var_sheets\Reserve_Level_Plotting_Variables_nar_2020.xlsx *** R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > target_year = c(2020) > year_range = c(2000,2020) > source('R/01_Load_Wrangle_Run.R') Loading required package: broom Loading required package: janitor Attaching package: 'janitor' The following objects are masked from 'package:stats': chisq.test, fisher.test Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: openxlsx Loading required package: readxl Loading required package: EnvStats Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default Loading required package: ggthemes Loading required package: RColorBrewer Loading required package: sf Linking to GEOS 3.9.1, GDAL 3.2.1, PROJ 7.2.1 Loading required package: ggmap Loading required package: ggplot2 Google's Terms of Service: https://cloud.google.com/maps-platform/terms/. Please cite ggmap if you use it! See citation("ggmap") for details. Loading required package: flextable Loading required package: officer Attaching package: 'officer' The following object is masked from 'package:readxl': read_xlsx Loading required package: SWMPr Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: SWMPrExtension Loading required package: devtools Loading required package: usethis There were 50 or more warnings (use warnings() to see the first 50) > closeAllConnections() > R call succeeded for nar ------------ * * Completed reserve 'nar' ******************************************************** ******************************************************** * Processing reserve 'niw' * *** Using updated spreadsheet: C:\NERRS\CDMO_Automation_2021\00_Annual_Update\Updated_reserve_var_sheets\Reserve_Level_Plotting_Variables_niw_2020.xlsx *** R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > target_year = c(2020) > year_range = c(2000,2020) > source('R/01_Load_Wrangle_Run.R') Loading required package: broom Loading required package: janitor Attaching package: 'janitor' The following objects are masked from 'package:stats': chisq.test, fisher.test Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: openxlsx Loading required package: readxl Loading required package: EnvStats Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default Loading required package: ggthemes Loading required package: RColorBrewer Loading required package: sf Linking to GEOS 3.9.1, GDAL 3.2.1, PROJ 7.2.1 Loading required package: ggmap Loading required package: ggplot2 Google's Terms of Service: https://cloud.google.com/maps-platform/terms/. Please cite ggmap if you use it! See citation("ggmap") for details. Loading required package: flextable Loading required package: officer Attaching package: 'officer' The following object is masked from 'package:readxl': read_xlsx Loading required package: SWMPr Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: SWMPrExtension Loading required package: devtools Loading required package: usethis There were 50 or more warnings (use warnings() to see the first 50) > closeAllConnections() > R call succeeded for niw ------------ * * Completed reserve 'niw' ******************************************************** ******************************************************** * Processing reserve 'noc' * *** Using updated spreadsheet: C:\NERRS\CDMO_Automation_2021\00_Annual_Update\Updated_reserve_var_sheets\Reserve_Level_Plotting_Variables_noc_2020.xlsx *** R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > target_year = c(2020) > year_range = c(2000,2020) > source('R/01_Load_Wrangle_Run.R') Loading required package: broom Loading required package: janitor Attaching package: 'janitor' The following objects are masked from 'package:stats': chisq.test, fisher.test Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: openxlsx Loading required package: readxl Loading required package: EnvStats Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default Loading required package: ggthemes Loading required package: RColorBrewer Loading required package: sf Linking to GEOS 3.9.1, GDAL 3.2.1, PROJ 7.2.1 Loading required package: ggmap Loading required package: ggplot2 Google's Terms of Service: https://cloud.google.com/maps-platform/terms/. Please cite ggmap if you use it! See citation("ggmap") for details. Loading required package: flextable Loading required package: officer Attaching package: 'officer' The following object is masked from 'package:readxl': read_xlsx Loading required package: SWMPr Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: SWMPrExtension Loading required package: devtools Loading required package: usethis There were 50 or more warnings (use warnings() to see the first 50) > closeAllConnections() > R call succeeded for noc ------------ * * Completed reserve 'noc' ******************************************************** ******************************************************** * Processing reserve 'owc' * *** Using updated spreadsheet: C:\NERRS\CDMO_Automation_2021\00_Annual_Update\Updated_reserve_var_sheets\Reserve_Level_Plotting_Variables_owc_2020.xlsx *** R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > target_year = c(2020) > year_range = c(2000,2020) > source('R/01_Load_Wrangle_Run.R') Loading required package: broom Loading required package: janitor Attaching package: 'janitor' The following objects are masked from 'package:stats': chisq.test, fisher.test Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: openxlsx Loading required package: readxl Loading required package: EnvStats Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default Loading required package: ggthemes Loading required package: RColorBrewer Loading required package: sf Linking to GEOS 3.9.1, GDAL 3.2.1, PROJ 7.2.1 Loading required package: ggmap Loading required package: ggplot2 Google's Terms of Service: https://cloud.google.com/maps-platform/terms/. Please cite ggmap if you use it! See citation("ggmap") for details. Loading required package: flextable Loading required package: officer Attaching package: 'officer' The following object is masked from 'package:readxl': read_xlsx Loading required package: SWMPr Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: SWMPrExtension Loading required package: devtools Loading required package: usethis There were 50 or more warnings (use warnings() to see the first 50) > closeAllConnections() > R call succeeded for owc ------------ * * Completed reserve 'owc' ******************************************************** ******************************************************** * Processing reserve 'pdb' * *** Using updated spreadsheet: C:\NERRS\CDMO_Automation_2021\00_Annual_Update\Updated_reserve_var_sheets\Reserve_Level_Plotting_Variables_pdb_2020.xlsx *** R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > target_year = c(2020) > year_range = c(2000,2020) > source('R/01_Load_Wrangle_Run.R') Loading required package: broom Loading required package: janitor Attaching package: 'janitor' The following objects are masked from 'package:stats': chisq.test, fisher.test Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: openxlsx Loading required package: readxl Loading required package: EnvStats Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default Loading required package: ggthemes Loading required package: RColorBrewer Loading required package: sf Linking to GEOS 3.9.1, GDAL 3.2.1, PROJ 7.2.1 Loading required package: ggmap Loading required package: ggplot2 Google's Terms of Service: https://cloud.google.com/maps-platform/terms/. Please cite ggmap if you use it! See citation("ggmap") for details. Loading required package: flextable Loading required package: officer Attaching package: 'officer' The following object is masked from 'package:readxl': read_xlsx Loading required package: SWMPr Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: SWMPrExtension Loading required package: devtools Loading required package: usethis There were 50 or more warnings (use warnings() to see the first 50) > closeAllConnections() > R call succeeded for pdb ------------ * * Completed reserve 'pdb' ******************************************************** ******************************************************** * Processing reserve 'rkb' * *** Using updated spreadsheet: C:\NERRS\CDMO_Automation_2021\00_Annual_Update\Updated_reserve_var_sheets\Reserve_Level_Plotting_Variables_rkb_2020.xlsx *** R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > target_year = c(2020) > year_range = c(2000,2020) > source('R/01_Load_Wrangle_Run.R') Loading required package: broom Loading required package: janitor Attaching package: 'janitor' The following objects are masked from 'package:stats': chisq.test, fisher.test Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: openxlsx Loading required package: readxl Loading required package: EnvStats Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default Loading required package: ggthemes Loading required package: RColorBrewer Loading required package: sf Linking to GEOS 3.9.1, GDAL 3.2.1, PROJ 7.2.1 Loading required package: ggmap Loading required package: ggplot2 Google's Terms of Service: https://cloud.google.com/maps-platform/terms/. Please cite ggmap if you use it! See citation("ggmap") for details. Loading required package: flextable Loading required package: officer Attaching package: 'officer' The following object is masked from 'package:readxl': read_xlsx Loading required package: SWMPr Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: SWMPrExtension Loading required package: devtools Loading required package: usethis There were 50 or more warnings (use warnings() to see the first 50) > closeAllConnections() > R call succeeded for rkb ------------ * * Completed reserve 'rkb' ******************************************************** ******************************************************** * Processing reserve 'sap' * *** Using updated spreadsheet: C:\NERRS\CDMO_Automation_2021\00_Annual_Update\Updated_reserve_var_sheets\Reserve_Level_Plotting_Variables_sap_2020.xlsx *** R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > target_year = c(2020) > year_range = c(2000,2020) > source('R/01_Load_Wrangle_Run.R') Loading required package: broom Loading required package: janitor Attaching package: 'janitor' The following objects are masked from 'package:stats': chisq.test, fisher.test Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: openxlsx Loading required package: readxl Loading required package: EnvStats Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default Loading required package: ggthemes Loading required package: RColorBrewer Loading required package: sf Linking to GEOS 3.9.1, GDAL 3.2.1, PROJ 7.2.1 Loading required package: ggmap Loading required package: ggplot2 Google's Terms of Service: https://cloud.google.com/maps-platform/terms/. Please cite ggmap if you use it! See citation("ggmap") for details. Loading required package: flextable Loading required package: officer Attaching package: 'officer' The following object is masked from 'package:readxl': read_xlsx Loading required package: SWMPr Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: SWMPrExtension Loading required package: devtools Loading required package: usethis There were 50 or more warnings (use warnings() to see the first 50) > closeAllConnections() > R call succeeded for sap ------------ * * Completed reserve 'sap' ******************************************************** ******************************************************** * Processing reserve 'sfb' * *** Using updated spreadsheet: C:\NERRS\CDMO_Automation_2021\00_Annual_Update\Updated_reserve_var_sheets\Reserve_Level_Plotting_Variables_sfb_2020.xlsx *** R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > target_year = c(2020) > year_range = c(2000,2020) > source('R/01_Load_Wrangle_Run.R') Loading required package: broom Loading required package: janitor Attaching package: 'janitor' The following objects are masked from 'package:stats': chisq.test, fisher.test Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: openxlsx Loading required package: readxl Loading required package: EnvStats Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default Loading required package: ggthemes Loading required package: RColorBrewer Loading required package: sf Linking to GEOS 3.9.1, GDAL 3.2.1, PROJ 7.2.1 Loading required package: ggmap Loading required package: ggplot2 Google's Terms of Service: https://cloud.google.com/maps-platform/terms/. Please cite ggmap if you use it! See citation("ggmap") for details. Loading required package: flextable Loading required package: officer Attaching package: 'officer' The following object is masked from 'package:readxl': read_xlsx Loading required package: SWMPr Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: SWMPrExtension Loading required package: devtools Loading required package: usethis There were 50 or more warnings (use warnings() to see the first 50) > closeAllConnections() > R call succeeded for sfb ------------ * * Completed reserve 'sfb' ******************************************************** ******************************************************** * Processing reserve 'sos' * *** Using updated spreadsheet: C:\NERRS\CDMO_Automation_2021\00_Annual_Update\Updated_reserve_var_sheets\Reserve_Level_Plotting_Variables_sos_2020.xlsx *** R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > target_year = c(2020) > year_range = c(2000,2020) > source('R/01_Load_Wrangle_Run.R') Loading required package: broom Loading required package: janitor Attaching package: 'janitor' The following objects are masked from 'package:stats': chisq.test, fisher.test Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: openxlsx Loading required package: readxl Loading required package: EnvStats Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default Loading required package: ggthemes Loading required package: RColorBrewer Loading required package: sf Linking to GEOS 3.9.1, GDAL 3.2.1, PROJ 7.2.1 Loading required package: ggmap Loading required package: ggplot2 Google's Terms of Service: https://cloud.google.com/maps-platform/terms/. Please cite ggmap if you use it! See citation("ggmap") for details. Loading required package: flextable Loading required package: officer Attaching package: 'officer' The following object is masked from 'package:readxl': read_xlsx Loading required package: SWMPr Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: SWMPrExtension Loading required package: devtools Loading required package: usethis There were 50 or more warnings (use warnings() to see the first 50) > closeAllConnections() > R call succeeded for sos ------------ * * Completed reserve 'sos' ******************************************************** ******************************************************** * Processing reserve 'tjr' * *** Using updated spreadsheet: C:\NERRS\CDMO_Automation_2021\00_Annual_Update\Updated_reserve_var_sheets\Reserve_Level_Plotting_Variables_tjr_2020.xlsx *** R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > target_year = c(2020) > year_range = c(2000,2020) > source('R/01_Load_Wrangle_Run.R') Loading required package: broom Loading required package: janitor Attaching package: 'janitor' The following objects are masked from 'package:stats': chisq.test, fisher.test Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: openxlsx Loading required package: readxl Loading required package: EnvStats Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default Loading required package: ggthemes Loading required package: RColorBrewer Loading required package: sf Linking to GEOS 3.9.1, GDAL 3.2.1, PROJ 7.2.1 Loading required package: ggmap Loading required package: ggplot2 Google's Terms of Service: https://cloud.google.com/maps-platform/terms/. Please cite ggmap if you use it! See citation("ggmap") for details. Loading required package: flextable Loading required package: officer Attaching package: 'officer' The following object is masked from 'package:readxl': read_xlsx Loading required package: SWMPr Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: SWMPrExtension Loading required package: devtools Loading required package: usethis There were 50 or more warnings (use warnings() to see the first 50) > closeAllConnections() > R call succeeded for tjr ------------ * * Completed reserve 'tjr' ******************************************************** ******************************************************** * Processing reserve 'wel' * *** Using updated spreadsheet: C:\NERRS\CDMO_Automation_2021\00_Annual_Update\Updated_reserve_var_sheets\Reserve_Level_Plotting_Variables_wel_2020.xlsx *** R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > target_year = c(2020) > year_range = c(2000,2020) > source('R/01_Load_Wrangle_Run.R') Loading required package: broom Loading required package: janitor Attaching package: 'janitor' The following objects are masked from 'package:stats': chisq.test, fisher.test Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: openxlsx Loading required package: readxl Loading required package: EnvStats Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default Loading required package: ggthemes Loading required package: RColorBrewer Loading required package: sf Linking to GEOS 3.9.1, GDAL 3.2.1, PROJ 7.2.1 Loading required package: ggmap Loading required package: ggplot2 Google's Terms of Service: https://cloud.google.com/maps-platform/terms/. Please cite ggmap if you use it! See citation("ggmap") for details. Loading required package: flextable Loading required package: officer Attaching package: 'officer' The following object is masked from 'package:readxl': read_xlsx Loading required package: SWMPr Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: SWMPrExtension Loading required package: devtools Loading required package: usethis There were 50 or more warnings (use warnings() to see the first 50) > closeAllConnections() > R call succeeded for wel ------------ * * Completed reserve 'wel' ******************************************************** ******************************************************** * Processing reserve 'wkb' * *** Using updated spreadsheet: C:\NERRS\CDMO_Automation_2021\00_Annual_Update\Updated_reserve_var_sheets\Reserve_Level_Plotting_Variables_wkb_2020.xlsx *** R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > target_year = c(2020) > year_range = c(2000,2020) > source('R/01_Load_Wrangle_Run.R') Loading required package: broom Loading required package: janitor Attaching package: 'janitor' The following objects are masked from 'package:stats': chisq.test, fisher.test Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: openxlsx Loading required package: readxl Loading required package: EnvStats Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default Loading required package: ggthemes Loading required package: RColorBrewer Loading required package: sf Linking to GEOS 3.9.1, GDAL 3.2.1, PROJ 7.2.1 Loading required package: ggmap Loading required package: ggplot2 Google's Terms of Service: https://cloud.google.com/maps-platform/terms/. Please cite ggmap if you use it! See citation("ggmap") for details. Loading required package: flextable Loading required package: officer Attaching package: 'officer' The following object is masked from 'package:readxl': read_xlsx Loading required package: SWMPr Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: SWMPrExtension Loading required package: devtools Loading required package: usethis There were 50 or more warnings (use warnings() to see the first 50) > closeAllConnections() > R call succeeded for wkb ------------ * * Completed reserve 'wkb' ******************************************************** ******************************************************** * Processing reserve 'wqb' * *** Using updated spreadsheet: C:\NERRS\CDMO_Automation_2021\00_Annual_Update\Updated_reserve_var_sheets\Reserve_Level_Plotting_Variables_wqb_2020.xlsx *** R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > target_year = c(2020) > year_range = c(2000,2020) > source('R/01_Load_Wrangle_Run.R') Loading required package: broom Loading required package: janitor Attaching package: 'janitor' The following objects are masked from 'package:stats': chisq.test, fisher.test Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: openxlsx Loading required package: readxl Loading required package: EnvStats Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default Loading required package: ggthemes Loading required package: RColorBrewer Loading required package: sf Linking to GEOS 3.9.1, GDAL 3.2.1, PROJ 7.2.1 Loading required package: ggmap Loading required package: ggplot2 Google's Terms of Service: https://cloud.google.com/maps-platform/terms/. Please cite ggmap if you use it! See citation("ggmap") for details. Loading required package: flextable Loading required package: officer Attaching package: 'officer' The following object is masked from 'package:readxl': read_xlsx Loading required package: SWMPr Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: SWMPrExtension Loading required package: devtools Loading required package: usethis There were 50 or more warnings (use warnings() to see the first 50) > closeAllConnections() > R call succeeded for wqb ------------ * * Completed reserve 'wqb' ******************************************************** ========== END OF RESERVE LOOP =========== --------------------------------------------------------- Check for Reserve-level processing errors IgnoreCase : True LineNumber : 16 Line : Error in res_local_map(nerr_site_id = res_abb, stations = sites_to_map, : Filename : hud_message.log Path : C:\NERRS\CDMO_Automation_2021\01_Reserve_working_files\all_logs\hud_message.log Pattern : Error Context : Matches : {0} IgnoreCase : True LineNumber : 16 Line : Error in res_local_map(nerr_site_id = res_abb, stations = sites_to_map, : Filename : mar_message.log Path : C:\NERRS\CDMO_Automation_2021\01_Reserve_working_files\all_logs\mar_message.log Pattern : Error Context : Matches : {0} End of Reserve-level processing error check --------------------------------------------------------- --------------------------------------------------------- * Processing national level reports * R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > logout <- file(paste0("national_output.log"), open = "wt") > logmess <- file(paste0("national_message.log"), open = "wt") > sink(logout, append = FALSE, type = "output", split = FALSE) > sink(logmess, append = FALSE, type = "message", split = FALSE) > > # Source files ------------ > source('R/00_nat_setup/00_load_analyses_variables.R') > > # ---------------------------------------------- > # Make system map -------------------------- > # ---------------------------------------------- > source('R/01_nat_plots/01-01_make_NERR_system_map.R') Check for National-level processing errors IgnoreCase : True LineNumber : 22 Line : Error in png_dev(..., res = dpi, units = "in") : Filename : national_message.log Path : C:\NERRS\CDMO_Automation_2021\01_National_Report\national_message.log Pattern : Error Context : Matches : {0} * * National level reports have been completed --------------------------------------------------------- ********************** Windows PowerShell transcript end End time: 20211109100045 **********************