This report is automatically generated with the R
package knitr
(version 1.39
)
.
--- title: '03_Wastewater Treatment Plants' subtitle: 'Data Fixes Associated with Control Study' author: "Mercury Program and Basin Planning Unit" date: "3/1/2022" output: html_document: code_folding: show toc: TRUE toc_float: TRUE toc_depth: 3 runtime: shiny assets: css: - "http://fonts.googleapis.com/css?family=Raleway:300" - "http://fonts.googleapis.com/css?family=Oxygen" --- --- <style> body{ font-family: 'Oxygen', sans-serif; font-size: 16px; line-height: 24px; } h1,h2,h3,h4 { font-family: 'Raleway', sans-serif; } .container { width: 1250px; } h3 { background-color: #D4DAEC; text-indent: 50px; } h4 { text-indent: 75px; margin-top: 35px; margin-bottom: 5px; } </style> ```{r setup, include=FALSE} knitr::opts_chunk$set(echo=TRUE, warning=FALSE, message=FALSE, fig.width=9.5) ``` ```{r Libraries, echo=FALSE} library(lubridate) library(readxl) library(kableExtra) # better formatting of tables library(shiny) # Had issue trying to set WD with Shiny in R project, reset working directory of rproj wd <- rstudioapi::getActiveProject() setwd(wd) source("R Functions/functions_estimate NDDNQ values.R") source("R Functions/functions_QA data.R") # Read MeHg Data set esmr <- read_excel("Reeval_Source_Analysis/Source Data/03a_Municipal WWTPs (NPDES)/Data/03_NPDES_eSMR MeHg Data.xlsx", guess_max = 300000, sheet = "OIMA eSMR FixErrors-AddLathrop") ``` ## Summarize Suspected Unit Error Fixes ```{r} StationErrorSummary <- esmr %>% filter(!is.na(ErrorCheck)) %>% group_by(StationName, ErrorCheck) %>% summarize(CountedErrors = n(), YearRange = ifelse(year(min(SampleDate)) == year(max(SampleDate)), paste0(year(min(SampleDate))), paste(year(min(SampleDate)), year(max(SampleDate)), sep="-")), Dates = grammaticList(SampleDate)) StationErrorSummary %>% kbl(align='lccc', caption='Fixed Errors by StationName') %>% kable_paper('hover', full_width=T) %>% kable_styling(fixed_thead = T) # setwd(wd) # writexl::write_xlsx(StationErrorSummary, paste0('Source Data/03a_Municipal WWTPs (NPDES)/Data/03_NPDES Unit Error Summary by SatationName_', today(), '.xlsx')) esmr %>% filter(`LOCATION PLACE TYPE` == 'Effluent Monitoring') %>% mutate(Result = if_else(Unit == 'ug/L', Result*1000, Result), Result = if_else(Unit == 'mg/L', Result*1000000, Result), MDL = if_else(Unit == 'ug/L', MDL*1000, MDL), MDL = if_else(Unit == 'mg/L', MDL*1000000, MDL), RL = if_else(Unit == 'ug/L', RL*1000, RL), RL = if_else(Unit == 'mg/L', RL*1000000, RL), origResult = if_else(origUnit == 'ug/L', origResult*1000, origResult), origResult = if_else(origUnit == 'mg/L', origResult*1000000, origResult), origMDL = if_else(origUnit == 'ug/L', origMDL*1000, origMDL), origMDL = if_else(origUnit == 'mg/L', origMDL*1000000, origMDL), origRL = if_else(origUnit == 'ug/L', origRL*1000, origRL), origRL = if_else(origUnit == 'mg/L', origRL*1000000, origRL) ) %>% group_by(StationName) %>% summarize(n = n(), ResultAvg_ngL = mean(Result, na.rm=T), OrigResultAvg_ngL = mean(origResult, na.rm=T), MDLAvg_ngL = mean(MDL, na.rm=T), OrigMDLAvg_ngL = mean(origMDL, na.rm=T), RLAvg_ngL = mean(RL, na.rm=T), OrigRLAvg_ngL = mean(origRL, na.rm=T), ResultNAs = sum(is.na(cur_data()$Result)), OrigResultNAs = sum(is.na(cur_data()$origResult))) %>% kbl(align='lccc', caption='NPDES MeHg Data Summary') %>% kable_paper('hover', full_width=T) %>% kable_styling(fixed_thead = T) ``` ## Show Suspect Data Based on Filter ```{r} esmr %>% filter(`LOCATION PLACE TYPE` == 'Effluent Monitoring') %>% filter(Unit != origUnit | ((Unit != 'ng/L' | origUnit != 'ng/L') & ((Result > 0.01 & Result < 5) | (origResult > 0.01 & origResult < 5)))) %>% mutate(Result = if_else(Unit == 'ug/L', Result*1000, Result), Result = if_else(Unit == 'mg/L', Result*1000000, Result), MDL = if_else(Unit == 'ug/L', MDL*1000, MDL), MDL = if_else(Unit == 'mg/L', MDL*1000000, MDL), RL = if_else(Unit == 'ug/L', RL*1000, RL), RL = if_else(Unit == 'mg/L', RL*1000000, RL), Unit = 'ng/L', origResult = if_else(origUnit == 'ug/L', origResult*1000, origResult), origResult = if_else(origUnit == 'mg/L', origResult*1000000, origResult), origMDL = if_else(origUnit == 'ug/L', origMDL*1000, origMDL), origMDL = if_else(origUnit == 'mg/L', origMDL*1000000, origMDL), origRL = if_else(origUnit == 'ug/L', origRL*1000, origRL), origRL = if_else(origUnit == 'mg/L', origRL*1000000, origRL), origUnit = 'ng/L' ) %>% group_by(StationName) %>% select(StationName, SampleDate, Unit, Result, MDL, RL, origUnit, origResult, origMDL, origRL) %>% kbl(align='lccc', caption='NPDES MeHg Data Summary') %>% kable_paper('hover', full_width=T) %>% kable_styling(fixed_thead = T) ```
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The R session information (including the OS info, R version and all packages used):
sessionInfo()
## R version 4.2.2 (2022-10-31 ucrt) ## Platform: x86_64-w64-mingw32/x64 (64-bit) ## Running under: Windows 10 x64 (build 22621) ## ## Matrix products: default ## ## locale: ## [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 ## [3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C ## [5] LC_TIME=English_United States.utf8 ## ## attached base packages: ## [1] stats graphics grDevices utils datasets methods base ## ## other attached packages: ## [1] lubridate_1.8.0 plotly_4.10.0 readxl_1.4.0 actuar_3.2-2 ## [5] NADA_1.6-1.1 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.9 ## [9] purrr_0.3.4 readr_2.1.2 tidyr_1.2.0 tibble_3.1.7 ## [13] ggplot2_3.3.6 tidyverse_1.3.1 fitdistrplus_1.1-8 survival_3.4-0 ## [17] MASS_7.3-58.1 ## ## loaded via a namespace (and not attached): ## [1] lattice_0.20-45 assertthat_0.2.1 digest_0.6.29 utf8_1.2.2 ## [5] R6_2.5.1 cellranger_1.1.0 backports_1.4.1 reprex_2.0.1 ## [9] evaluate_0.15 httr_1.4.3 highr_0.9 pillar_1.7.0 ## [13] rlang_1.0.2 lazyeval_0.2.2 rstudioapi_0.13 data.table_1.14.2 ## [17] Matrix_1.5-1 rmarkdown_2.14 labeling_0.4.2 splines_4.2.2 ## [21] htmlwidgets_1.5.4 munsell_0.5.0 broom_0.8.0 compiler_4.2.2 ## [25] modelr_0.1.8 xfun_0.31 pkgconfig_2.0.3 htmltools_0.5.2 ## [29] tidyselect_1.1.2 viridisLite_0.4.0 fansi_1.0.3 crayon_1.5.1 ## [33] tzdb_0.3.0 dbplyr_2.2.0 withr_2.5.0 grid_4.2.2 ## [37] jsonlite_1.8.0 gtable_0.3.0 lifecycle_1.0.1 DBI_1.1.2 ## [41] magrittr_2.0.3 scales_1.2.0 writexl_1.4.0 cli_3.3.0 ## [45] stringi_1.7.6 farver_2.1.0 fs_1.5.2 xml2_1.3.3 ## [49] ellipsis_0.3.2 generics_0.1.2 vctrs_0.4.1 expint_0.1-7 ## [53] RColorBrewer_1.1-3 tools_4.2.2 glue_1.6.2 hms_1.1.1 ## [57] yaml_2.3.5 fastmap_1.1.0 colorspace_2.0-3 rvest_1.0.2 ## [61] knitr_1.39 haven_2.5.0
Sys.time()
## [1] "2023-12-27 10:09:00 PST"