This report is automatically generated with the R
package knitr
(version 1.39
)
.
--- title: "01_Tributaries" author: "Mercury Program and Basin Planning Unit" date: '2022-07-08' 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(shiny) # Had issue with runtime:shiny resetting the WD of rproj so used getActiveProject() wd <- rstudioapi::getActiveProject() source(paste0(wd, "/R Functions/functions_estimate NDDNQ values.R")) source(paste0(wd, "/R Functions/functions_QA data.R")) ``` # Load and Tidy Data ## MeHg: Tributary Data ###Define columns variable for repeat use later ```{r} # # Columns to select # columns_select <- c("StationCode", "StationName", "Tributary", "SampleDate", "SampleTime", "Unit", "Result", "MDL", "RL", "ResultQualCode", "MeHgDataSource", "SourceRow", "SampleMonth", "SampleYear", "WaterYear") ``` ###Load data ```{r} trib_data <- readxl::read_xlsx(paste0(wd, "/Reeval_Source_Analysis/Source Data/01_Tributaries/01_Tributaries_MeHg.xlsx"), sheet = "All_MeHg") %>% chara_to_NumDate ``` ###Tidy data ```{r} trib_clean_format <- trib_data %>% #Clean up dates mutate(SampleDate = as.Date(SampleDate, origin = "1899-12-30")) ``` ###Find Daily MeHg Median and Mean Concentrations by Tributary ```{r} trib_dailymedian <- trib_clean_format %>% group_by(Tributary, SampleDate) %>% mutate(DailyMedian = median(Result, na.rm=T), DailyMean = mean(Result, na.rm=T)) %>% distinct(Tributary, DailyMedian, .keep_all = TRUE) %>% select(Tributary, DailyMedian, DailyMean, Unit, SampleMonth) ``` ###Create CCSB OUtflow and Weir Data Frame ```{r} ccsb <- trib_dailymedian %>% filter(Tributary %in% c("Cache Creek Settling Basin Outflow", "Cache Creek Settling Basin Weir")) %>% mutate(Month = month(SampleDate)) ``` ###Find CCSB Monthly Median and Mean Concentrations ```{r} ccsb_median <- ccsb %>% group_by(Tributary, Month) %>% summarise(MonthlyMedian = median(DailyMedian, na.rm=T), MonthlyMean = mean(DailyMean, na.rm=T), N = n(), MonthlyMax = max(DailyMedian, na.rm=T), MonthlyMin = min(DailyMedian, na.rm=T)) ``` ###Create Tributary Data Frame, no CCSB ```{r} trib_noCCSB <- trib_dailymedian %>% filter(Tributary %are not% c("Cache Creek Settling Basin Outflow", "Cache Creek Settling Basin Weir")) ``` ###Find Tributary Monthly MeHg Median and Mean Concentrations for all but CCSB ```{r} trib_monthlymedian <- trib_noCCSB %>% group_by(Tributary, SampleMonth) %>% summarise(TributaryMedian = median(DailyMedian, na.rm=T), TributaryMean = mean(DailyMean, na.rm=T), N = n(), TributaryMax = max(DailyMedian, na.rm=T), TributaryMin = min(DailyMedian, na.rm=T)) ``` ###Find Tributary MeHg Median and Mean Concentrations ```{r} trib_median <- trib_dailymedian %>% group_by(Tributary) %>% summarise(TributaryMedian = median(DailyMedian, na.rm=T), TributaryMean = mean(DailyMean, na.rm=T), N = n(), TributaryMax = max(DailyMedian, na.rm=T), TributaryMin = min(DailyMedian, na.rm=T)) ``` ### Export CCSB to excel ```{r} writexl::write_xlsx(ccsb_median, paste0(wd, '/Reeval_Source_Analysis/Source Data/01_Tributaries/Output/01_CCSB Monthly MeHg Median Concentration', today(), '.xlsx')) ``` ### Export Tributaries to excel ```{r} # Save MeHg Data Used for Trib Calculations trib_data_save <- trib_clean_format %>% filter(!is.na(Tributary) & !grepl("Settling Basin Outflow|Settling Basin Weir", Tributary)) %>% # exclude unlabeled tributaries and outflows of CCSB # rename(ReferenceCode = Project) %>% mutate(SourceID = case_when(grepl("CEDEN", SourceID) ~ "CEDEN", T ~ SourceID), ReferenceCode = case_when(SourceID == "R5AQ" ~ Project, SourceID == "AR" ~ CitationCode, T ~ NA_character_), ) %>% select(Tributary, SourceID, ReferenceCode, StationCode, StationName, SampleDate, Unit, Result, MDL, RL, ResultQualCode) %>% arrange(Tributary, SampleDate) writexl::write_xlsx(list("6.2.1 Tributary Inflows"=trib_data_save), paste0(wd, '/Reeval_Source_Analysis/Source Data/01_Tributaries/Output/Appdx A_Data Compilation_Tributaries.xlsx')) # Save MeHg Data Used for CCSB Calculations ccsb_data_save <- trib_clean_format %>% filter(grepl("Settling Basin Outflow|Settling Basin Weir", Tributary)) %>% # use only outflows of CCSB select(Tributary, SourceID, Project, StationCode, StationName, SampleDate, Unit, Result, MDL, RL, ResultQualCode) %>% rename(ReferenceCode = Project) %>% mutate(ReferenceCode = case_when(ReferenceCode == "0" ~ NA_character_, SourceID == "R5AQ" ~ ReferenceCode, T ~ NA_character_), ) %>% arrange(Tributary, SampleDate) writexl::write_xlsx(list("6.3.7 CCSB"=ccsb_data_save), paste0(wd, '/Reeval_Source_Analysis/Source Data/01_Tributaries/Output/Appdx A_Data Compilation_CCSB.xlsx')) # output tributary monthly median/mean concentration writexl::write_xlsx(trib_monthlymedian, paste0(wd, '/Reeval_Source_Analysis/Source Data/01_Tributaries/Output/01_Tributaries Monthly MeHg Median Concentration', today(), '.xlsx')) # output tributary pooled median/mean concentration writexl::write_xlsx(trib_median, paste0(wd, '/Reeval_Source_Analysis/Source Data/01_Tributaries/Output/01_Tributaries MeHg Median Concentration', today(), '.xlsx')) ```
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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 ## ## loaded via a namespace (and not attached): ## [1] rstudioapi_0.13 knitr_1.39 magrittr_2.0.3 tidyselect_1.1.2 ## [5] R6_2.5.1 rlang_1.0.2 fastmap_1.1.0 fansi_1.0.3 ## [9] stringr_1.4.0 highr_0.9 dplyr_1.0.9 tools_4.2.2 ## [13] xfun_0.31 utf8_1.2.2 DBI_1.1.2 cli_3.3.0 ## [17] htmltools_0.5.2 ellipsis_0.3.2 assertthat_0.2.1 yaml_2.3.5 ## [21] readxl_1.4.0 digest_0.6.29 tibble_3.1.7 lifecycle_1.0.1 ## [25] crayon_1.5.1 RColorBrewer_1.1-3 purrr_0.3.4 vctrs_0.4.1 ## [29] glue_1.6.2 evaluate_0.15 rmarkdown_2.14 stringi_1.7.6 ## [33] compiler_4.2.2 pillar_1.7.0 cellranger_1.1.0 generics_0.1.2 ## [37] writexl_1.4.0 pkgconfig_2.0.3
Sys.time()
## [1] "2023-12-26 16:03:57 PST"