This report is automatically generated with the R
package knitr
(version 1.40
)
.
source("R Functions/functions_QA data.R") ### LOAD DATA ### exclude_cols <- c("AnalyteGroup", "AutoID", "Basis", "BlankCorrected", "Coelutions", "COMMENTS_DL", "DisplayCode", "DL_ORIG", "FieldResultBatchVerCode", "FieldResultCalibrationDate", "LabResultComments", "PARAMETER_ORIG", "QACode_ORIG", "SFEIContractID", "SITE_CODE_ORIG", "Species", "StationName", "Unit_Orig" ) DRMP_16_Hg_Anc <- readxl::read_excel('Reeval_Impl_Goals_Linkage_Analysis/Data/DRMP FY16-19/DRMP_2016-17_Hg_Anc_Aq_Sed.xlsx', sheet=1, guess_max = 30000) %>% mutate(SourceID = 'DRMP_2016-17_Hg_Anc_Aq_Sed', SourceRow = rownames(.), ChemResultRowID = NA_character_, LabResultRowID = NA_character_) %>% rename(LabCollectionComments = CollectionComments, PrepPreservationDate = PreparationPreservationDate, PrepPreservationName = PreparationPreservation, Replicate = SampleReplicate, ResQualCode = ResultQualCode, UnitName = Unit) %>% select(-one_of(exclude_cols)) #Remove excluded columns not shared in the data sheets below DRMP_17_Hg_Anc <- readxl::read_excel('Reeval_Impl_Goals_Linkage_Analysis/Data/DRMP FY16-19/DRMP_2017-18_Hg_Anc_Aq_Sed.xlsx', sheet='ChemResults', guess_max = 30000) %>% mutate(SourceID = 'DRMP_2017-18_Hg_Anc_Aq_Sed', SourceRow = rownames(.), ChemResultRowID = NA_character_) DRMP_18_Hg <- readxl::read_excel('Reeval_Impl_Goals_Linkage_Analysis/Data/DRMP FY16-19/DRMP_2018-19_Hg_Aq.xlsx', sheet='ChemResults', guess_max = 30000)%>% mutate(SourceID = 'DRMP_2018-19_Hg_Aq', SourceRow = rownames(.)) DRMP_18_Anc <- readxl::read_excel('Reeval_Impl_Goals_Linkage_Analysis/Data/DRMP FY16-19/DRMP_2018-19_Anc_Aq.xlsx', sheet='ChemResults', guess_max = 30000) %>% mutate(SourceID = 'DRMP_2018-19_Anc_Aq', SourceRow = rownames(.)) %>% select(-AnalysisDate_original, -PrepPreservationDate_original, -DigestExtractDate_original) DRMP_19Jul_Hg <- readxl::read_excel('Reeval_Impl_Goals_Linkage_Analysis/Data/DRMP FY16-19/DRMP_2019-Jul_chem_template_final.xls', sheet='ChemResults', guess_max = 30000) %>% mutate(SourceID = 'DRMP_19Jul_Hg', SourceRow = rownames(.), ChemResultRowID = NA_character_) %>% select(-CollectionTime_original) DRMP_19Aug_Hg <- readxl::read_excel('Reeval_Impl_Goals_Linkage_Analysis/Data/DRMP FY16-19/DRMP_2019-Aug_chem_template_final.xls', sheet='ChemResults', guess_max = 30000) %>% mutate(SourceID = 'DRMP_19Aug_Hg', SourceRow = rownames(.), ChemResultRowID = NA_character_) %>% select(-CollectionTime_original) DRMP_19Sep_Hg <- readxl::read_excel('Reeval_Impl_Goals_Linkage_Analysis/Data/DRMP FY16-19/DRMP_2019-Sep_chem_template_final.xls', sheet='ChemResults', guess_max = 30000) %>% mutate(SourceID = 'DRMP_19Sep_Hg', SourceRow = rownames(.), ChemResultRowID = NA_character_) %>% select(-CollectionTime_original) DRMP_19Oct_Hg <- readxl::read_excel('Reeval_Impl_Goals_Linkage_Analysis/Data/DRMP FY16-19/DRMP_2019-Oct_chem_template_final.xls', sheet='ChemResults', guess_max = 30000) %>% mutate(SourceID = 'DRMP_19Oct_Hg', SourceRow = rownames(.), ChemResultRowID = NA_character_) %>% select(-CollectionTime_original) sort(names(DRMP_16_Hg_Anc)); nrow(DRMP_16_Hg_Anc)
## [1] "AgencyCode" "AnalysisDate" "AnalyteName" ## [4] "ChemResultRowID" "CollectionDepth" "CollectionDeviceName" ## [7] "CollectionMethodCode" "CollectionTime" "ComplianceCode" ## [10] "DigestExtractDate" "DigestExtractMethod" "DilutionFactor" ## [13] "EventCode" "ExpectedValue" "FractionName" ## [16] "GeometryShape" "LabBatch" "LabCollectionComments" ## [19] "LabReplicate" "LabResultRowID" "LabSampleID" ## [22] "LocationCode" "MatrixName" "MDL" ## [25] "MethodName" "PositionWaterColumn" "PrepPreservationDate" ## [28] "PrepPreservationName" "ProjectCode" "ProtocolCode" ## [31] "QACode" "Replicate" "ResQualCode" ## [34] "Result" "RL" "SampleComments" ## [37] "SampleDate" "SampleID" "SampleTypeCode" ## [40] "SourceID" "SourceRow" "StationCode" ## [43] "UnitCollectionDepth" "UnitName"
## [1] 394
sort(names(DRMP_17_Hg_Anc)); nrow(DRMP_17_Hg_Anc)
## [1] "AgencyCode" "AnalysisDate" "AnalyteName" ## [4] "ChemResultRowID" "CollectionDepth" "CollectionDeviceName" ## [7] "CollectionMethodCode" "CollectionTime" "ComplianceCode" ## [10] "DigestExtractDate" "DigestExtractMethod" "DilutionFactor" ## [13] "EventCode" "ExpectedValue" "FractionName" ## [16] "GeometryShape" "LabBatch" "LabCollectionComments" ## [19] "LabReplicate" "LabResultRowID" "LabSampleID" ## [22] "LocationCode" "MatrixName" "MDL" ## [25] "MethodName" "PositionWaterColumn" "PrepPreservationDate" ## [28] "PrepPreservationName" "ProjectCode" "ProtocolCode" ## [31] "QACode" "Replicate" "ResQualCode" ## [34] "Result" "RL" "SampleComments" ## [37] "SampleDate" "SampleID" "SampleTypeCode" ## [40] "SourceID" "SourceRow" "StationCode" ## [43] "UnitCollectionDepth" "UnitName"
## [1] 1311
sort(names(DRMP_18_Hg)); nrow(DRMP_18_Hg)
## [1] "AgencyCode" "AnalysisDate" "AnalyteName" ## [4] "ChemResultRowID" "CollectionDepth" "CollectionDeviceName" ## [7] "CollectionMethodCode" "CollectionTime" "ComplianceCode" ## [10] "DigestExtractDate" "DigestExtractMethod" "DilutionFactor" ## [13] "EventCode" "ExpectedValue" "FractionName" ## [16] "GeometryShape" "LabBatch" "LabCollectionComments" ## [19] "LabReplicate" "LabResultComments" "LabSampleID" ## [22] "LocationCode" "MatrixName" "MDL" ## [25] "MethodName" "PositionWaterColumn" "PrepPreservationDate" ## [28] "PrepPreservationName" "ProjectCode" "ProtocolCode" ## [31] "QACode" "Replicate" "ResQualCode" ## [34] "Result" "RL" "SampleComments" ## [37] "SampleDate" "SampleID" "SampleTypeCode" ## [40] "SourceID" "SourceRow" "StationCode" ## [43] "UnitCollectionDepth" "UnitName"
## [1] 632
sort(names(DRMP_18_Anc)); nrow(DRMP_18_Anc)
## [1] "AgencyCode" "AnalysisDate" "AnalyteName" ## [4] "ChemResultRowID" "CollectionDepth" "CollectionDeviceName" ## [7] "CollectionMethodCode" "CollectionTime" "ComplianceCode" ## [10] "DigestExtractDate" "DigestExtractMethod" "DilutionFactor" ## [13] "EventCode" "ExpectedValue" "FractionName" ## [16] "GeometryShape" "LabBatch" "LabCollectionComments" ## [19] "LabReplicate" "LabResultComments" "LabSampleID" ## [22] "LocationCode" "MatrixName" "MDL" ## [25] "MethodName" "PositionWaterColumn" "PrepPreservationDate" ## [28] "PrepPreservationName" "ProjectCode" "ProtocolCode" ## [31] "QACode" "Replicate" "ResQualCode" ## [34] "Result" "RL" "SampleComments" ## [37] "SampleDate" "SampleID" "SampleTypeCode" ## [40] "SourceID" "SourceRow" "StationCode" ## [43] "UnitCollectionDepth" "UnitName"
## [1] 572
sort(names(DRMP_19Jul_Hg)); nrow(DRMP_19Jul_Hg)
## [1] "AgencyCode" "AnalysisDate" "AnalyteName" ## [4] "ChemResultRowID" "CollectionDepth" "CollectionDeviceName" ## [7] "CollectionMethodCode" "CollectionTime" "ComplianceCode" ## [10] "DigestExtractDate" "DigestExtractMethod" "DilutionFactor" ## [13] "EventCode" "ExpectedValue" "FractionName" ## [16] "GeometryShape" "LabBatch" "LabCollectionComments" ## [19] "LabReplicate" "LabResultComments" "LabSampleID" ## [22] "LocationCode" "MatrixName" "MDL" ## [25] "MethodName" "PositionWaterColumn" "PrepPreservationDate" ## [28] "PrepPreservationName" "ProjectCode" "ProtocolCode" ## [31] "QACode" "Replicate" "ResQualCode" ## [34] "Result" "RL" "SampleComments" ## [37] "SampleDate" "SampleID" "SampleTypeCode" ## [40] "SourceID" "SourceRow" "StationCode" ## [43] "UnitCollectionDepth" "UnitName"
## [1] 119
sort(names(DRMP_19Aug_Hg)); nrow(DRMP_19Aug_Hg)
## [1] "AgencyCode" "AnalysisDate" "AnalyteName" ## [4] "ChemResultRowID" "CollectionDepth" "CollectionDeviceName" ## [7] "CollectionMethodCode" "CollectionTime" "ComplianceCode" ## [10] "DigestExtractDate" "DigestExtractMethod" "DilutionFactor" ## [13] "EventCode" "ExpectedValue" "FractionName" ## [16] "GeometryShape" "LabBatch" "LabCollectionComments" ## [19] "LabReplicate" "LabResultComments" "LabSampleID" ## [22] "LocationCode" "MatrixName" "MDL" ## [25] "MethodName" "PositionWaterColumn" "PrepPreservationDate" ## [28] "PrepPreservationName" "ProjectCode" "ProtocolCode" ## [31] "QACode" "Replicate" "ResQualCode" ## [34] "Result" "RL" "SampleComments" ## [37] "SampleDate" "SampleID" "SampleTypeCode" ## [40] "SourceID" "SourceRow" "StationCode" ## [43] "UnitCollectionDepth" "UnitName"
## [1] 114
sort(names(DRMP_19Sep_Hg)); nrow(DRMP_19Sep_Hg)
## [1] "AgencyCode" "AnalysisDate" "AnalyteName" ## [4] "ChemResultRowID" "CollectionDepth" "CollectionDeviceName" ## [7] "CollectionMethodCode" "CollectionTime" "ComplianceCode" ## [10] "DigestExtractDate" "DigestExtractMethod" "DilutionFactor" ## [13] "EventCode" "ExpectedValue" "FractionName" ## [16] "GeometryShape" "LabBatch" "LabCollectionComments" ## [19] "LabReplicate" "LabResultComments" "LabSampleID" ## [22] "LocationCode" "MatrixName" "MDL" ## [25] "MethodName" "PositionWaterColumn" "PrepPreservationDate" ## [28] "PrepPreservationName" "ProjectCode" "ProtocolCode" ## [31] "QACode" "Replicate" "ResQualCode" ## [34] "Result" "RL" "SampleComments" ## [37] "SampleDate" "SampleID" "SampleTypeCode" ## [40] "SourceID" "SourceRow" "StationCode" ## [43] "UnitCollectionDepth" "UnitName"
## [1] 112
sort(names(DRMP_19Oct_Hg)); nrow(DRMP_19Oct_Hg)
## [1] "AgencyCode" "AnalysisDate" "AnalyteName" ## [4] "ChemResultRowID" "CollectionDepth" "CollectionDeviceName" ## [7] "CollectionMethodCode" "CollectionTime" "ComplianceCode" ## [10] "DigestExtractDate" "DigestExtractMethod" "DilutionFactor" ## [13] "EventCode" "ExpectedValue" "FractionName" ## [16] "GeometryShape" "LabBatch" "LabCollectionComments" ## [19] "LabReplicate" "LabResultComments" "LabSampleID" ## [22] "LocationCode" "MatrixName" "MDL" ## [25] "MethodName" "PositionWaterColumn" "PrepPreservationDate" ## [28] "PrepPreservationName" "ProjectCode" "ProtocolCode" ## [31] "QACode" "Replicate" "ResQualCode" ## [34] "Result" "RL" "SampleComments" ## [37] "SampleDate" "SampleID" "SampleTypeCode" ## [40] "SourceID" "SourceRow" "StationCode" ## [43] "UnitCollectionDepth" "UnitName"
## [1] 112
DRMP_2016_2019_Aq_Sed_Data <- bind_rows(DRMP_16_Hg_Anc, DRMP_17_Hg_Anc, DRMP_18_Hg, DRMP_18_Anc, DRMP_19Jul_Hg, DRMP_19Aug_Hg, DRMP_19Sep_Hg, DRMP_19Oct_Hg) %>% select(SourceID, SourceRow, everything()) ## SAVE MERGED DATA## #Save to Aqueous Data folder writexl::write_xlsx(DRMP_2016_2019_Aq_Sed_Data, path='Reeval_Impl_Goals_Linkage_Analysis/Data/Aqueous/DRMP_2016_2019_Aq_Sed_Data.xlsx') #Save to Ancillary Data folder writexl::write_xlsx(DRMP_2016_2019_Aq_Sed_Data, path='Reeval_Impl_Goals_Linkage_Analysis/Data/Ancillary/DRMP_2016_2019_Aq_Sed_Data.xlsx')
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] mgcv_1.8-41 nlme_3.1-160 lubridate_1.8.0 plotly_4.10.0 ## [5] readxl_1.4.1 actuar_3.3-0 NADA_1.6-1.1 forcats_0.5.2 ## [9] stringr_1.4.1 dplyr_1.0.9 purrr_0.3.4 readr_2.1.2 ## [13] tidyr_1.2.0 tibble_3.1.8 ggplot2_3.3.6 tidyverse_1.3.2 ## [17] fitdistrplus_1.1-8 survival_3.4-0 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_2.0.2 ## [9] evaluate_0.16 highr_0.9 httr_1.4.4 pillar_1.8.1 ## [13] rlang_1.0.5 lazyeval_0.2.2 googlesheets4_1.0.1 rstudioapi_0.14 ## [17] data.table_1.14.2 Matrix_1.5-1 splines_4.2.2 webshot_0.5.3 ## [21] googledrive_2.0.0 htmlwidgets_1.5.4 munsell_0.5.0 broom_1.0.1 ## [25] compiler_4.2.2 modelr_0.1.9 xfun_0.32 pkgconfig_2.0.3 ## [29] htmltools_0.5.3 tidyselect_1.1.2 viridisLite_0.4.1 fansi_1.0.3 ## [33] crayon_1.5.1 tzdb_0.3.0 dbplyr_2.2.1 withr_2.5.0 ## [37] grid_4.2.2 jsonlite_1.8.0 gtable_0.3.1 lifecycle_1.0.1 ## [41] DBI_1.1.3 magrittr_2.0.3 scales_1.2.1 writexl_1.4.0 ## [45] cli_3.3.0 stringi_1.7.8 fs_1.5.2 xml2_1.3.3 ## [49] ellipsis_0.3.2 generics_0.1.3 vctrs_0.4.1 expint_0.1-7 ## [53] tools_4.2.2 glue_1.6.2 crosstalk_1.2.0 hms_1.1.2 ## [57] yaml_2.3.5 fastmap_1.1.0 colorspace_2.0-3 gargle_1.2.0 ## [61] rvest_1.0.3 knitr_1.40 haven_2.5.1
Sys.time()
## [1] "2024-01-04 15:50:28 PST"