This report is automatically generated with the R
package knitr
(version 1.40
)
.
source("R Functions/functions_QA data.R") ### LOAD DATA ### DRMP_17_TIResults <- readxl::read_excel('Reeval_Impl_Goals_Linkage_Analysis/Data/DRMP FY16-19/DRMP_2017_Hg_Fish.xlsx', sheet='TIResults', guess_max = 30000) %>% mutate(SourceID = 'DRMP_2017_Hg_Fish', SourceRow = rownames(.), BlankCorrected = NA_character_, QACodeLab = NA_character_, SFEISampleID = NA_character_) %>% rename(UIDTIR = TissueResultRowID) DRMP_17_FishComposite <- readxl::read_excel('Reeval_Impl_Goals_Linkage_Analysis/Data/DRMP FY16-19/DRMP_2017_Hg_Fish.xlsx', sheet='FishComposite', guess_max = 30000)
DRMP_18_TIResults <- readxl::read_excel('Reeval_Impl_Goals_Linkage_Analysis/Data/DRMP FY16-19/DRMP_2018_Hg_Fish.xlsx', sheet='TIResults', guess_max = 30000) %>% mutate(SourceID = 'DRMP_2018_Hg_Fish', SourceRow = rownames(.), BlankCorrected = NA_character_, QACodeLab = NA_character_, SFEISampleID = NA_character_) DRMP_18_FishComposite <- readxl::read_excel('Reeval_Impl_Goals_Linkage_Analysis/Data/DRMP FY16-19/DRMP_2018_Hg_Fish.xlsx', sheet='FishComposite', guess_max = 30000) DRMP_19_TIResults <- readxl::read_excel('Reeval_Impl_Goals_Linkage_Analysis/Data/DRMP FY16-19/DRMP_2019_Hg_Fish.xlsx', sheet='TIResults', guess_max = 30000) %>% mutate(SourceID = 'DRMP_2019_Hg_Fish', SourceRow = rownames(.), ComplianceCode = NA_character_) DRMP_19_FishComposite <- readxl::read_excel('Reeval_Impl_Goals_Linkage_Analysis/Data/DRMP FY16-19/DRMP_2019_Hg_Fish.xlsx', sheet='FishComposite', guess_max = 30000) # TIResults sort(names(DRMP_17_TIResults)); nrow(DRMP_17_TIResults)
## [1] "AnalysisDate" "AnalyteName" "BlankCorrected" ## [4] "ComplianceCode" "CompositeComments" "CompositeID" ## [7] "CompositeReplicate" "CompositeType" "DigestExtractDate" ## [10] "DigestExtractMethod" "DilutionFactor" "ExpectedValue" ## [13] "FractionName" "LabBatch" "LabReplicate" ## [16] "LabSampleID" "MatrixName" "MDL" ## [19] "MethodName" "OrganismGroup" "PrepPreservationDate" ## [22] "PrepPreservationName" "QACode" "QACodeLab" ## [25] "ResQualCode" "Result" "RL" ## [28] "SampleTypeCode" "SFEISampleID" "SourceID" ## [31] "SourceRow" "TissueResultComments" "UIDTIR" ## [34] "UnitName"
## [1] 207
sort(names(DRMP_18_TIResults)); nrow(DRMP_18_TIResults)
## [1] "AnalysisDate" "AnalyteName" "BlankCorrected" ## [4] "ComplianceCode" "CompositeComments" "CompositeID" ## [7] "CompositeReplicate" "CompositeType" "DigestExtractDate" ## [10] "DigestExtractMethod" "DilutionFactor" "ExpectedValue" ## [13] "FractionName" "LabBatch" "LabReplicate" ## [16] "LabSampleID" "MatrixName" "MDL" ## [19] "MethodName" "OrganismGroup" "PrepPreservationDate" ## [22] "PrepPreservationName" "QACode" "QACodeLab" ## [25] "ResQualCode" "Result" "RL" ## [28] "SampleTypeCode" "SFEISampleID" "SourceID" ## [31] "SourceRow" "TissueResultComments" "UIDTIR" ## [34] "UnitName"
## [1] 258
sort(names(DRMP_19_TIResults)); nrow(DRMP_19_TIResults)
## [1] "AnalysisDate" "AnalyteName" "BlankCorrected" ## [4] "ComplianceCode" "CompositeComments" "CompositeID" ## [7] "CompositeReplicate" "CompositeType" "DigestExtractDate" ## [10] "DigestExtractMethod" "DilutionFactor" "ExpectedValue" ## [13] "FractionName" "LabBatch" "LabReplicate" ## [16] "LabSampleID" "MatrixName" "MDL" ## [19] "MethodName" "OrganismGroup" "PrepPreservationDate" ## [22] "PrepPreservationName" "QACode" "QACodeLab" ## [25] "ResQualCode" "Result" "RL" ## [28] "SampleTypeCode" "SFEISampleID" "SourceID" ## [31] "SourceRow" "TissueResultComments" "UIDTIR" ## [34] "UnitName"
## [1] 278
DRMP_2017_2019_TIResults <- bind_rows(DRMP_17_TIResults, DRMP_18_TIResults, DRMP_19_TIResults) %>% select(SourceID, SourceRow, everything()) # FishComposite sort(names(DRMP_17_FishComposite)); nrow(DRMP_17_FishComposite)
## [1] "Age" "AgencyCode...49" ## [3] "AgencyCode...6" "Anomaly" ## [5] "CollectionDeviceName" "CollectionMethodCode" ## [7] "CollectionTime" "CompositeComments" ## [9] "CompositeID" "CompositeReplicate" ## [11] "CompositeRowID" "CompositeType" ## [13] "CompositeWeight" "EntryDateTime" ## [15] "EventCode" "ForkLength" ## [17] "GeometryShape" "HomogDate" ## [19] "LengthSource" "LifeStageCode" ## [21] "LocationCode" "OrganismGroup" ## [23] "OrganismID" "OrganismName" ## [25] "PartCreated" "PartsComments" ## [27] "PrepPreservationName" "ProcessedOrganismsExpandedFishComments" ## [29] "ProjectCode" "ProtocolCode" ## [31] "Replicate" "SampleComments" ## [33] "SampleDate" "SampleID" ## [35] "Sex" "SizeDescr" ## [37] "StationCode" "TagNumber" ## [39] "TisSource" "TissueCollectionComments" ## [41] "TissueID" "TissueName" ## [43] "TissueWeight" "TotalCount" ## [45] "TotalLength" "UnitCompositeWeight" ## [47] "UnitLengthFish" "UnitTissueWeight" ## [49] "UnitWeightFish" "Weight" ## [51] "WeightSource"
## [1] 96
sort(names(DRMP_18_FishComposite)); nrow(DRMP_18_FishComposite)
## [1] "Age" "AgencyCode" ## [3] "Anomaly" "CollectionDeviceName" ## [5] "CollectionMethodCode" "CollectionTime" ## [7] "CompAgencyCode" "CompositeComments" ## [9] "CompositeID" "CompositeReplicate" ## [11] "CompositeType" "CompositeWeight" ## [13] "EntryDateTime" "EventCode" ## [15] "ForkLength" "GeometryShape" ## [17] "HomogDate" "LengthSource" ## [19] "LifeStageCode" "LocationCode" ## [21] "OrganismGroup" "OrganismID" ## [23] "OrganismName" "PartCreated" ## [25] "PartsComments" "PrepPreservationName" ## [27] "ProcessedOrganismsExpandedFishComments" "ProjectCode" ## [29] "ProtocolCode" "Replicate" ## [31] "SampleComments" "SampleDate" ## [33] "SampleID" "Sex" ## [35] "SizeDescr" "SQLServerID" ## [37] "StationCode" "TagNumber" ## [39] "TisSource" "TissueCollectionComment" ## [41] "TissueID" "TissueName" ## [43] "TissueWeight" "TotalCount" ## [45] "TotalLength" "UnitCompositeWeight" ## [47] "UnitLengthFish" "UnitTissueWeight" ## [49] "UnitWeightFish" "Weight" ## [51] "WeightSource"
## [1] 291
sort(names(DRMP_19_FishComposite)); nrow(DRMP_19_FishComposite)
## [1] "Age" "AgencyCode" ## [3] "Anomaly" "CollectionDeviceName" ## [5] "CollectionMethodCode" "CollectionTime" ## [7] "CompAgencyCode" "CompositeComments" ## [9] "CompositeID" "CompositeReplicate" ## [11] "CompositeType" "CompositeWeight" ## [13] "EntryDateTime" "EventCode" ## [15] "ForkLength" "GeometryShape" ## [17] "HomogDate" "LengthSource" ## [19] "LifeStageCode" "LocationCode" ## [21] "OrganismGroup" "OrganismID" ## [23] "OrganismName" "PartCreated" ## [25] "PartsComments" "PrepPreservationName" ## [27] "ProcessedOrganismsExpandedFishComments" "ProjectCode" ## [29] "ProtocolCode" "Replicate" ## [31] "SampleComments" "SampleDate" ## [33] "SampleID" "Sex" ## [35] "SizeDescr" "SQLServerID" ## [37] "StationCode" "TagNumber" ## [39] "TisSource" "TissueCollectionComment" ## [41] "TissueID" "TissueName" ## [43] "TissueWeight" "TotalCount" ## [45] "TotalLength" "UnitCompositeWeight" ## [47] "UnitLengthFish" "UnitTissueWeight" ## [49] "UnitWeightFish" "Weight" ## [51] "WeightSource"
## [1] 324
DRMP_2017_2019_FishComposite <- bind_rows(DRMP_17_FishComposite, DRMP_18_FishComposite, DRMP_19_FishComposite) %>% distinct(CompositeID, .keep_all=T) # rows are duplicated for some CompositeIDs ## SAVE MERGED DATA## #Save to Fish Linkage folder writexl::write_xlsx(list(TIResults=DRMP_2017_2019_TIResults, FishComposite=DRMP_2017_2019_FishComposite), path='Reeval_Impl_Goals_Linkage_Analysis/Data/Fish/DRMP_2017_2019_Hg_Fish.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 16:06:24 PST"