This report is automatically generated with the R
package knitr
(version 1.40
)
.
source("R Functions/functions_QA data.R") ## RUN 1st & 2nd SCRIPTS TO LOAD & MERGE CEDEN FORMATTED DATA ## source('Reeval_Impl_Goals_Linkage_Analysis/Data/Fish/AppK_Fish MeHg_format-to-ceden.R')
There were 50 or more warnings (use warnings() to see the first 50)
## "50 or more warnings" result from Date column having years and not a full day, month, year date. The "Format Date & Time" section addresses this issue ## 'Result' column is in numeric format ## 'MDL' column is in numeric format ## 'RL' column is in numeric format
source('Reeval_Impl_Goals_Linkage_Analysis/Data/Fish/CEDENFish_format-to-ceden.R')
## 'Result' column is in numeric format ## 'MDL' column is in numeric format ## 'RL' column is in numeric format
sort(names(AppK_new)); nrow(AppK_new)
## [1] "Analyte" "BatchVerification" "CitationCode" "CommonName" ## [5] "ComplianceCode" "CompositeID" "CompositeRowID" "CoordSystem" ## [9] "LabSubmissionCode" "MDL" "Method" "NumberFishPerComp" ## [13] "ParentProjectName" "ProgramName" "ProjectCode" "ProjectName" ## [17] "QACode" "Result" "ResultComments" "ResultQualCode" ## [21] "RL" "SampleDate" "SampleDateTime" "SampleID" ## [25] "SampleTime" "SourceID" "SourceRow" "StationCode" ## [29] "StationName" "TargetLatitude" "TargetLongitude" "TaxonomicName" ## [33] "TissueName" "TLAvgLength mm" "TLMax mm" "TLMin mm" ## [37] "Unit" "WBT" "WeightAvg g"
## [1] 1816
sort(names(CEDENFish_new)); nrow(CEDENFish_new)
## [1] "Analyte" "BatchVerification" "CitationCode" "CommonName" ## [5] "ComplianceCode" "CompositeID" "CompositeRowID" "CoordSystem" ## [9] "LabSubmissionCode" "MDL" "Method" "NumberFishPerComp" ## [13] "ParentProjectName" "ProgramName" "ProjectCode" "ProjectName" ## [17] "QACode" "Result" "ResultComments" "ResultQualCode" ## [21] "RL" "SampleDate" "SampleDateTime" "SampleID" ## [25] "SampleTime" "SourceID" "SourceRow" "StationCode" ## [29] "StationName" "TargetLatitude" "TargetLongitude" "TaxonomicName" ## [33] "TissueName" "TLAvgLength mm" "TLMax mm" "TLMin mm" ## [37] "Unit" "WBT" "WeightAvg g"
## [1] 8414
FishMaster <- rbind(AppK_new, CEDENFish_new) rm(list=setdiff(ls(), 'FishMaster')) #removes all objects except 'FishMaster' ## RUN 3rd SCRIPT TO LOAD & MERGE CEDEN FORMATTED DATA ## source('Reeval_Impl_Goals_Linkage_Analysis/Data/Fish/DRMP_2016_CEDENfish_format-to-ceden.R')
## 'Result' column is in numeric format ## 'MDL' column is in numeric format ## 'RL' column is in numeric format
sort(names(FishMaster)); nrow(FishMaster)
## [1] "Analyte" "BatchVerification" "CitationCode" "CommonName" ## [5] "ComplianceCode" "CompositeID" "CompositeRowID" "CoordSystem" ## [9] "LabSubmissionCode" "MDL" "Method" "NumberFishPerComp" ## [13] "ParentProjectName" "ProgramName" "ProjectCode" "ProjectName" ## [17] "QACode" "Result" "ResultComments" "ResultQualCode" ## [21] "RL" "SampleDate" "SampleDateTime" "SampleID" ## [25] "SampleTime" "SourceID" "SourceRow" "StationCode" ## [29] "StationName" "TargetLatitude" "TargetLongitude" "TaxonomicName" ## [33] "TissueName" "TLAvgLength mm" "TLMax mm" "TLMin mm" ## [37] "Unit" "WBT" "WeightAvg g"
## [1] 10230
sort(names(DRMP_2016_new)); nrow(DRMP_2016_new)
## [1] "Analyte" "BatchVerification" "CitationCode" "CommonName" ## [5] "ComplianceCode" "CompositeID" "CompositeRowID" "CoordSystem" ## [9] "LabSubmissionCode" "MDL" "Method" "NumberFishPerComp" ## [13] "ParentProjectName" "ProgramName" "ProjectCode" "ProjectName" ## [17] "QACode" "Result" "ResultComments" "ResultQualCode" ## [21] "RL" "SampleDate" "SampleDateTime" "SampleID" ## [25] "SampleTime" "SourceID" "SourceRow" "StationCode" ## [29] "StationName" "TargetLatitude" "TargetLongitude" "TaxonomicName" ## [33] "TissueName" "TLAvgLength mm" "TLMax mm" "TLMin mm" ## [37] "Unit" "WBT" "WeightAvg g"
## [1] 66
FishMaster <- rbind(FishMaster, DRMP_2016_new) rm(list=setdiff(ls(), 'FishMaster')) #removes all objects except 'FishMaster' ## RUN 4th SCRIPT TO LOAD & MERGE CEDEN FORMATTED DATA ## source('Reeval_Impl_Goals_Linkage_Analysis/Data/Fish/DRMP_2017_2019_Fish_format-to-ceden.R')
## 'Result' column is in numeric format ## 'MDL' column is in numeric format ## 'RL' column is in numeric format
sort(names(FishMaster)); nrow(FishMaster)
## [1] "Analyte" "BatchVerification" "CitationCode" "CommonName" ## [5] "ComplianceCode" "CompositeID" "CompositeRowID" "CoordSystem" ## [9] "LabSubmissionCode" "MDL" "Method" "NumberFishPerComp" ## [13] "ParentProjectName" "ProgramName" "ProjectCode" "ProjectName" ## [17] "QACode" "Result" "ResultComments" "ResultQualCode" ## [21] "RL" "SampleDate" "SampleDateTime" "SampleID" ## [25] "SampleTime" "SourceID" "SourceRow" "StationCode" ## [29] "StationName" "TargetLatitude" "TargetLongitude" "TaxonomicName" ## [33] "TissueName" "TLAvgLength mm" "TLMax mm" "TLMin mm" ## [37] "Unit" "WBT" "WeightAvg g"
## [1] 10296
sort(names(DRMP_2017_19_new)); nrow(DRMP_2017_19_new)
## [1] "Analyte" "BatchVerification" "CitationCode" "CommonName" ## [5] "ComplianceCode" "CompositeID" "CompositeRowID" "CoordSystem" ## [9] "LabSubmissionCode" "MDL" "Method" "NumberFishPerComp" ## [13] "ParentProjectName" "ProgramName" "ProjectCode" "ProjectName" ## [17] "QACode" "Result" "ResultComments" "ResultQualCode" ## [21] "RL" "SampleDate" "SampleDateTime" "SampleID" ## [25] "SampleTime" "SourceID" "SourceRow" "StationCode" ## [29] "StationName" "TargetLatitude" "TargetLongitude" "TaxonomicName" ## [33] "TissueName" "TLAvgLength mm" "TLMax mm" "TLMin mm" ## [37] "Unit" "WBT" "WeightAvg g"
## [1] 330
FishMaster <- rbind(FishMaster, DRMP_2017_19_new) rm(list=setdiff(ls(), 'FishMaster')) #removes all objects except 'FishMaster' ## RUN 5th SCRIPT TO LOAD & MERGE CEDEN FORMATTED DATA ## source('Reeval_Impl_Goals_Linkage_Analysis/Data/Fish/MasterFish_format-to-ceden.R') sort(names(FishMaster)); nrow(FishMaster)
## [1] "Analyte" "BatchVerification" "CitationCode" "CommonName" ## [5] "ComplianceCode" "CompositeID" "CompositeRowID" "CoordSystem" ## [9] "LabSubmissionCode" "MDL" "Method" "NumberFishPerComp" ## [13] "ParentProjectName" "ProgramName" "ProjectCode" "ProjectName" ## [17] "QACode" "Result" "ResultComments" "ResultQualCode" ## [21] "RL" "SampleDate" "SampleDateTime" "SampleID" ## [25] "SampleTime" "SourceID" "SourceRow" "StationCode" ## [29] "StationName" "TargetLatitude" "TargetLongitude" "TaxonomicName" ## [33] "TissueName" "TLAvgLength mm" "TLMax mm" "TLMin mm" ## [37] "Unit" "WBT" "WeightAvg g"
## [1] 10626
sort(names(MasterFish_new)); nrow(MasterFish_new)
## [1] "Analyte" "BatchVerification" "CitationCode" "CommonName" ## [5] "ComplianceCode" "CompositeID" "CompositeRowID" "CoordSystem" ## [9] "LabSubmissionCode" "MDL" "Method" "NumberFishPerComp" ## [13] "ParentProjectName" "ProgramName" "ProjectCode" "ProjectName" ## [17] "QACode" "Result" "ResultComments" "ResultQualCode" ## [21] "RL" "SampleDate" "SampleDateTime" "SampleID" ## [25] "SampleTime" "SourceID" "SourceRow" "StationCode" ## [29] "StationName" "TargetLatitude" "TargetLongitude" "TaxonomicName" ## [33] "TissueName" "TLAvgLength mm" "TLMax mm" "TLMin mm" ## [37] "Unit" "WBT" "WeightAvg g"
## [1] 7328
FishMaster <- rbind(FishMaster, MasterFish_new) rm(list=setdiff(ls(), 'FishMaster')) #removes all objects except 'FishMaster' ## RUN 6h SCRIPT TO LOAD & MERGE CEDEN FORMATTED DATA ## source('Reeval_Impl_Goals_Linkage_Analysis/Data/Fish/SNIP_FISH_format-to-ceden.R')
## 'Result' column converted to numeric format ## 'MDL' column converted to numeric format ## 'RL' column converted to numeric format
sort(names(FishMaster)); nrow(FishMaster)
## [1] "Analyte" "BatchVerification" "CitationCode" "CommonName" ## [5] "ComplianceCode" "CompositeID" "CompositeRowID" "CoordSystem" ## [9] "LabSubmissionCode" "MDL" "Method" "NumberFishPerComp" ## [13] "ParentProjectName" "ProgramName" "ProjectCode" "ProjectName" ## [17] "QACode" "Result" "ResultComments" "ResultQualCode" ## [21] "RL" "SampleDate" "SampleDateTime" "SampleID" ## [25] "SampleTime" "SourceID" "SourceRow" "StationCode" ## [29] "StationName" "TargetLatitude" "TargetLongitude" "TaxonomicName" ## [33] "TissueName" "TLAvgLength mm" "TLMax mm" "TLMin mm" ## [37] "Unit" "WBT" "WeightAvg g"
## [1] 17954
sort(names(SNIPFISH_new)); nrow(SNIPFISH_new)
## [1] "Analyte" "BatchVerification" "CitationCode" "CommonName" ## [5] "ComplianceCode" "CompositeID" "CompositeRowID" "CoordSystem" ## [9] "LabSubmissionCode" "MDL" "Method" "NumberFishPerComp" ## [13] "ParentProjectName" "ProgramName" "ProjectCode" "ProjectName" ## [17] "QACode" "Result" "ResultComments" "ResultQualCode" ## [21] "RL" "SampleDate" "SampleDateTime" "SampleID" ## [25] "SampleTime" "SourceID" "SourceRow" "StationCode" ## [29] "StationName" "TargetLatitude" "TargetLongitude" "TaxonomicName" ## [33] "TissueName" "TLAvgLength mm" "TLMax mm" "TLMin mm" ## [37] "Unit" "WBT" "WeightAvg g"
## [1] 4333
FishMaster <- rbind(FishMaster, SNIPFISH_new) rm(list=setdiff(ls(), 'FishMaster')) #removes all objects except 'FishMaster' ## RUN 7th SCRIPT TO LOAD & MERGE CEDEN FORMATTED DATA ## source('Reeval_Impl_Goals_Linkage_Analysis/Data/Fish/USGSFISH_format-to-ceden.R')
## 'Result' column should be numeric but some cells contain <.1 and NA ## . ## ACTIONS TAKEN: ## For numeric values with '<': 'ND' put in ResultQualCode column, numeric value moved to MDL column, & made Result blank. ## For NA's: 'ND' put in ResultQualCode column, MDL column value converted to mg/Kg, & made Result blank. ## ## 'MDL' column should be numeric but some cells contain 1.33 ng/g, 1.5 ng/g, 0.26 ng/g, and 0.07 ng/g. ## ACTIONS TAKEN: ## The 'ng/g' text dropped and value converted to mg/Kg. ## ## 'RL' column is all blanks and was converted to numeric format
sort(names(FishMaster)); nrow(FishMaster)
## [1] "Analyte" "BatchVerification" "CitationCode" "CommonName" ## [5] "ComplianceCode" "CompositeID" "CompositeRowID" "CoordSystem" ## [9] "LabSubmissionCode" "MDL" "Method" "NumberFishPerComp" ## [13] "ParentProjectName" "ProgramName" "ProjectCode" "ProjectName" ## [17] "QACode" "Result" "ResultComments" "ResultQualCode" ## [21] "RL" "SampleDate" "SampleDateTime" "SampleID" ## [25] "SampleTime" "SourceID" "SourceRow" "StationCode" ## [29] "StationName" "TargetLatitude" "TargetLongitude" "TaxonomicName" ## [33] "TissueName" "TLAvgLength mm" "TLMax mm" "TLMin mm" ## [37] "Unit" "WBT" "WeightAvg g"
## [1] 22287
sort(names(USGSFISH_new)); nrow(USGSFISH_new)
## [1] "Analyte" "BatchVerification" "CitationCode" "CommonName" ## [5] "ComplianceCode" "CompositeID" "CompositeRowID" "CoordSystem" ## [9] "LabSubmissionCode" "MDL" "Method" "NumberFishPerComp" ## [13] "ParentProjectName" "ProgramName" "ProjectCode" "ProjectName" ## [17] "QACode" "Result" "ResultComments" "ResultQualCode" ## [21] "RL" "SampleDate" "SampleDateTime" "SampleID" ## [25] "SampleTime" "SourceID" "SourceRow" "StationCode" ## [29] "StationName" "TargetLatitude" "TargetLongitude" "TaxonomicName" ## [33] "TissueName" "TLAvgLength mm" "TLMax mm" "TLMin mm" ## [37] "Unit" "WBT" "WeightAvg g"
## [1] 381
FishMaster <- rbind(FishMaster, USGSFISH_new) rm(list=setdiff(ls(), 'FishMaster')) #removes all objects except 'FishMaster' ## RUN 8th SCRIPT TO LOAD & MERGE CEDEN FORMATTED DATA ## source('Reeval_Impl_Goals_Linkage_Analysis/Data/Fish/WQP_FISH_format-to-ceden.R')
## 'Result' column is in numeric format ## 'MDL' column is in numeric format ## 'RL' column is in numeric format
sort(names(FishMaster)); nrow(FishMaster)
## [1] "Analyte" "BatchVerification" "CitationCode" "CommonName" ## [5] "ComplianceCode" "CompositeID" "CompositeRowID" "CoordSystem" ## [9] "LabSubmissionCode" "MDL" "Method" "NumberFishPerComp" ## [13] "ParentProjectName" "ProgramName" "ProjectCode" "ProjectName" ## [17] "QACode" "Result" "ResultComments" "ResultQualCode" ## [21] "RL" "SampleDate" "SampleDateTime" "SampleID" ## [25] "SampleTime" "SourceID" "SourceRow" "StationCode" ## [29] "StationName" "TargetLatitude" "TargetLongitude" "TaxonomicName" ## [33] "TissueName" "TLAvgLength mm" "TLMax mm" "TLMin mm" ## [37] "Unit" "WBT" "WeightAvg g"
## [1] 22668
sort(names(WQP_FISH_new)); nrow(WQP_FISH_new)
## [1] "Analyte" "BatchVerification" "CitationCode" "CommonName" ## [5] "ComplianceCode" "CompositeID" "CompositeRowID" "CoordSystem" ## [9] "LabSubmissionCode" "MDL" "Method" "NumberFishPerComp" ## [13] "ParentProjectName" "ProgramName" "ProjectCode" "ProjectName" ## [17] "QACode" "Result" "ResultComments" "ResultQualCode" ## [21] "RL" "SampleDate" "SampleDateTime" "SampleID" ## [25] "SampleTime" "SourceID" "SourceRow" "StationCode" ## [29] "StationName" "TargetLatitude" "TargetLongitude" "TaxonomicName" ## [33] "TissueName" "TLAvgLength mm" "TLMax mm" "TLMin mm" ## [37] "Unit" "WBT" "WeightAvg g"
## [1] 99
FishMaster <- rbind(FishMaster, WQP_FISH_new) rm(list=setdiff(ls(), 'FishMaster')) #removes all objects except 'FishMaster' # Order columns FishMaster <- FishMaster %>% #rename columns with complex names rename( WeightAvg = `WeightAvg g`, TLAvgLength = `TLAvgLength mm`, TLMin =`TLMin mm`, TLMax = `TLMax mm` ) %>% mutate(SourceRow = as.numeric(SourceRow)) %>% #reorder columns select(SourceID, SourceRow, StationName, SampleDateTime, Analyte, Result, MDL, RL, Unit, ResultQualCode, WBT, CommonName, TaxonomicName, NumberFishPerComp, TissueName, WeightAvg, TLAvgLength, TLMin, TLMax, CompositeID, CompositeRowID, TargetLatitude, TargetLongitude, CoordSystem, QACode, SampleID, ResultComments, LabSubmissionCode, Method, BatchVerification, ComplianceCode, ProjectCode, ProgramName, ParentProjectName, ProjectName, CitationCode, StationCode, SampleDate, SampleTime) %>% arrange(SourceID, SourceRow) ## SAVE MERGED CEDEN FORMATTED DATA - STILL NEEDS QA/QC FOR GIS SCOPING## writexl::write_xlsx(FishMaster, path='Reeval_Impl_Goals_Linkage_Analysis/Data/Fish/1a_FishMaster_merged.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 16:17:09 PST"