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Type 'q()' to quit R. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(normfluodbf) == Welcome to normfluodbf - Developed by Tingwei Adeck and Tesla Adeck (Jesus Followers) =========================================================================== If you find this package useful, please leave a star: https://github.com/AlphaPrime7/normfluodbf If you want to support me in my learning and development journey: https://www.buymeacoffee.com/tingweiadeck If you encounter a bug or want to request an enhancement please file an issue at: https://github.com/AlphaPrime7/normfluodbf/issues Thank you for using normfluodbf! Attaching package: 'normfluodbf' The following object is masked from 'package:stats': step The following object is masked from 'package:utils': demo The following object is masked from 'package:base': subset > > test_check("normfluodbf") Crikee, some values in your original data violate thresholds 🐷 🐫 [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "C9" Crikee, some values in your original data violate thresholds 🐷 🐫 [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "C9" Crikee, some values in your original data violate thresholds 🐷 🐫 [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "C9" Crikee, some values in your original data violate thresholds 🐷 🐫 [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "C9" Crikee, some values in your original data violate thresholds 🐷 🐫 [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "27" Crikee, some values in your original data violate thresholds 🐷 🐫 Crikee, some values in your original data violate thresholds 🐷 🐫 [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "A01" [[2]] [1] "A02" [[3]] [1] "A03" [[4]] [1] "B01" [[5]] [1] "B02" [[6]] [1] "B03" [[7]] [1] "C01" [[8]] [1] "C02" [[9]] [1] "C03" Crikee, some values in your original data violate thresholds 🐷 🐫 [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "A01" [[2]] [1] "A02" [[3]] [1] "A03" [[4]] [1] "B01" [[5]] [1] "B02" [[6]] [1] "B03" [[7]] [1] "C01" [[8]] [1] "C02" [[9]] [1] "C03" The upload_data step needs to be completed Initializing Data ... [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "C9" Data Initialized step DONE... DONE (1 seconds) The upload_data step needs to be completed Initializing Data ... [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "A01" [[2]] [1] "A02" [[3]] [1] "A03" [[4]] [1] "B01" [[5]] [1] "B02" [[6]] [1] "B03" [[7]] [1] "C01" [[8]] [1] "C02" [[9]] [1] "C03" Data Initialized step DONE... DONE (0 seconds) The upload_data step needs to be completed Initializing Data ... [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "C9" Data Initialized step DONE... DONE (0 seconds) [1] "Steps left:4" [1] "Next step function: format_plate_data" Formating Plate Data ... Data Formatted step DONE... DONE (0 seconds) [1] "Next step function: normalize_by_well" Normalizing Data ... Data Normalized step DONE... DONE (0 seconds) [1] "Next step function: modify_plate_data" [1] "Next step function: analyze_ready" Process complete The upload_data step needs to be completed Initializing Data ... [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "C9" Data Initialized step DONE... DONE (1 seconds) [1] "Steps left:4" [1] "Next step function: format_plate_data" Formating Plate Data ... Data Formatted step DONE... DONE (0 seconds) [1] "Next step function: normalize_by_well" Normalizing Data ... Data Normalized step DONE... DONE (0 seconds) [1] "Next step function: modify_plate_data" [1] "Next step function: analyze_ready" Process complete List of 9 $ plate_meta : tibble [96 x 5] (S3: tbl_df/tbl/data.frame) ..$ well : chr [1:96] "A1" "A2" "A3" "A4" ... ..$ sample : logi [1:96] NA NA NA NA NA NA ... ..$ well_row: Factor w/ 8 levels "A","B","C","D",..: 1 1 1 1 1 1 1 1 1 1 ... ..$ well_col: Factor w/ 12 levels "1","2","3","4",..: 1 2 3 4 5 6 7 8 9 10 ... ..$ used : logi [1:96] FALSE FALSE FALSE FALSE FALSE FALSE ... $ plate_data : md_nrmf_ [1,500 x 8] (S3: mod_normfluodbf_data/tbl_df/tbl/data.frame) ..$ well : chr [1:1500] "A1" "A1" "A1" "A1" ... ..$ well_row : chr [1:1500] "A" "A" "A" "A" ... ..$ well_col : Factor w/ 12 levels "1","10","11",..: 1 1 1 1 1 1 1 1 1 1 ... ..$ used : logi [1:1500] TRUE TRUE TRUE TRUE TRUE TRUE ... ..$ Cycle_Number : num [1:1500] 1 2 3 4 5 6 7 8 9 10 ... ..$ fluor_values : num [1:1500] 1 0.872 0.788 0.715 0.731 ... ..$ outlier : logi [1:1500] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ outlier_color: chr [1:1500] "#EE3B3B" "#EE3B3B" "#EE3B3B" "#EE3B3B" ... $ steps : num 0 $ status : num 5 $ dirty : logi TRUE $ version : chr "2.0.0" $ params :List of 3 ..$ GENERAL :List of 5 .. ..$ X_VAR_ONE : chr "Time" .. ..$ X_VAR_TWO : chr "Cycle_Number" .. ..$ Y_VAR : chr "FLUORESCENCE" .. ..$ X_VAR_ONE_LABEL: chr "TIME" .. ..$ X_VAR_TWO_LABEL: chr "CYCLE NUMBER" ..$ THRESHOLDS:List of 4 .. ..$ MAX_FLUOR : num 65536 .. ..$ MIN_FLUOR : num 128 .. ..$ CUTOFF_UPPER_LIMIT: num 32768 .. ..$ CUTOFF_LOWER_LIMIT: num 4096 ..$ COLORS :List of 4 .. ..$ POS : chr "#7FFFD4" .. ..$ TEST : chr "#0000CD" .. ..$ NEG : chr "#EE3B3B" .. ..$ NEUTRAL: chr "#BF3EFF" $ dataset_name: chr "dat_1" $ data_summary: chr "36 Wells Used" - attr(*, "class")= chr [1:3] "96well_plate" "normfluodbf_plate" "list" The upload_data step needs to be completed Initializing Data ... [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "C9" Data Initialized step DONE... DONE (1 seconds) [1] "Steps left:4" [1] "Next step function: format_plate_data" Formating Plate Data ... Data Formatted step DONE... DONE (0 seconds) [1] "Next step function: normalize_by_well" Normalizing Data ... Data Normalized step DONE... DONE (0 seconds) [1] "Next step function: modify_plate_data" [1] "Next step function: analyze_ready" Process complete The upload_data step needs to be completed Initializing Data ... [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "C9" Data Initialized step DONE... DONE (1 seconds) [1] "Steps left:4" [1] "Next step function: format_plate_data" Formating Plate Data ... Data Formatted step DONE... DONE (0 seconds) [1] "Next step function: normalize_by_well" Normalizing Data ... Data Normalized step DONE... DONE (0 seconds) [1] "Next step function: modify_plate_data" [1] "Next step function: analyze_ready" Process complete Crikee, some values in your original data violate thresholds 🐷 🐫 [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "C9" The upload_data step needs to be completed Initializing Data ... [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)" [[1]] [1] "C9" Data Initialized step DONE... DONE (0 seconds) [1] "Steps left:5" [1] "Next step function: format_plate_data" Formating Plate Data ... Data Formatted step DONE... DONE (0 seconds) [1] "Next step function: remove_outliers" [1] "Next step function: normalize_by_well" Normalizing Data ... Data Normalized step DONE... DONE (0 seconds) [1] "Next step function: modify_plate_data" [1] "Next step function: analyze_ready" Process complete [ FAIL 0 | WARN 617 | SKIP 0 | PASS 24 ] [ FAIL 0 | WARN 617 | SKIP 0 | PASS 24 ] > > proc.time() user system elapsed 15.98 1.57 17.20