Open mrustl opened 3 years ago
As now @chsprenger introduced new columns (partly based on qmra.db, i.e.:
Notes
ReferenceName
ReferenceLink
ReferenceNameInfection
ReferenceNameDalys
This currently leads to parsing errors when kwb.qmra::config_read() is executed. Fixing requires refactoring input structure!
kwb.qmra::config_read()
install.packages("remotes") remotes::install_github("kwb-r/kwb.qmra@patch-christoph") kwb.qmra::config_read(system.file("extdata/configs/default", package = "kwb.qmra")) #> #> -- Column specification -------------------------------------------------------- #> cols( #> name = col_character(), #> type = col_character(), #> value = col_double(), #> min = col_double(), #> max = col_double(), #> mode = col_double(), #> mean = col_logical(), #> sd = col_logical(), #> meanlog = col_logical(), #> sdlog = col_logical() #> ) #> #> -- Column specification -------------------------------------------------------- #> cols( #> PathogenID = col_double(), #> PathogenName = col_character(), #> PathogenGroup = col_character(), #> simulate = col_double(), #> type = col_character(), #> value = col_logical(), #> min = col_double(), #> max = col_double(), #> mode = col_logical(), #> mean = col_logical(), #> sd = col_logical(), #> meanlog = col_logical(), #> sdlog = col_character(), #> Notes = col_character(), #> ReferenceName = col_character(), #> ReferenceLink = col_character() #> ) #> Warning: 1 parsing failure. #> row col expected actual file #> 34 -- 16 columns 15 columns 'C:/Users/mrustl/Documents/R/win-library/4.0/kwb.qmra/extdata/configs/default/inflow.csv' #> #> -- Column specification -------------------------------------------------------- #> cols( #> TreatmentID = col_double(), #> TreatmentName = col_character(), #> TreatmentGroup = col_character(), #> PathogenGroup = col_character(), #> type = col_character(), #> value = col_double(), #> min = col_double(), #> max = col_double(), #> mode = col_logical(), #> mean = col_double(), #> sd = col_logical(), #> meanlog = col_logical(), #> sdlog = col_character(), #> ReferenceName = col_character(), #> ReferenceLink = col_character() #> ) #> Warning: 3 parsing failures. #> row col expected actual file #> 33 -- 15 columns 14 columns 'C:/Users/mrustl/Documents/R/win-library/4.0/kwb.qmra/extdata/configs/default/treatment_processes.csv' #> 34 -- 15 columns 14 columns 'C:/Users/mrustl/Documents/R/win-library/4.0/kwb.qmra/extdata/configs/default/treatment_processes.csv' #> 35 -- 15 columns 14 columns 'C:/Users/mrustl/Documents/R/win-library/4.0/kwb.qmra/extdata/configs/default/treatment_processes.csv' #> #> -- Column specification -------------------------------------------------------- #> cols( #> TreatmentSchemeID = col_double(), #> TreatmentSchemeName = col_character(), #> TreatmentID = col_double(), #> TreatmentName = col_character() #> ) #> #> -- Column specification -------------------------------------------------------- #> cols( #> PathogenID = col_double(), #> PathogenName = col_character(), #> PathogenGroup = col_character(), #> `Best fit model*` = col_character(), #> k = col_double(), #> alpha = col_double(), #> N50 = col_double(), #> `Host type` = col_character(), #> `Dose units` = col_character(), #> Route = col_character(), #> Response = col_character(), #> Reference = col_character(), #> Link = col_character() #> ) #> #> -- Column specification -------------------------------------------------------- #> cols( #> PathogenID = col_double(), #> PathogenName = col_character(), #> infection_to_illness = col_double(), #> dalys_per_case = col_double(), #> ReferenceNameInfection = col_character(), #> ReferenceNameDalys = col_character() #> ) #> Warning: 1 parsing failure. #> row col expected actual file #> 34 -- 6 columns 4 columns 'C:/Users/mrustl/Documents/R/win-library/4.0/kwb.qmra/extdata/configs/default/health.csv' #> $exposure #> # A tibble: 3 x 10 #> name type value min max mode mean sd meanlog sdlog #> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <lgl> <lgl> <lgl> <lgl> #> 1 number_of_repeati~ value 1000 NA NA NA NA NA NA NA #> 2 number_of_exposur~ value 100 NA NA NA NA NA NA NA #> 3 volume_perEvent triang~ NA 0.001 0.01 0.005 NA NA NA NA #> #> $inflow #> # A tibble: 37 x 16 #> PathogenID PathogenName PathogenGroup simulate type value min max #> <dbl> <chr> <chr> <dbl> <chr> <lgl> <dbl> <dbl> #> 1 1 Bacillus an~ Bacteria 0 log1~ NA 10 1.00e4 #> 2 2 Burkholderi~ Bacteria 0 log1~ NA 10 1.00e4 #> 3 3 Campylobact~ Bacteria 0 log1~ NA 100 1.00e6 #> 4 4 Coxiella bu~ Bacteria 0 log1~ NA 10 1.00e4 #> 5 5 Escherichia~ Bacteria 0 log1~ NA 10 1.00e4 #> 6 6 Escherichia~ Bacteria 1 log1~ NA 170000 1.70e9 #> 7 7 Francisella~ Bacteria 0 log1~ NA 10 1.00e4 #> 8 8 Legionella ~ Bacteria 0 log1~ NA 10 1.00e4 #> 9 9 Listeria mo~ Bacteria 0 log1~ NA 10 1.00e4 #> 10 10 Listeria mo~ Bacteria 0 log1~ NA 10 1.00e4 #> # ... with 27 more rows, and 8 more variables: mode <lgl>, mean <lgl>, #> # sd <lgl>, meanlog <lgl>, sdlog <chr>, Notes <chr>, ReferenceName <chr>, #> # ReferenceLink <chr> #> #> $treatment #> $treatment$processes #> # A tibble: 72 x 15 #> TreatmentID TreatmentName TreatmentGroup PathogenGroup type value min #> <dbl> <chr> <chr> <chr> <chr> <dbl> <dbl> #> 1 1 Conventional~ Coagulation, ~ Bacteria unif~ NA 0.2 #> 2 1 Conventional~ Coagulation, ~ Protozoa unif~ NA 1 #> 3 1 Conventional~ Coagulation, ~ Viruses unif~ NA 0.1 #> 4 2 Dissolved ai~ Coagulation, ~ Protozoa unif~ NA 0.6 #> 5 3 High-rate cl~ Coagulation, ~ Protozoa unif~ NA 2 #> 6 4 Lime softeni~ Coagulation, ~ Bacteria unif~ NA 1 #> 7 4 Lime softeni~ Coagulation, ~ Protozoa unif~ NA 0 #> 8 4 Lime softeni~ Coagulation, ~ Viruses unif~ NA 2 #> 9 5 Granular hig~ Filtration Bacteria unif~ NA 0.2 #> 10 5 Granular hig~ Filtration Protozoa unif~ NA 0.4 #> # ... with 62 more rows, and 8 more variables: max <dbl>, mode <lgl>, #> # mean <dbl>, sd <lgl>, meanlog <lgl>, sdlog <chr>, ReferenceName <chr>, #> # ReferenceLink <chr> #> #> $treatment$schemes #> # A tibble: 5 x 4 #> TreatmentSchemeID TreatmentSchemeName TreatmentID TreatmentName #> <dbl> <chr> <dbl> <chr> #> 1 1 default 16 Primary treatment #> 2 1 default 17 Secondary treatment #> 3 1 default 13 Chlorine dioxide #> 4 1 default 18 Soil-Aquifer passage #> 5 1 default 24 Filtration #> #> #> $doseresponse #> # A tibble: 37 x 13 #> PathogenID PathogenName PathogenGroup `Best fit model~ k alpha #> <dbl> <chr> <chr> <chr> <dbl> <dbl> #> 1 1 Bacillus an~ Bacteria exponential 1.65e-5 NA #> 2 2 Burkholderi~ Bacteria beta-Poisson NA 0.328 #> 3 3 Campylobact~ Bacteria beta-Poisson NA 0.144 #> 4 4 Coxiella bu~ Bacteria beta-Poisson NA 0.357 #> 5 5 Escherichia~ Bacteria exponential 2.18e-4 NA #> 6 6 Escherichia~ Bacteria beta-Poisson NA 0.155 #> 7 7 Francisella~ Bacteria exponential 4.73e-2 NA #> 8 8 Legionella ~ Bacteria exponential 5.99e-2 NA #> 9 9 Listeria mo~ Bacteria exponential 1.15e-5 NA #> 10 10 Listeria mo~ Bacteria beta-Poisson NA 0.253 #> # ... with 27 more rows, and 7 more variables: N50 <dbl>, `Host type` <chr>, #> # `Dose units` <chr>, Route <chr>, Response <chr>, Reference <chr>, #> # Link <chr> #> #> $health #> # A tibble: 37 x 6 #> PathogenID PathogenName infection_to_il~ dalys_per_case ReferenceNameIn~ #> <dbl> <chr> <dbl> <dbl> <chr> #> 1 1 Bacillus an~ NA NA <NA> #> 2 2 Burkholderi~ NA NA <NA> #> 3 3 Campylobact~ NA NA <NA> #> 4 4 Coxiella bu~ NA NA <NA> #> 5 5 Escherichia~ NA NA <NA> #> 6 6 Escherichia~ 0.25 0.0547 Bartak et al. (~ #> 7 7 Francisella~ NA NA <NA> #> 8 8 Legionella ~ NA NA <NA> #> 9 9 Listeria mo~ NA NA <NA> #> 10 10 Listeria mo~ NA NA <NA> #> # ... with 27 more rows, and 1 more variable: ReferenceNameDalys <chr>
Created on 2021-02-05 by the reprex package (v0.3.0)
Was not handled in #39
mrustl
commented
3 years ago mrustl
commented
3 years ago
As now @chsprenger introduced new columns (partly based on qmra.db, i.e.:
Notes,ReferenceName,ReferenceLinkReferenceName,ReferenceLinkReferenceNameInfection,ReferenceNameDalysThis currently leads to parsing errors when
kwb.qmra::config_read()is executed. Fixing requires refactoring input structure!Created on 2021-02-05 by the reprex package (v0.3.0)