code-refactoring: new "input" structure (due to new columns in "default") #37
Description
As now @chsprenger introduced new columns (partly based on qmra.db, i.e.:
- inflow.csv:
Notes,ReferenceName,ReferenceLink - treatment_processes.csv:
ReferenceName,ReferenceLink - health.csv:
ReferenceNameInfection,ReferenceNameDalys
This currently leads to parsing errors when kwb.qmra::config_read() is executed. Fixing requires refactoring input structure!
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)