babsim.hospital

11.8.8

• NEW:
  • function funBabsimHospital() added (moved from package SPOT)
  • updateRkidatafile.R: Formatting improved

11.8.6

• CHANGES
  • updateRkidataFile.R updated
  • updateIcudataFile

11.8.4

• CHANGES
  • Roxygen note: 7.1.2
  • Typos in vignette

11.8.2

• CHANGES
  • ‘rmarkdown’ package declared as a dependency (in the suggests field)

11.8.0

• CHANGES
  • Minor typos fixed

11.7.26

• NEW:
  • UK data analysis added:
    • vignette-NumericalMethods

11.7.24

• NEW:
  • runoptUK accept new argument factorUK to adapt the probabilities for ventilated patients.

11.7.22

• NEW:
  • getTrainTestFunction accepts additional argument simRepeats (default=1 for Windows)

11.7.20

• NEW:
  • getAndCheckTrainData() function
  • checkTrainConfig()
  • checkTestData()
  • getTestData()
  • checkTestConf()

11.7.18

• CHANGES:
  • getTrainTestObjFun.R from develop to master.

11.7.16

• CHANGES:
  • logLevel <- 0 in getTrainTestObjFun.R

11.7.14

• BUGFIX: as.Date() provides origin (origin = “1970-01-01”) to fix error: Quitting from lines 618-626 (babsim-vignette-introduction.Rmd) Error: processing vignette ‘babsim-vignette-introduction.Rmd’ failed with diagnostics: ‘origin’ must be supplied:

11.7.12

• BUGFIX: Found the following (possibly) invalid URLs: URL: https://www.destatis.de/DE/Themen/Laender-Regionen/Regionales/Gemeindeverzeichnis/_inhalt.html From: man/GermanCounties.Rd man/GermanStates.Rd Status: 400 Message: Bad Request

11.7.10

• CHANGES:
  • icudata.R, icudataFull.R, rkidata.R, and rkidataFull.R files added

11.7.24

• NEW:
  • runoptUK accept new argument factorUK to adapt the probabilities for ventilated patients.

11.7.22

• NEW:
  • getTrainTestFunction accepts additional argument simRepeats (default=1 for Windows)

11.7.20

• NEW:
  • getAndCheckTrainData() function
  • checkTrainConfig()
  • checkTestData()
  • getTestData()
  • checkTestConf()

11.7.18

• Cleanup: code, vignette master

11.7.14

• CHANGES:
  • getTrainTestObjFunctions: logLevel <- 0

11.7.12

• NEWS
  • Vignette updated

11.7.10

• NEWS
  • ukpara added
  • vignette for master students

11.7.8

• BUGFIX
  • mc.coresN is handled correctly
  • babsimHospital example uses conf correctly

11.7.6

• BUGFIX:
  • meesagef messageDataRange are exported

11.7.4

• NEW:
  • vaccine counts added

11.7.2

• package plotly not suggested anymore

11.7.0

• New data structures

11.6.0

• Improved prediction /conf intervals

11.5.18

• more regions
• envToTibble does not use a default conf argument

11.5.16

• Faster evalutions:
  • getDecision() rewritten
  • updateP() rewritten

11.5.14

• CRAN comments fixed

11.5.12

• CHANGES:
  • Cleanup
  • Accelerate testing (region is set to 5374 whenever possible)

11.5.10

• CHANGES:
  • babsimrun returns list

11.5.8

• CHANGES:
  • importFrom dependencies reduced. The following packages were removed from the DESCRIPTION Imports list:
    • Metrics, simmer.plot, rpart.plot
  • examples use smaller data sets

11.5.6

new para file: obkpara with 29 variables (135 obs)

11.5.4

• new para file:
  • nrwpara with 29 variables (5 results)

11.5.2

• new para file:
  • koelnpara with 29 variables

11.5.0

• WARNING: runoptDirect() uses x0 <- getStartParameter(region= -1), because there is no previous region parameter set
• NEW:
  • edge: IntensiveAftercare -> Healthy
• UPDATE:
  • Probabilities and Durations refined based on feedback from doctors

11.4.6.

* R0 ranges from 0.1
* Error function tests
* Hall of Fame

11.4.4

* CHANGES
   * getBounds(): new lower limit (1 instead of 0.5) for Risk Male

11.4.2

* CHANGES:
   * funEvalsFactor = 0 

11.4.0

* UPDATES:
   * config for new local runs (over)

11.3.10

* UPDATES
   * local koeln results (maans03)

11.3.8

* UPDATES:
   * local obkresults (maans05)

11.3.6

* UPDATES:
   * rkidata, icudata 25.11.2020
   * local nrwresults (maans04)

11.3.4

* NEWS:
   * *over run configurations

11.3.2

• CHANGES:
  • koelnpara.R and nrwpara.R use the same run config as obkpara (initial designs, funevals, ..)
• UPDATES:
  • rkidata 24.11.2020

11.3.0

• BUGFIX
  • getError fixed

11.2.2

• UPDATE:
  • new obkpara

11.2.0

• CHANGES:
  • New train/test set splittimg procedure
  • runoptDirect uses new parameter: tryOnTestSet (default: TRUE)

11.1.16

• UPDATES:
  • locally optimized parameter sets koelnpara (tbb)

11.1.14

• UPDATES
  • locally optimized parameter sets (tbb)

11.1.12

• UPDATES:
  • Cleanup results

11.1.10

• UPDATES:
  • rkidata 22.11.2020
  • icudata 22.11.2020

11.1.8

• BUGFIX:
  • getStartParameter() generates vector, not a list

11.1.6

• CHANGES: Typo fixed

11.1.4

• UPDATES:
  • getStartParameter() uses region information (new arg “region”)
  • nrwpara, nrwarchive fixed

11.1.2

* UPDATES:
   * current best parameter setting: 
      * obkpara.rda, koelnpara.rda, and nrwpara.rda contain the current best
     known parameter set
   * archived parameter sets:
      * results from all runs in obkarchive, koelnarchive, nrwarchive

11.1.0

• CHANGES:
  • nrwpara.R
    • funevals = 2000 (before: 1000)
    • size = 500 (before: 300)
    • simrepeats = 5 (before: 10)

11.0.64

• CHANGES:
  • Organize results

11.0.62

• NEW:
  • results dir added

11.0.60

• NEW:
  • First draft of analysis script

11.0.58

• CHANGES:
  • *para.R files use “_” instead of “-” as separator
  • archive folder

11.0.56

• NEW:
  • testing archive

11.0.54

• CHANGES:
  • obkpara.R uses 1000 repeats (complete opt. runs)

11.0.52

• CHANGES:
  • meta runs uses icuWeights = c(1,1)

11.0.50

• CHANGES: testRepeats = 10

11.0.48:

• UPDATES:
  • nrwpara 20.11.20 (17 obs) with y min = 912.14

11.0.46:

• UPDATES:
  • koelnpara with icuWeights (1,1) (73 obs) with min y = 12.40

11.0.44

• UPDATES:
  • nrwpara 20.11.20 (28 obs) with y min = 912.14

11.0.42:

• UPDATES:
  • koelnpara 20.11.20 (100 obs) with min y = 71.14

11.0.40

* CHANGES:
   * koelnpara.R uses: icuWeights = c(1,1)  

10.0.38:

• UPDATES:
  • koelnpara 20.11.20 (100 obs)

11.0.36

* CHANGES:
   * obkpara.R uses: icuWeights = c(1,1)  

11.0.34

* CHANGES:
   * nrwpara.R uses: icuWeights = c(1,1)  
   

11.0.32

* UPDATES:
   * koelnpara 20.11.20 (42 obs.)

11.0.28

* UPDATES:
   * nrwpara 20.11.20 

11.0.26:

• UPDATES:
  • koelnpara 20.11.20 (28 obs.)

11.0.24:

• NEWS:
  • koelnparameta.R
  • obkpara.R

11.0.22:

• CHANGES:
  • Slightly increased bounds (constraints)
  • Risk male = 1.5 (from 2)

11.0.20

• UPDATES:
  • koelnpara (version 11 format, 27 variables, 100 observations)

11.0.18:

• CHANGES:
  • Training and testing times modiefied (extended warm-up periods)
  • Prob./duration graphs updated

11.0.16

• UPDATES:
  • nrwpara (10 observations)

11.0.14

• UPDATES:
  • koelnpara (version 11 format, 27 variables, 67 observations)

11.0.12

• UPDATES:
  • koelnpara (version 11 format, 27 variables, 47 observations)

11.0.10

• BUGFIX:
  • preloadFunctions.R handles parameterfiles with flexible dimensions

11.0.8

• BUGFIX:
  • ggVisualizeRkiAge: Day <- value <- variable <- NULL

11.0.6:

• BUGFIX:
  • app_server.R handles parameterfiles with flexible dimensions

11.0.4

• UPDATES:
  • koelnpara (version 11 foramt, 27 variables)

11.0.2

• UPDATES:
  • obkpara (version 11 format, 27 variables)

11.0.0

• CHANGES:
  • Transitions removed: Intensive -> Healthy, Ventilation -> Aftercare, and IntensiveAftercare -> Healthy
  • This affects variables: x9, x25, x10, x28, and x14
  • The number of states remains the same

10.6.6

• UPDATE:
  • nrwpara 18.11.2020

10.6.4

• UPDATE:
  • obkpara 18.11.2020

10.6.2

• BUGFIX:
  • icudata, icudataFull: double entries removed using unique

10.6.0

• UPDATES:
  • New parameter bounds (2nd Update)

10.5.2

• UPDATES:
  • nrwpara 18.11.2020

10.5.0

• CHANGES:
  • Modified parameter bounds (stricter)
• NEWS: * Old bound values can be accessed via getBoundsOld()

10.4.8

• UPDATES:
  • deutschlandpara from 15.11.2020 run
  • nrwpara from 15.11.2020 run
  • koelnpara from 15.11.2020 run
  • obkpara from 15.11.2020 run

10.4.6

• CHANGES:
  • Optimization runs use no overlap and shorter warm-up period (2 weeks)

10.4.4

• UPDATES:
  • rkidata, icudata from 15.11.2020

10.4.2

• UPDATES:
  • obk, koeln, nrw: first results from 15.11.2020

10.4.0

• CHANGES:
  • new upper bound AmntDaysInfectedToHospital: 14 instead of 21 days

10.3.6

• BUGFIX:
  • Correct End Days in runoptDirect()

10.3.4

• BUGFIX:
  • Correct Starting Days in runoptDirect()

10.3.2

• BUGFIX:
  • Correct order in getRkiData()

10.3.0

• BUGFIX:
  • Perform data correction after the one case per row only correction in getRkiData()

10.2.22

• koelnpara, nrwpara, deutschlandpara results

10.2.20

• obkpara.R uses 400 funevals

10.2.18

• obkpara

10.2.16

• visualizeGraph() imports plot.igraph from igraph

10.2.14

• BUGFIX:
  • rkidata manually fixed (should be done automatically, see issue 37)

10.2.12

• CHANGES
  • testRepeats accepts new parameter: testRepeats. Default value = 3

10.2.10

• UPDATES:
  • new obkpara.R, koelnpara.R, nrwpara.R and deutschlandpara.R settings

10.2.8

• BUGFIX:
  • runoptDirect:
    • date handling fixed

10.2.6

• BUGFIX:
  • updateRkidataFile() uses Meldedatum to select rkidata:
    rkidata <- rkidataFull[which(rkidataFull$Meldedatum >= as.Date(“2020-09-01”)), ]
  • getRkiData() checks if (length(date_range[!date_range %in% rki$Refdatum]) >0)
• CHANGES:
  • run configs (dates) in obk, koeln, nrw, deutschland modified (dates mut be later than Sep 1)

10.2.4

• CHANGES:
  • print/verbosity restructured
  • The following functions require an explicit specification of their parameters:
    • getRegionRki(): region

babsimHospital 10.2.2

• CHANGES:
  • runopt() replaced by runoptdirect()

babsimHospital 10.2.0

• CHANGES:
  • The following functions require an explicit specification of the conf parameter (no default is used to prevent errors):
    • getConfFromData() does not provide an default settings
    • getDailyMaxResults()
    • babsimHospital()

babsim.hospital 10.1.0.6

• CHANGES:
  • getParameterDataFrame() returns min max values

babsim.hospital 10.1.0.4

• CHANGES:
  • reorganization of file contents:
    • new files babsimPara.R and babsimConf.R for parameter (optmization) and configuration
  • new version numbering

babsim.hospital 10.11.13.2

• UPDATES:
  • obkpara from obk-2020-Nov.13-01.23-V10.11.12.10.RData

babsim.hospital 10.11.13.0

• CHANGES:
  • getError() does not use a default conf
  • babsimToolsConf() implements verbosity (default: 0)
  • runoptDirect() uses verbosity

babsim.hospital 10.11.12.10

• CHANGES:
  • babsimHospital() detects OS (Win, Linux, Mac) and turns of parallel processing for Win systems

babsim.hospital 10.11.12.8

• UPDATES:
  • obkpara
  • koelnpara
  • nrwpara
  • deutschlandpara

babsim.hospital 10.11.12.6

• UPDATES:
  • obkpara
  • koelnpara
  • nrwpara

babsim.hospital 10.11.12.4

• BUGIXES:
  • icudata: double entries manually removed (develop branch)

babsim.hospital 10.11.12.2

• UPDATES:
  • icudata (DIVI) 12.11.2020
  • rkidata 12.11.2020

babsim.hospital 10.11.12.0

• UPDATE:
  • cleanup interfaces and default parameters
• NEW:
  • babsimFun.R collects optimization functions

babsim.hospital 10.11.11.0

• NEW:
  • direct option in SPOT used

babsim.hospital 10.11.10.2

• UPDATES:
  • obkpara 20201109PM
  • nrwpara 20201109PM

babsim.hospital 10.11.10.0

• UPDATES:
  • icudata (DIVI) 9.11.2020
  • rkidata 10.11.2020

babsim.hospital 10.11.9.0

• UPDATES:
  • obkpara 20201108PM
• NEWS:
  • runoptLasso(): Optimization using Lasso instead of Kriging (experimental)

babsim.hospital 10.11.8.2

• UPDATES:
  • icudata (DIVI) 8.11.2020
  • rkidata 8.11.2020

babsim.hospital 10.11.8.0

• CHANGES:
  • data download and handling for icudata and rkidata reorganized:
    • rkidata and rkidataFull
    • icudata and icudataFull

babsim.hospital 10.11.7.0

• CHANGES:
  • modelOptimizeHospital() removed
  • visualizeGraph() uses checkSimPara()
• UPDATES:
  • icudata (DIVI) 7.11.2020

babsim.hospital 10.11.6.12

• UPDATES:
  • parameter sets updated (optimization results from 5. Nov. 2020):
    • nrwpara
    • koelnpara
    • obkpara

babsim.hospital 10.11.6.10

• UPDATES:
  • icudata DIVI 6.11.2020

babsim.hospital 10.11.6.8

• CHANGES:
  • simmerplot mv to man/figures

babsim.hospital 10.11.6.6

• CHANGES:
  • simmerplot mv to man/figures

babsim.hospital 10.11.6.4

• CHANGES:
  • vignette PDF compacted via tools::compactPDF(“vignettes”, gs_quality = “ebook”)

babsim.hospital 10.11.6.2

• CHANGES:
  • cleanup:
    • vignettes renamed
    • subfolder ForTheExpert
    • INTERNAL_DATA.md included in bundeslanddata.R
    • INTERNAL_DATA.md removed
    • README.Rmd: fig.path = “man/figures/README-” changed to fig.path = “.”,

babsim.hospital 10.11.6.0

• CHANGES:
  • rkidata (switched Refdatum <-> Meldedatum) 6.11.2020

babsim.hospital 10.11.5.8

• CHANGES:
  • sysdata.rda removed, were replaced by bundeslanddata.rda

babsim.hospital 10.11.5.6

• UPDATE:
  • icudata 5.11.2020

babsim.hospital 10.11.5.4

• UPDATE:
  • results koelnpara 2020.11.4 PM

babsim.hospital 10.11.5.2

• NEW:
  • runopt() accepts argument funEvalsFactor with default value 0

babsim.hospital 10.11.5.0

• CHANGES:
  • rkidata (switched Refdatum <-> Meldedatum) 5.11.2020
  • switchRkiRefdatumToMeldedatum updated

babsim.hospital 10.11.4.18

• NEW:
  • getBestParameter()
  • smoothParameter()

babsim.hospital 10.11.4.16

• deutschlandpara 20201103PM

babsim.hospital 10.11.4.14

• runopt() uses
  • retries=100
  • designControl does not use inequalityConstraint=g anymore

babsim.hospital 10.11.4.12

• CHANGES:
• ggVisualizeIcu() considers theat faelle_covid_aktuell include faelle_covid_aktuell_beatmet, so we substract faelle_covid_aktuell_beatmet

babsim.hospital 10.11.4.10

• CHANGES:
  • koelnpara 20201103PM2
  • nrwpara 20201103PM2
  • deutschlandpara 20201103PM

babsim.hospital 10.11.4.8

• CHANGES:
  • obkpara 20201104AM-5
  • icudata DIVI 4.11.2020

babsim.hospital 10.11.4.6

• CHANGES:
  • rkidata uses Meldedatum

babsim.hospital 10.11.4.4

* CHANGES:
 * rkidata as provided by RKI from 4.11.2020

babsim.hospital 10.11.4.2

• BUG (partially fixed):
  • TestSimStartDate = “2020-09-20” does not work for OBK data. Use TestSimStartDate = “2020-09-21” instead. Possible reason: not suffient data in obkdata?

babsim.hospital 10.11.4.0

• NEWS:
  • runopt() accepts Overlap (= 7)

babsim.hospital 10.11.03.14

• NEWS:
  • runopt() accepts TestFieldStartDate = “2020-10-20” and TestSimStartDate = “2020-09-20”

babsim.hospital 10.11.03.12

• CHANGES:
  • examples reduced (dontrun)

babsim.hospital 10.11.03.10

• CHANGES:
  • runopt() stores results in subfolder results

babsim.hospital 10.11.03.8

• CHANGES:
  • runopt() stops if dates are incorrect

babsim.hospital 10.11.03.6

• CHANGES:
  • icudata (DIVI) Stand 3.11.2020

babsim.hospital 10.11.03.4

• CHANGES:
  • rkidata uses Meldedatum

babsim.hospital 10.11.03.2

• BUGFIX:
  • runopt() uses correct configuration
• CHANGES:
  • rkidata as provided by RKI
  • nowcast vignette: eval = FALSE for all snipplets

babsim.hospital 9.11.03.0

• BUGFIX:
  • runopt() uses train and test data

babsim.hospital 9.11.02.2

• BUGFIX:
  • runopt() uses corrected data

babsim.hospital 9.11.02.0

• BUGFIX:
  • runopt() uses full simData and fieldData

babsim.hospital 8.11.02.10

• CHANGES:
  • runoptsynth() accepts data argument

babsim.hospital 8.11.02.08

• CHANGES:
  • koelnpara20201102AM-7

babsim.hospital 8.11.02.06

• CHANGES:
  • getObkData() accepts data argument

babsim.hospital 8.11.02.04

• UPDATE:
  • icudata (DIVI) 2.11.2020
  • obkpara 20201102AM-10

babsim.hospital 8.11.02.02

• UPDATE:
  • Vignette Nowcast updated

babsim.hospital 8.11.02.00

• UPDATE:
  • rkidata (switched to Meldedatum) from Nov 2nd 2020
• NEW:
  • Vignette Nowcast
  • koelnpara run 20201102AM

babsim.hospital 8.11.01.20

CHANGES: extendRki uses median( tail(dataAgg, 7)$Freq)

babsim.hospital 8.11.01.18

• UPDATE:
  • obkpara 20201031PM-22

babsim.hospital 8.11.01.16

• NEW:
  • ggVisualizeIcu()
  • ggVisualizeRki()

babsim.hospital 8.11.01.14

• NEW:
  • app has analysis tab

babsim.hospital 8.11.01.12

• CHANGES:
  • typos fixed: rkidata uses Meldedatum

babsim.hospital 8.11.01.10

• NEW:
  • switchRkiRefdatumToMeldedatum()
  • switchRkiMeldedatumToRefdatum()
  • rkidata uses Meldedatum

babsim.hospital 8.11.01.8

• CHANGES:
  • icudata (DIVI) 1.11.2020

babsim.hospital 8.11.01.6

• CHANGES:
  • new plot arrangement for simulations

babsim.hospital 8.11.01.4

• CHANGES:
  • ggVisualize functions accept option simplify. Defaault is true.

babsim.hospital 8.11.01.2

• CHANGES:
  • rkidata

babsim.hospital 8.11.01.0

• NEW:
  • App display preview (extended data)

babsim.hospital 7.10.31.18

• NEW:
  • function ggVisualizeRkiExtended()

babsim.hospital 7.10.31.16

• NEW:
  • function ggVisualizeRkiAge()

babsim.hospital 7.10.31.14

• CHANGES:
  • deutschlandpara AM 20201031A-8

babsim.hospital 7.10.31.12

• NEW:
  • preparing new function ggVisualizeRkiAge()

babsim.hospital 7.10.31.10

• CHANGES:
  • nrwpara20201031A-8

babsim.hospital 7.10.31.8

• CHANGES:
  • bundeslanddata (replacement for sysdata.rda)
    • bundeslanddata uses ASCII characters only

babsim.hospital 7.10.31.6

• CHANGES:
  • icudata 20201031 update
  • obkpara 20201031-17 update
  • rkiToBabsimData() handles age and gender

babsim.hospital 7.10.31.4

• CHANGES:
  • under preparation: ggVisualizeRkiEvents()

babsim.hospital 7.10.31.2

• CHANGES:
  • nrwpara 20201030-26

babsim.hospital 7.10.31.0

• CHANGES:
  • obkpara20201031-23
  • rkidata

babsim.hospital 7.10.30.2

• CHANGES:
  • obkpara 30.10.2020

babsim.hospital 7.10.30.0

• CHANGES:
  • new bounds based on info from OBK

babsim.hospital 6.10.30.2

• CHANGES:
  • obkpara20201030-16

babsim.hospital 6.10.30.0

• CHANGES:
  • icudata 30.10.2020
  • rkidata 30.10.2020
  • compacted ‘babsim-vignette-RKI-DIVI.pdf’ via tools::compactPDF(gs_quality = “ebook”, paths = “/Users/bartz/workspace/babsim.hospital/vignettes”)
• BUGFIX:
  • getError() fixed and extended

babsim.hospital 5.10.29.18

• CHANGES:
  • koelnpara202010262 (required by vignette RKI/DIVI)

babsim.hospital 5.10.29.16

• CHANGES:
  • koelnpara20201029-19

babsim.hospital 5.10.29.14

• CHANGES:
  • koelnpara20201029-13

babsim.hospital 5.10.29.12

• CHANGES:
  • obkdata20201028-122

babsim.hospital 5.10.29.10

• CHANGES:
  • obkpara20201028-118
  • icudata 29.20.2020

babsim.hospital 5.10.29.8

• CHANGES:
  • deutschlandpara and
  • nrwpara combined TBB+FR

babsim.hospital 5.10.29.6

• CHANGES:
  • deutschlandpara20201028-113

babsim.hospital 5.10.29.4

• CHANGES:
  • nrwpara20201028-210

babsim.hospital 5.10.29.2

• CHANGES:
  • obkdata20201028-117
  • koelnpara20201028-114

babsim.hospital 5.10.29.0

• CHANGES:
  • rkidata 29.10.2020

babsim.hospital 5.10.28.26

• CHANGES:
  • deutschlandpara20201028-16

babsim.hospital 5.10.28.24

• CHANGES:
  • vignette updated

babsim.hospital 5.10.28.22

• CHANGES:
  • README.Rmd updated

babsim.hospital 5.10.28.20

• CHANGES:
  • app() does not show Bochum

babsim.hospital 5.10.28.18

• CHANGES:
  • nrwpara20201028-21

babsim.hospital 5.10.28.16

• CHANGES:
  • extendRkiData accepts R0 vector (start, end)
  • app implements R0 ranges, e.g., value = c(1.4, 1.5),

babsim.hospital 5.10.28.14

• CHANGES:
  • deutschlandpara 20201028-14

babsim.hospital 5.10.28.12

• CHANGES:
  • visualizeGraph() uses babsim.hospital::synthpara

babsim.hospital 5.10.28.10

• CHANGES:
  • deutschlandpara 20201028-12

babsim.hospital 5.10.28.8

• CHANGES:
  • extendRki() first ideas on how to use a dynamic R0 value (only comments)
  • app() shows Germany

babsim.hospital 5.10.28.6

• CHANGES:
  • deutschlandpara 20201027 (many short runs)

babsim.hospital 5.10.28.4

• CHANGES:
  • icudata (DIVI) 28.10.2020
  • rkidata 28.10.2020

babsim.hospital 5.10.28.2

• CHANGES:
  • owos version

babsim.hospital 5.10.28.0

• CHANGES:
  • merged owos+bab10 version

babsim.hospital 5.10.27.4

• CHANGES:
  • vignette updated/extended

babsim.hospital 5.10.27.2

• CHANGES:
  • code cleanup
  • icudata (DIVI) 27.20.2020

babsim.hospital 5.10.27.0

• CHANGES:
  • renamed babsim -> babsim.hospital
  • moved to OWOS

babsim.hospital 4.10.26.22

• CHANGES: cleanup

babsim.hospital 4.10.26.20

• CHANGES: vignette-rki-dvi sources fixed

babsim.hospital 4.10.26.18

• NEW: koelnpara202010262

babsim.hospital 4.10.26.16

• CHANGES:
  • runopt returns reslist

babsim.hospital 4.10.26.14

• CHANGES
  • koelnpara 20201026-12

babsim.hospital 4.10.26.12

• NEW
  • visualizeRkiEvents() can handle StartDate and Region

babsim.hospital 4.10.26.10

• NEW
  • visualizeRkiEvents() to visualize preprocessed RKI data

babsim.hospital 4.10.26.8

• CHANGES:
  • getError() reverted
  • icuWeight conf$w2 is a vector with default setting: w2 = c(1,10)

babsim.hospital 4.10.26.6

• CHANGES: getError() was rewritten

babsim.hospital 4.10.26.4

• CHANGES: icudata 26.10.2020

babsim.hospital 4.10.26.2

• CHANGES: rkidata 26.10.2020

babsim.hospital 4.10.26.0

• CHANGES: koelnpara 20201025 updated

babsim.hospital 4.10.25.10

• CHANGES: tests run faster

babsim.hospital 4.10.25.8

• NEW: updateParaFile()

babsim.hospital 4.10.25.6

• NEW:
• vignettes added

babsim.hospital 4.10.25.4

• NEW:
  • babsim.hospitalconstraints with constraintG()
  • icudata 25.20.2020
  • runopt() modified

babsim.hospital 4.10.25.2

• CHANGES:
  • rkidata 25.10.2020

babsim.hospital 4.10.24.8

• CHANGES: icudata 24.10.2020, bochumdata 20201023

babsim.hospital 4.10.24.6

• CHANGES:
  • deutschland, koeln, nrw, obk 202010231

babsim.hospital 4.10.24.4

• CHANGES:
  • bochum 2nd run

babsim.hospital 4.10.24.2

• CHANGES:
  • rkidata 24.10.2020

babsim.hospital 4.10.24.0

• NEW:
  • bochum

babsim.hospital 4.10.23.0

• CHANGES:
  • icu
  • rki

babsim.hospital 4.10.22.2

• CHANGES:
  • getBounds(): upper bound for x1 AmntDaysInfectedToHospital changed from 14 back to 21

babsim.hospital 4.10.22.0

• CHANGES:
  • koelnpara
  • nrwpara
  • obkpara
  • rkidata

babsim.hospital 4.10.21.4

• CHANGES:
  • rkidata 21.10.2020
  • obkpara20201020
  • nrwpara (1st run)
  • koelnpara (1st run)
  • resulceNames, resourceEval in babsim.hospitalrun

babsim.hospital 4.10.21.0

• BUGFIX:
  • funOptimizeSim(): Missing conf=conf argument added to call getError(res=res, conf=conf)

babsim.hospital 3.10.20.2

• CHANGES:
  • icudata updated 2020-10-20

babsim.hospital 3.10.20.0

• CHANGES:
  • getBounds(): upper bound for x1 AmntDaysInfectedToHospital changed from 21 to 14
  • English version

babsim.hospital 2.10.20.2

• CHANGES:
  • nrwpara 20.1.2020

babsim.hospital 2.10.20.0

• CHANGES:
  • rkidata 20.1.2020

babsim.hospital 2.10.19.8

• CHANGES:
  • icudata 19.10.2020

babsim.hospital 2.10.19.6

• CHANGES:
  • obkpara 19.10.2020
  • deutschlandpara 19.10.2020
  • rkidata 19.10.2020
  • Impressum

babsim.hospital 2.10.19.4

• CHANGES:
  • rkidata 19.10.2020

babsim.hospital 2.10.19.2

• CHANGES:
  • koelnpara 18.10.2020

babsim.hospital 2.10.19.0

• CHANGES:
  • Versionsnummern anhand der Tage

babsim.hospital 2.2.22

• CHANGES:
  • berlinpara, koelnpara, magdeburgpara, obkpara

babsim.hospital 2.2.20

• CHANGES:
  • nrwpara

babsim.hospital 2.2.18

• CHANGES:
  • dividata 18.10.2020 hinzugefuegt
  • farben angepasst
  • App aktualisiert

babsim.hospital 2.2.16

• CHANGES:
  • deutschlandpara update

babsim.hospital 2.2.14

• CHANGES:
  • nrwdata update

babsim.hospital 2.2.12

• CHANGES:
  • rkidata update

babsim.hospital 2.2.10

• CHANGES:
  • koelnpara update

babsim.hospital 2.2.8

• CHANGES:
  • icudata fixed

babsim.hospital 2.2.6

• CHANGES:
  • Added Berlin and Magdeburg

babsim.hospital 2.2.4

• CHANGES:
  • Naming

babsim.hospital 2.2.2

• CHANGES:
  • New file structure

babsim.hospital 2.2.0

• CHANGES:
  • getIcuBeds() erzeugt intensiveBed statt bed
  • getError() uses resource <- conf$ResourceEval
  • getDailyMaxResults() loscht nicht mehr die bed Kategorie
  • envToTibble() loscht nicht mehr die bed Kategorie
• NEW:
  • conf$ResourceEval spezifiziert die auszuwertenden Ressourcen, z.B. c(“intensiveBed”, “intensiveBedVentilation”) für DIVI

babsim.hospital 2.1.8

• CHANGES:
  • MC Plots added

babsim.hospital 2.1.6

• CHANGES:
  • Titel ergaenzt

babsim.hospital 2.1.4

• BUG FIXED
  • dailyMaxResults() and envToTibble() can handle empty resources

babsim.hospital 2.1.2

• CHANGES
  • Koeln data

babsim.hospital 2.1.0

• NEW
  • Shiny App
• CHANGES
  • ifelse fixed

babsim.hospital 2.0.6

• CHANGES
  • data bug fixed in extendRki()

babsim.hospital 2.0.4

• CHANGES
  • envToTibble() uses fieldEvent information

babsim.hospital 2.0.2

• NEW
  • envToTibble()
• CHANGES
  • Wahrscheinlichkeiten angepasst
  • getDailyMaxResults: bed labels changed * no bed, only intensiveBed and intensiveBedVentilation

babsim.hospital 1.8.2

• CHANGES
  • Fixed S4 class problem

babsim.hospital 1.8.0

• NEW
  • getMatrixD()
  • plotting results

babsim.hospital 1.7.8

• CHANGES
  • Data importing and archiving strategy

babsim.hospital 1.7.6

• CHANGES
  • Consistent data handling via conf

babsim.hospital 1.7.4

• NEW:
  • icu20201001
  • rki20201001

babsim.hospital 1.7.2

• CHANGES:
  • babsim.hospitalHospital(): sim.repeats bug fix

babsim.hospital 1.7.0

• CHANGES:
  • babsim.hospitalHospital(): new parallel / sequential handling
• NEW:
  • constraint handling (experimental), see runQuickConstraints.R

babsim.hospital 1.6.4

• CHANGES:
  • risk factor B adapted

babsim.hospital 1.6.2

• CHANGES:
  • updateMatrixP(): value check for risk multiplier

babsim.hospital 1.6.0

• CHANGES:
  • train/test data
  • weighted error
  • test script runICU100TrainTest.R

babsim.hospital 1.5.6

• CHANGES:
  • parallel option works again

babsim.hospital 1.5.4

• CHANGES
  • otimization interface can be used with SPOT

babsim.hospital 1.5.2

• NEW
  • risk attributes are used to update probabilities

babsim.hospital 1.5.0

• NEW
  • risk attributes implemented

babsim.hospital 1.4.2

Merged Versions TBB+FR

babsim.hospital 1.4.0

Testing, not stable version.

• CHANGES
  • new traj hadling in babsim.hospitalHospital()

babsim.hospital 1.3.10

• NEW
  • getRkiData() preprocesses raw RKI data
  • getRkiRisk() determines risk for RKI patients based on age and gender

babsim.hospital 1.3.8

• CHANGES
  • trajList is generated from with babsim.hospitalHospital()

babsim.hospital 1.3.6

• NEW
  • Parameter extended: risk factors are included

babsim.hospital 1.3.4

• NEW
  • Preparing risk calculations for RKI data

babsim.hospital 1.3.2

• CHANGES
  • getRealBeds() uses resource=c(“bed”, “intensiveBed”, “intensiveBedVentilation”) as default parameter

babsim.hospital 1.3.0

• NEW:
  • data structures:
  1. simData
  2. fieldData

babsim.hospital 1.2.22

• NEW:
  • getConfFromData()

babsim.hospital 1.2.20

• CHANGES:
  • ICUBeds20200822 geloescht

babsim.hospital 1.2.18

• NEW:
  • Aktualisierte RKI/DIVI Daten

babsim.hospital 1.2.16

• CHANGES:
  • getDailyMaxResults() uses conf list

babsim.hospital 1.2.14

• CHANGES:
  • getRealBeds() handles getIcuBeds()

babsim.hospital 1.2.12

• CHANGES:
  • getError() handles getIcuError()
  • getIcuError() deleted

babsim.hospital 1.2.10

• CHANGES:
  • getError() simplified

babsim.hospital 1.2.8

• CHANGES:
  • getRealBedsOLD() removed
  • simulateHospital() removed, use the following code instead: x <- rep(0.2,30) para <- mapXToPara(x) conf <- babsim.hospitalToolsConf() res <- modelResultHospital(para=para, conf=conf) getError(res) p <- plotDailyMaxResults(res) print(p)

babsim.hospital 1.2.6

• NEWS:
  • getBounds()
  • Sim100 data
• CHANGES
  • Default values of x15 and x19 modified
  • Default values of DurationInfected2Hospital (shift = 1) changed

babsim.hospital 1.2.4

• NEWS:
  • mapXToPara (replaces simulateHospital)
  • synthSimCovid20201130: synthetic data
  • synthBeds20201130: synthetic data
• CHANGES:
  • babsim.hospitalToolsConf implements
    • simulationData = babsim.hospital::dataCovidBeds20200624,
    • fieldData = babsim.hospital::GABeds220200624

babsim.hospital 1.2.3*

• CHANGES:
  • babsim.hospitalToolsConf has the following additional list entries: * logLevel (int) 0 = no logging, 1 = logging. Default: 0. * maxCapacity (num) Maximum capacity used for babsim.hospitalHospital resources. Default: 1e6. * dataset (chr) Can be “GA” or “ICU”. Default: “GA”. * infectionDates List with the following entries: * StartDate (chr) Start date of the infection data, first day. Default: “2020-03-03” * EndDate (chr) End date of the infection data, last day. Default: “2020-06-24” * bedDates List with the following entries: * StartDate (chr) Start date of the bed data, first day. Default: “2020-03-03” * EndDate (chr) End date of the bed data, last day. Default: “2020-06-24” * predictionDates List with the following entries: * StartDate (chr) Start date of the prediction interval, first day. Default: “2020-03-03” * EndDate (chr) End date of the prediction interval, last day. Default: “2020-06-24”

babsim.hospital 1.2.1

• CHANGES:
  • Aktualisierung der Ergebnisdateien der Simulationslaeufe
  • bart20h.Rmd aktualisiert

babsim.hospital 1.2.0

• CHANGES:
  • Tests fur getError und getIcuError hinzugefuegt

babsim.hospital 1.1.10

• CHANGES:
  • getDailyMaxResults errors fixed (simStartDay anstelle von StartDay)
  • test.getDailyMaxResults hinzugefuegt fuer GA und ICU

babsim.hospital 1.1.8

• CHANGES
  • getIcuBeds benötigt kein Start- und EndDate als eigenstaendige Parameter
  • getRealBeds erzeugt time Information, die mit 0 (und nicht, wie vorher, bei 1) anfaengt
  • getIcuBeds erzeugt time Information, die mit 0 (und nicht, wie vorher, bei 1) anfaengt
  • checkSimPara verwendet minDays = 1e-6 statt minDays = 0
• NEWS:
  • test.bed testet ICU Betten
• ERRORS:
  • Das R-Skript source(“runICU1000NotParallel.R”) (Verzeichnis babsim.hospital/bart20h/Runs.d) stuerzt mit der folgenden Fehlermeldung ab: Error: ‘patient112184’ at 107.42 in [Branch]->Timeout->[Release]: missing value (NA or NaN returned)
    In addition: Warning message: qgamma(u, shape = shape, rate = rate) : NaNs produced

babsim.hospital 1.1.4

• CHANGES
  • babsim.hospitalHospitalControl renamed to babsim.hospitalHospitalPara
  • babsim.hospitalHospitalPara uses minVal instead of 0.0 to avoid division by zero
  • ICU Betten verwenden Date Format: ICUBeds20200822$date <- as.Date(ICUBeds20200822)
  • rkiTobabsim.hospitalArrivals uses time label: return(data.frame(time = getArrivalTimes( rkiAgg\(Freq ))) instead return(data.frame(getArrivalTimes( rkiAgg\)Freq )))
  • conf$maxCapacity = 1e6 (increased from 1e4)
  • getArrivalTimes verwendet RNGkind(“Wich”)
  • rtgamma verwendet RNGkind(“Wich”)
• NEW:
  • test.bed Bettendaten werden getestet
  • test.trajectories hat einen Test fuer riesige Datenmengen (bundesweite COVID-19 Faelle)
• ERRORS:
  • Bei grossen Datensaetzen (> 200.000): arrival Times nicht eindeutig, z.B.: dim(arrivalTimes) ergibt 230187 aber dim(unique(arrivalTimes)) ergibt 230186. Daher : RNGkind(“Wich”) . sum(duplicated(runif(1e8))) >0, aber RNGkind(“Wich”) sum(duplicated(runif(1e8))) == 0. Siehe: https://stackoverflow.com/questions/51425656/why-does-runif-have-less-unique-values-than-rnorm

babsim.hospital 1.1.2

• CHANGES:
  • New: arrivalTimes <- c(arrivalTimes, runif(xDaily[i],0,1) + (i -1) )
  • Old: arrivalTimes <- c(arrivalTimes, runif(xDaily[i],0,1) + i )
• ERRORS:
  • source(“runGA1000.R”) ergibt (packageVersion(“SPOT”) ‘2.0.62’):
  • Warnmeldungen: 1: In duplicateAndReplicateHandling(xnew, x, lower, upper, control) : SPOT created a duplicated solution. This can be due to early convergence or bad configuration. Duplicate is replaced by random solution. 2: In duplicateAndReplicateHandling(xnew, x, lower, upper, control) : SPOT created a duplicated solution. This can be due to early convergence or bad configuration. Duplicate is replaced by random solution. 3: In duplicateAndReplicateHandling(xnew, x, lower, upper, control) : SPOT created a duplicated solution. This can be due to early convergence or bad configuration. Duplicate is replaced by random solution. 4: In duplicateAndReplicateHandling(xnew, x, lower, upper, control) : SPOT created a duplicated solution. This can be due to early convergence or bad configuration. Duplicate is replaced by random solution.
• source(“runICU1000.R”) ergibt:
  • Error in UseMethod(“get_mon_resources”, unlist(list(.envs))[[1]]) : no applicable method for ‘get_mon_resources’ applied to an object of class “character” In addition: Warning message: In mclapply(1:simRepeats, function(i) { : scheduled core 1 encountered error in user code, all values of the job will be affected

babsim.hospital 1.1.0

• CHANGES:
  • babsim.hospitalHospitalTrajectories() benutzt getDecision()

babsim.hospital 1.0.46

• COMMENT:
  • ICU data does crash
• CHANGES:
  • getDailyMaxResults() clean up
• NEW:
  • getDecision() to prepare babsim.hospital 1.1.0
  • more test functions

babsim.hospital 1.0.44

• NEW:
  • checkSimPara()
  • ensureRangeOpen()
  • weitere Tests in test.tools
• CHANGES:
  • maxCapacity wird in conf und nicht mehr in para gespeichert
  • modelResultHospital korrigiert para Werte mittels checkSimPara

babsim.hospital 1.0.42

• NEW:
  • data GABeds20200624
  • data dataICUBeds20200821
  • function getRealBedsOLD (compatibility)
  • test rtgamma

CHANGES function getIcuBeds simplified * function getRealBeds simplified

babsim.hospital 1.0.40

• CHANGES:
  • modelResultHospital uses rkiTobabsim.hospitalArrivals
• NEW
  • function rkiTobabsim.hospitalArrivals

babsim.hospital 1.0.38

• CHANGES:
  • rtgamma implements a shift 8Translation) parameter and alpha upper quantile of gamma distribution. All values above alpha are truncated.

babsim.hospital 1.0.36

• NEW:
  • babsim.hospitalToolsConf to configure conf
• CHANGES:
  • babsim.hospitalHospitalPara list speichert GammaShapeParameter
  • funOptimizeSim erzeugt para mit GammaShapeParameter
  • Durchgaengig conf und para

babsim.hospital 1.0.34

• NEWS:
  • resRki data added
  • Abstract vorbereitet
  • babsim.hospital benutzt trunkierte Gamma Verteilung mit 0.95 Grenze
  • experiment runSPOTICU1000TruncDist

babsim.hospital 1.0.32

• CHANGES: gamma dist

babsim.hospital 1.0.30

• CHANGES:
  • funWrapOptimize: new parameter

babsim.hospital 1.0.28

• NEW:
  • getIcuBeds()
  • getDailyMaxResults() has new parameter ICU

babsim.hospital 1.0.26

• NEW:
  • readCsvRecursively()
  • getDiviData()
  • Data: icu20200822 und rki 20200822

babsim.hospital 1.0.24

• Cleanup:
  • babsim.hospitalHospital does not use argument GammaShapeParameter
  • babsim.hospitalHospitalTrajectories does not use arguments arrivalTimes and simRepeats
  • babsim.hospitalHospitalTrajectories used truncated Gamma dist. (rtgamma) Max. val = alpha x mean value
  • DurationInfected2Hospital hat eine untere Grenze (min = 2 Tage)
  • Ergebnisse von runSpot500b hinzugefügt

babsim.hospital 1.0.22

• Grundgerüst des Reports bart20h erstellt.

babsim.hospital 1.0.20

• Report bart20h bis SPOT Aufruf (Optimierung)

babsim.hospital 1.0.18

• new: postprocessEnvs()

babsim.hospital 1.0.16:

• new: Dokumentation und Tests funktionieren mit babsim.hospitalHospitalTrajectories()

babsim.hospital 1.0.14

• new: babsim.hospitalHospitalTrajectories

babsim.hospital 1.0.12

• Last version before “cleanup”

babsim.hospital 1.0.10

• New state “healthy” added
• Documentation and new examples

babsim.hospital 1.0.8

• Only cleanup. Added res250.rda

babsim.hospital 1.0.7

• new option parallel in babsim.hospitalHospitalPara

babsim.hospital 1.0.6

• new data dataCovidBeds20200624

babsim.hospital 1.0.4

• SPOT optimization as an example

babsim.hospital 1.0.0:

• Initial version