NEWS

Version 1.1.0 (2019/11/..)

* Update dependencies


Version 1.0.9 (2019/10/30)

* Update dependencies
* Support single Gender and DateOfDiagnosisYear data


Version 1.0.8 (2019/09/20)

* HIV Model: Initial implementation
* HIV Model: Implement UI for diagnosis rate modelling


Version 1.0.7 (2019/05/31)

* RD: Adjust VarT and Tf by plus one


Version 1.0.6 (2019/05/23)

* Do not overwrite Weight for VarX equal 0


Version 1.0.5 (2019/05/20)

* RD: Set MissingData to FALSE for VarX equal 0
* RD: Estimate the number of rows in the RD intermediate report based on
  ggplot_built object
* RD: Let GetRDPlots return ggplot_built object instead of ggplot object


Version 1.0.4 (2019/05/20)

* RD: Droplevels of Stratum after filter in RD adjustments
* Misc: Implement matching original columns using adist function
* RD: In RD adjustment replace infinite variance by 0


Version 1.0.3 (2019/05/18)

* Misc: Update dependencies


Version 1.0.2 (2019/02/02)

* Report: Fix creating plots where number of categories is more than 8.
* Report: Fix missing "IsEmptyString" function on Windows.
* Misc: Update dependencies


Version 1.0.1 (2019/01/19)

* Misc: Update manual
* Misc: Update dependencies
* Misc: Build using R 3.5.2


Version 1.0.0 (2018/11/30)
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* Misc: Invalidate data when risk origing grouping changed
* Summary: Add plot of proportion of missing in key variables
* Misc: Show number of instances open


Version 0.11.0 (2018/11/24)
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* MI: Rename tabs of intermediate results
* Main Report: add ECDC logo to pdf output
* Misc: Seed for random number generator for imputations can be set
* Misc: Make filtering on notification quarter effective
* Manual: Draft manual added as pdf file
* Adjustments: Fix infinity in LogitVarX for jomo adjustment
* Summary: Set min/max for filters based on input data
* Main Report: Allow cancelling creating the report
* RD adjustments: Update reporting delays adjustments to support missing
  DiagnosisTime or NotificationTime
* RD adjustments: Title of the parameters dialog updated
* Misc: Enforce no missings in DateOfDiagnosisYear
* Summary: Show message when start notification quarter is before start diagnosis
  year
* Misc: Support gender "Other"
* Misc: Updates to formatting and user experience


Version 0.10.0 (2018/11/11)
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* Input data: custom mapping module for GroupedRegionOfOrigin implemented
* Input data: additional country codes incorporated
* Adjustments: Remodel adjustment specification control to have fixed order
* Main Report: Rename "confidence interval" to "inter-quartile range"
* Main Report: Change and fix column names of report tables to include proper
  unit indicator
* Input data: Fix typo in "Assignment of input..."
* Reporting Delays: Initial implementation of univariate analysis
* Reporting Delays: Initial implementation of modelling time trend
* Intermediate report for RD: fixes in plotting stratified data
* Misc: Add "reportingDelaysRegressionScript.R" in inst folder
* Input data summary: titles of plots adjusted, comments added. PLot for trends
  in reporting delay for last 5 years removed. Histogram of data below filter
  added.
* Misc: Initial implementation of application state saving
* Adjustments: Allow filtering adjusted data
* Misc: Implement opening a new window
* Intermediate reports for MI: Distributions of imputed data added
* Summary: Initialize filter to min and max of Diagnosis Year on data load
* Summary: Clear adjusted data on filter change if applicable
* Main page: Implement draft dialog for setting random seed
* Main Report: Display detailed information on performed adjustments and input
  data file name
* Diagnostic reports: Display tabbed plots
* Misc: Header styling adjusted according to ECDC request
* Main Report: Latex figures naming adjusted to be more intuitive
* RD adjustments: Remove records with NotificationTime < DiagnosisTime
* Summary page: Remove records with NotificationTime < DiagnosisTime
* RD: Ensure weight is 1 if after fit it is NA or infinite
* MICE: Default degree of freedom set to 4
* Input data upload: Filter redundant columns from the input data.


Version 0.9.11 (2018/09/05)
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* General: initial implementation of Google Analytics data collection
* Adjustments: parallel execution disabled for now until it is better tested
* Main report: show results by Migrant
* Main report: pre-render plots for faster downloading
* Main report: adjust total/overall columns/rows in the tables
* Main report: increase quality of plots in html output (switch from png to svg)
* Main report: fix printing "mu" (micro) symbol
* Main report: print estimated unreported and total with confidence interval
  bounds


Version 0.9.10 (2018/08/29)
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* Do not filter records in RD adjustment.
* New naming convention for migrant variables.
* Implement RD missingness plot in the summary page.
* Implement adaptive "badCategories" detection mechanism in the main report.
* Implement "Download as Latex" option for the main report.
* Completely redesigned Markdown source report with caching of tables and plots.
* Redesigned output report with data presented per Gender and Transmission.
* Option to include confidence intervals in the report plots.


Version 0.9.9 (2018/07/25)
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* Default selected years in summary page are 2000 and current year.
* Parameter dialogs can be closed only by clicking buttons.
* Adjustments renamed.
* Maximum number of mice chains increased to 5. Text added in the intermediate
  report.
* Interface and processing of grouping of FullMigr implemented.


Version 0.9.8 (2018/07/23)
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* Summary page filtering reimplemented with plots supporting no data and error
  messages removed.
* FullMigr variable implemented in the pre-processing.


Version 0.9.7 (2018/07/23)
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* Cancellable adjustment runs implemented.
* Summary data filtering implemented.
* Diagnostic plots for mice adjustments implemented.
* Notification end quarter parameter for reporting delays is split into year
  and quarter.
* Placeholder page for the manual created.
* The dependencies of the tool are updated to their latest versions and
  tested with the latest R version 3.5.1.


Version 0.9.6 (2018/04/22)
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* Reporting delays table in the main report to be sorted by year of diagnosis
  and include totals.
* jomo imputations have only 10 burn-in samples for the imputations, but full
  number of burn-in samples for the diagnosis plots.


Version 0.9.5 (2018/04/20)
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* Missing data summary plot stratified by gender.
* Fix in the main report glm fit for unsmoothed plots - non-conformable arrays.
* Reporting delays table added to the main report if only RD performed.
* Adjusted data section title in the main report includes performed adjustment
  types.
* RD adjustment returns reporting delays distributions as artifact.
* Output page contains download links to the final data and the reporting delays
  distributions (if RD performed).
* Output page contains table showing the adjusted data.


Version 0.9.4 (2018/04/19)
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* Main report parameters split into two - count correction and smoothing.
* Show reporting delays diagnostic plot under caption.
* Remove redundant "Parameters" member of data list.
* jomo intermediate report updated to have plots ordered alphabetically.
* Add table to RD intermediate report.
* Styling of tables in intermediate reports made consistent with the main report.
* Allow saving data as R rds file.
* Completely reimplemented main report.
* Allow running the main report only with RD adjustment carried out.
* Handle 100% missing CD4 in the main report.
* Allow any count of transmission categories in the main report.


Version 0.9.3 (2018/04/18)
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* Width of navigation panel reduced to 180px in order to maximize content area.
* Regression "missing success and warning icons in the mapping overview" fixed.
* Regression "missing input data table in the summary page" fixed.
* Plots have all years printed.
* Plots start from 0.
* Upper bound for the main report plots fixed.
* Adjusted styling of input data table in the summary page.
* Introduction text added.
* Main report adjusted to support reporting delays count adjustment and
  smoothing.


Version 0.9.2 (2018/04/17)
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* Stratified RD intermediate plots styling and height adjusted.
* Add execution timestamp to every adjustment.
* Move download links to page "Outputs". Download file names adjusted to include
  adjustment order, adjustment name and adjustment execution end time.
* Progress of attribute mapping and pre-processing.
* Single imputation for Gender always applied.
* Header adjusted and intro page removed.


Version 0.9.1 (2018/04/14)
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* "Multiple Imputations" report name changed to "Main Report". Generalization
  of the report to handle all possible scenarios and ECDC styling applied.
* Remove dependency on package "coda"


Version 0.9.0 (2018/04/10)
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* Pages "Introductions" and "Outputs" added.
* Run logs of adjustments formatting updated.
* Reporting Delays estimated total counts of cases plot adjusted visually.
* "Diagnostic run" option removed.


Version 0.8.12 (2018/03/30)
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* Bug in creating final report when Reporting Delays was run - nsdf was NULL.
* Adjustments for making it compatible with ShinyApps.io.


Version 0.8.11 (2018/03/04)
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* Allow providing default values for non-mapped attributes.
* Read all text data as character and convert to proper column types afterwards.
* Hide summary plots and tables if input data is not uploaded.
* Compute all missingness pattern details using own code, not port from VIM
  package.
* Recreate missingness pattern using ggplot2.
* Align all summary plots with ECDC house style (colours).


Version 0.8.10 (2018/01/24)
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* Fix missing template for Word report.
* Labels for tables in Multiple Imputations report updated.


Version 0.8.9 (2018/01/24)
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* Multiple Imputations report updated.


Version 0.8.8 (2018/01/23)
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* Multiple Imputations report updated to have non-fixed column names in tables
  (support for dummy data set).


Version 0.8.7 (2018/01/22)
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* Reporting delays adjustment returns proper data with columns "VarT", "Stratum"
  and "Weight" appended.
* MI report, figures 6 and 7 have y axis title changed to "Median CD4 cell count
  (cells/microL)".
* MI (mice) and MI (jomo) parameter nsdf specified as a slider input with
  minimum 3 and maximum 5.
* MI (mice) and MI (jomo) adjustments run in parallel fixed - extra functions
  exported to computation nodes.
* MI (mice) implements same checks on data the jomo version does.
* Experimental support for uploading zipped csv, txt, xls and xlsx files.


Version 0.8.6 (2018/01/21)
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* Reporting delays adjustment corrected and generalized.
* Allow exporting intermediate data as stata file.


Version 0.8.5 (2018/01/18)
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* Multiple imputations (jomo) adjustment filters out covariates columns if less
  than two distinct values are present in those columns.
* Multiple imputations (jomo) adjustment filters out outcome columns if they
  contain only NAs.
* Intermediate reports headers styling updated.
* Intermediate report for "Multiple imputations (jomo)" shows information on
  covariate and imputed columns filtered out due to data not sufficient.


Version 0.8.4 (2018/01/18)
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* All data sets tested against every adjustment.
* Reporting delays adjustment updated to support empty data sets (ES) and
  dealing with missing data (SE).
* Plots for reporting delay densities ("Summary" page) are implemented using
  ggplot2. This fixes error "need at least 2 points to select a bandwidth
  automatically" on ES data.
* Mean delay plot ("Summary" page) is produced with NotificationTime == NA
  filtered out. This fixes error "'delta' must be finite and > 0" on ES and SE
   data.
* "Summary" page plots are not printed if the input data does not support them.
* "Summary" page includes pre-processed input data table.
* Attribute "FirstCD4Count" automatically mapped to "cd4_num" if such column
  exists in the provided input data.


Version 0.8.3 (2018/01/15)
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* Variable "Stage" removed from the attributes mapping.
* Fixed printing stratified plots in the Reporting Delays adjustment artifacts
  report.
* Reporting Delays adjustment updated to support input data after Multiple
  Imputations.
* Specify stratifaction columns for the reporting delay adjustment by checkboxes
  (columns "Gender", "Transmission" and "Migr" allowed for selection).


Version 0.8.2 (2018/01/11)
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* Support data with only one value for AIDS column
  (function PreProcessInputData adjusted).
* Support data with NotificationTime equal DiagnosisTime
  (function GetDataSummaryArtifacts adjusted)


Version 0.8.1 (2018/01/11)
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* Updated reporting delay adjustment to support stratification (optional).
* Input data value check moved to page "Data upload".
* Interface of "Adjustments" and "Reports" pages updated to new design (headers
  background white, collapsible boxes, inactive elements not visible).
* Disable adjustment runs without input data uploaded.
* Multiple imputations report adjusted with dynamic limits for CD4 plots and
  order of Transmission labels corrected.
* Increase maximum file upload size to 70MB.
* Fix report "Multiple Imputations" - show proper year in Table 1 and 3 instead
  of index.


Version 0.8.0 (2018/01/08)
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* Issue #23: Argument "endQrt" added to reporting delays adjustment.
* Issue #24: Stratified reporting delay adjustment added.
* Issue #25: Displaying reporting delay summary.


Version 0.7.8 (2018/01/04)
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* Updated functionality and styling of page "Data upload"
* Reporting delays adjustment script updated to the version submitted by Magda
  on 2018/01/03.


Version 0.7.7 (2017/12/21)
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* Fixing output of the multiple imputations adjustment using mice package to
  make it compatible with the multiple imputations report.


Version 0.7.6 (2017/12/12)
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* Input data mapping to required columns
* Intermediate reports
* Reporting delays adjustment (initial implementation)
* Multiple imputations adjustment using mice package


Version 0.7.5 (2017/12/03)
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* Fixed path to diagnosis reports


Version 0.7.4
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* Framework for running diagnosis implemented


Version 0.7.3
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* Styling in reports adjusted


Version 0.7.2
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* Missingness plot added.
* Fixed plots 6 and 7 in the standard report.
* Better styling of tables in the report.


Version 0.7.1
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* First release of deployment procedure.