v 2.0.0 (30/12/2019)
Download links:
- 64-bit BCoDE_v2.0.0.zip, 69MB
Note: This is general public deployment version to be released on ECDC website.
Software is digitally signed with EV Code Signing certificate issued by Certum.pl to NextPage Software.
The executable has been tested against viruses: https://www.virustotal.com/gui/file/a51a93785fa021c7b115fd15acc9af61fe2497024ab6b0dc135dc5334563c24b/detection
v 1.7.0 (15/02/2019)
Download links:
- 32-bit BCoDE_190215_v1.7.0_x86.zip, 45.7MB
- 64-bit BCoDE_190215_v1.7.0_x64.zip, 55MB
Note: This is general public deployment version to be released on ECDC website.
Software is digitally signed with EV Code Signing certificate issued by Certum.pl to NextPage Software
v 1.5.1 (30/01/2018)
Download links:
- 32-bit BCoDE_180130_v1.5.1_x86.zip, 41.5MB
- 64-bit BCoDE_180130_v1.5.1_x64.zip, 49.9MB
Changed:
- "Model Maintenance tool" renamed to "Model Create tool".
Fixed ("Model Create tool"):
- Health outcomes were disappearing from the outcome tree when re-rendering.
v 1.5.0 (03/01/2018)
Download links:
- 32-bit BCoDE_180103_v1.5.0_x86.zip, 42MB
- 64-bit BCoDE_180103_v1.5.0_x64.zip, 51MB
New:
- Initial integration of "Model Maintenance tool" in the BCoDE toolkit (menu Tools -> "Open Model Maintenance tool").
- Totals for the aggregated results view computed.
Changed:
- Upgrade to Qt framework 5.10. This is latest release of Qt C++ framework providing:
a) better performance (15% calculation time reduction)
b) more recent platform for future updates. Previously used version 4.8.7 of the Qt framework is deprecated and not maintained any more.
c) support for high DPI screens. Previous versions of the BCoDE toolkit have been rendered incorrectly (tiny text) on modern, high-resolution screens with high pixel density.
d) 32 and 64 bit builds produced of the toolkit produced with the latest version of Microsoft Visual C++ compiler (msvc2017).
- Switching from WebKit to WebEngine web browser (user interface is implemented as web page with JavaScript).
- A complete rewrite of the bridge between C++ engine and JavaScript user interface.
- A substantial update of the JavaScript user interface code for easier maintenance. Code has been reviewed and modularized.
- List of available disease models is no longer hard-coded in the interface, but provided by the C++ engine.
- Minor update of the visual style (fonts, colours).
v 1.4.11 (28/09/2017)
Changed:
- Export of aggregated results table to Excel includes only one row (2.5%, 50%, 97.5%) per model.
Fixed:
- Disease models "Klebsiella pneumoniae 3GCRKP SSI" and "Klebsiella pneumoniae 3GCRKP OTH" where called "Klebsiella pneumoniae CRKP SSI" and "Klebsiella pneumoniae CRKP OTH" respectively.
v 1.4.10 (27/09/2017)
Updated:
- Improved performance of saving models to Excel.
v 1.4.9 (20/09/2017)
Fixed:
- Tuberculosis disease models were not recognized by the toolkit.
v 1.4.8 (19/09/2017)
Fixed:
- 3GCRKP SSI and OTH are available in the "Select disease" but are called "CRKP SSI" and "CRKP OTH" in the "Models" once they're created.
- ColRKP BSI duration of complicated is slightly wrong and should be aligned with uncomplicated.
- CREC BSI case fatality proportio, parameter says "RandUniform(.2, 0.513)" without the "0" before the ".2".
Updated:
- CRPA OTH (all 3 models) – the upper bound duration is 19 days (not 18).
v 1.4.7 (18/09/2017)
New:
- Columns "Case per year", "Incidence per 100,000", "Deaths per year", "Mortality per 100,000"
added to "Aggregated results table".
v 1.4.6 (17/09/2017)
New:
Tuberculosis models implemented:
- Pulmonary tuberculosis (DS, mono-/poly resistant, MDR, XDR)
- Low-mortality extra-pulmonary tuberculosis (DS, mono-/poly resistant, MDR, XDR)
- High-mortality extra-pulmonary tuberculosis (DS, mono-/poly resistant, MDR, XDR)
v 1.4.5 (29/08/2017)
Updated:
- Liechtenstein country removed from the tool and data sets.
v 1.4.4 (28/08/2017)
New:
Burden of antimicrobial resistance models implemented (BSI, RESP, SSI, UTI, OTH variants):
- Escherichia coli (CREC, ColREC)
- Acinetobacter spp. (MDRACI, CRACI, ColRACI)
- Pseudomonas aeruginosa (MDRPA, CRPA, ColRPA)
- Staphylococcus aureus (MRSA)
- Enterococcus faecalis and E. faecium (VRE)
- Streptococcus pneumoniae (PRSP, PMRSP)
v 1.4.3 (17/08/2017)
New:
Burden of antimicrobial resistance models implemented (BSI, RESP, SSI, UTI, OTH variants):
- Baseline model
- Klebsiella pneumoniae (3GCRKP, CRKP, ColRKP)
- Escherichia coli (3GCREC)
v 1.4.2 (06/04/2017)
Updated:
Healthcare-associated P-BSI Burden of HAIs, transition gamma changed to RandUniform(0.198, 0.734).
v 1.4.1 (28/03/2017)
New:
Healthcare-associated P-BSI Burden of HAIs
v 1.4 (05/10/2016) (update 1)
Changed:
- Page "What's new" updated.
v 1.4 (04/10/2016)
Changed:
- Healthcare-associated pneumonia (HAP) beta transition changed to RandPert(0.001, 0.035, 0.09). Disease report updated accordingly.
v 1.3 (13/09/2016) (update 1)
Changed:
- Tutorial includes a reference to the Normal distribution.
v 1.3 (12/09/2016)
Changed:
- Chlamydia disease report adjusted per email (Alessandro, 30/08/2016)
- Mumps beta transition adjusted per email (Alessandro, 30/08/2016)
- HAP beta transition adjusted per email (Alessandro, 30/08/2016)
- Default value of time discounting set to 0
- Heading of the 'Help' menu changed the to 'About'.
- Life expectancy table updated per email (Alessandro, 30/08/2016)
- Normal distibution implemented with input parameters mu (mean) and sigma (standard deviation).
Can be used by specifying "RandNormal" in the tool.
v 1.2 (01/03/2016) (update 2)
Changed:
- Chlamydia Women OT: Ectopic pregnancy and Tubal infertility connected to Asymptomatic infection as well
v 1.2 (29/02/2016) (update 1)
Changed:
- Tutorial includes now text about possibility to paste data from Excel "as Uniform" or "as Pert" distribution.
v 1.2 (27/02/2016)
New:
- Option to paste data into table as "Constant", "RandUniform", or "RandPert".
- Separate entries in "Help" menu for descriptions of the toolkit, the 3rd party libraries and changelog.
- Support for input data (for instance demographic) including "Newborn" age category.
Changed:
- Disease report for "HAI-CDI" updated.
- Disease report and transition "gamma" for "HA Neonatal sepsis" updated.
- Logo changed to high resolution.
- Acknowledgements added.
- Demographic data updated to EU/EEA 2014 data from Eurostat.
v 1.1 (30/12/2015)
Fixed:
- The toolkit was not supporting Windows XP. Now it is.
- On certain instances of Windows the program logo was not displayed. Now veryfied to work on Windows XP, Windows 7 and Windows 10.
v 1.0 (21/12/2015) (update 2)
Changed:
- Disease report of "UTI" updated with content of "DR_UTI_for Daniel.docx"
v 1.0 (18/12/2015) (update 1)
Changed:
- Menu "Help" removed. "About" button placed instead.
- Citation section added in "About" page.
- Reference to publication "Assessing disability weights..." added to "About" page.
- All disease reports include title "Disability Weight (DW) (Haagsma, 2015)" in Table 2 and reference "Haagsma JA, Maertens de Noordhout C..." in the references sections.
- Disease reports of Diphtheria, Syphilis and Tuberculosis adjusted by removing paragraphs with internal discussions.
- Disease report of HAP updated with content of file "HAP for Daniel.docx". Transition "beta" changed to "RandUniform(0.001, 0.09)".
- New logo placed on the main page.
- Final link added to "About" page.
- Typos in "About" page fixed.
v 1.0 (13/12/2015)
Changed:
- HAI reports updated
- "Model parameters" changed to "Incidence data"
v 0.992 (03/11/2015)
Changed:
- Names of "healthcare-associated" models adjusted according to email of Alessandro (03/11/2015) (this includes changes to the disease reports).
- "Create models" view: long names of diseases are displayed in tooltips.
- Size of file "BCoDE.exe" reduced by 0.3MB due to compression of tutorial images (no loss of quality).
v 0.991 (01/11/2015)
Fixed:
- Dynamic walkthrough: element not properly exposed in step 19
Changed:
- Flowchart: rewritten and expanded slides on "Detailed results", "Aggregated results" and "Exporting results" (refreshed images)
- Dynamic walkthrough: All steps for "View aggregated results" redone to reflect current design of the view and the displayed results.
v 0.990 (29/10/2015)
Changed:
- "About" dialog:
a) First sentence changed to the first paragraph of "BCoDE toolkit_TEXT FOR WEBSITE_AC_DL.docx"
b) Affiliations with abbreviations added
c) Disclaimer added
- Tutorial flow chart:
a) corrected assignment of content to buttons
- Dynamic walkthrough:
a) rewritten transitioning between steps
b) buttons for "previous", "next", "close" moved to the bottom of the walkthrough dialog
- Command "Import reference data" removed.
Comments received on 23/10/2015
- Comments from "BCoDE" toolkit tutorial POP-UP comments.docx" handled
v 0.132 (09/10/2015)
Changed:
- Aggregated results per age/sex category: denominator computed as average also for total population.
v 0.131 (08/10/2015)
Changed:
- Aggregated view: detailed results section title changed from "Results details" to "Detailed results of total DALYs".
- Aggregated results per age/sex category: denominator computed as average population.
v 0.130 (07/10/2015)
Comments received on 02/10/2015
I`ve reviewed all the models and here are some final comments:
1. (checked, no need to fix) Giardiasis: Fatal cases in the model is set to 100%. It should actually be set to 0.014%. (the age re-distribution still applies)
2. (checked, no need to fix) Under your point 8. Toxoplasmosis: in the "Disease report" tab, Table 2, "Acquired". Please add a row: 1st column "Permanent disability due to chorioretinitis", 2nd column "0.015 (0.011-0.019)", 3rd column "Conjunctivitis without corneal scar", 4th column "rem life exp.", 5th column "Kemmeren, 2006". – this was not done, please implement.
3. (done) P-BSI: "Disease report" tab, Table 2, last line ("Renal failure and renal replacement therapy following severe sepsis or septic shock"): can you please invert the 2 numbers in the 2nd column. It should read "0.030-0.487" (instead of the current "0.487-0.030").
4. (done) SSI: "beta" transition probability of >=65 years old is 3.6% (and not 3.9% as it is currently in the model). Please change.
I`ve also reviewed the general feel of the toolkit and here are some final comments:
1. (no action needed) In your change log you state that you forgot point 7 of part 3 ("Please also remember to re-establish interactivity in the "Aggregated results table" of "Aggregate results".). We were talking about the possibility of changing the order of the diseases according to the metric. This has been re-established anyway and no action is required.
2. In all transition probabilities in the explanation of ATP and LTP you write "Parameter "Lifetime transition probability" indicates whether the transition probability is of type "Lifetime transition probability (LTP)". If not then it is assumed it is "Annual transition probability (ATP)" and parameter "Duration" is applicable. Specify "-1" in "Duration" to specify remaining life expectancy”. Is it correct that if the user decides to apply an ATP, the user can decide to change the amount of years this is applicable? E.g. the user wants to apply an ATP for 10 years all the user needs to do is change the duration to 10?
DL RESPONSE:
The general formula used for calculation of transition probability for ATP is:
1 - (1-s)^d * t/s
where:
t: transition probability as specified in the reference data,
s: sum of all transition probabilities (as in the reference data) leaving this health state,
d: duration.
By default d = remaining life expectancy. This can be overridden in the transition probability settings, but the code ensures that it never exceeds the remaining life expectancy.
3. (done) In aggregate results, please move the bubble charts under the histogram of all diseases and before the age-gender specific total results.
I`ve reviewed the wording of the embedded explanations and have some edits to be implemented please:
1. (done) ? on the input tables: please change to:
"In the table you can specify the number of cases per age group and gender.
The formula can include arithmetic operations ("+", "-", "*", "/"), constants ("0.3", "3.14", etc) and the following uncertainty ranges that will be evaluated at each iteration of the modelling sampling by Monte Carlo simulations:
· Rand (same until "with this formula"")
It`s also possible to paste a table already prepared on another software (e.g. Windows Excel©) by copying the table on that software and right-clicking on the table below and selecting "Paste table from clipboard"."
2. (done) ? on the input tables: next to the bullet points listing the possible random distributions can you please add the links to their Wiki explanation pages? (e.g. http://en.wikipedia.org/wiki/Uniform_distribution_(continuous) )?
3. (done) Selection of multipliers: Title to change from "Select multiplication factors to set" to "Multiplication factors adjusting for under-estimation of number of cases".
Explication below when hovering on the ? to change to: "In this table you can input multipliers adjusting for under-estimation either by defining one number or set of numbers (1 table to fill) or by adjusting for under-ascertainment and under-reporting separately (2 tables to fill).
By default the multiplier is 1; if you do not change the table you consider there's no under-estimation of number of cases you`ve inputted in the table on the left."
v 0.129 (28/09/2015)
Disease model updates:
- Giardiasis updated according to "Giardiasis.docx" (version 29/09/2015)
v 0.128 (20/09/2015)
PART 1: Comments received on 15/09/2015
1. (done) Rubella: in the "Disease report" tab, in Table 1, Congenital. Can you please add a row called "Fatal cases" in the first column, nothing in the second column, 10% in the third column and "Reef, 2000" in the fourth column?
2. Salmonellosis:
a) (done) please use the updated table for the re-distribution of fatal cases according to age-groups which I attach to this email on the powerpoint;
b) (done) in the "Disease report" tab, in Table 1, please add a new row. 1st column: "Reactive arthritis", 2nd column nothing, 3rd column "1.31% (0.29-5.43%)", 4th column "Kemmeren, 2006".
3. Shigellosis:
a) (done) please update the case fatality. The CFP is 0.06-0.97% of all cases, re-distributed according to Table 3 in the powerpoint attached;
b) (done) please update the age-group redistribution of the risk of developing HUS (0.008-0.011%) according the Table 4 of the ppt attached;
c) (done) transition probabilities lambda 1 and 2 from 45 to 65 years old has a higher limit of 44% (not 41%), please update;
d) in the outcome tree, please correct "Transplanted (remaining of transplanation)" to "Transplanted (remaining of transplantation)"
4 STEC/VTEC:
a) (done) please update the age-group redistribution of the case fatality following symptomatic infection (0.03-0.045%) according the Table 3 of the ppt attached;
b) (done) please update the age-group redistribution of the risk of developing HUS (0.94-1.25%) according the Table 4 of the ppt attached;
c) (done) please update the age-group specific CFP following HUS according to Table 5 of the ppt attached;
d) (done) transition probabilities lambda 1 and 2 from 45 to 65 years old has a higher limit of 44% (not 41%), please update;
e) (done) in the "Disease report" tab, Table 2 there`s a first row missing, please update as following: 1st column "Symptomatic infection (Gastroenteritis)", 2nd column "0.149 (0.12-0.182)", 3rd column "Diarrhoea, moderate", 4th column "0.008-0.014", 5th column "Havelaar, 2004; Cressey & Lake, 2007";
f) (done) in the outcome tree, please correct "Transplanted (remaining of transplanation)" to "Transplanted (remaining of transplantation)"
5. Syphilis:
a) (done) in the "Disease report" tab, Table 1, acquired. Can you please change "Primary syphilis from symptomatic infection" to "Primary syphilis from infections".
b) (done) in the "Disease report" tab, Table 1, acquired. Can you please change "Secondary syphilis" to "Secondary syphilis from symptomatic infection"
6. (done) Tetanus: in the "Disease report" tab, Table 2. Under "Symptomatic infection", please invert "(Localised tetanus)" and "(Generalised tetanus)".
7. (done) TBE: in the "Disease report" tab, Table 1. In "Symptomatic infection", please change "20-24%" to "20-34%".
8. Toxoplasmosis: in the "Disease report" tab, Table 2, "Acquired". Please add a row: 1st column "Permanent disability due to chorioretinitis", 2nd column "0.015 (0.011-0.019)", 3rd column "Conjunctivitis without corneal scar", 4th column "rem life exp.", 5th column "Kemmeren, 2006".
9. Tuberculosis:
a) (done) In the outcome tree, when clicking on "beta2" or "beta3" the pop-up window reads "beta1", although the parameters are correct. Please adjust.
b) (done) beta2 is "12.8% (2.3-23.3%)" (not "12.3% (2.3-23.3%)").
10. (done) DSSI-CABG now becomes simply SSI and the outcome tree follows the report attached.
PART 2: Comments received on: 11/09/2015
1. (done, reintroduced) Healthcare associated clostridium difficile is not created, the error message is "Model creation - Data is missing for the selected combination of country and disease."
2. (done, redistribution table updated) Table 3 of campylobacteriosis (distribution of CFR) is wrong, please find attached the tables;
3. (done, dw updated) The disability weight for Chlamydia, women, PID is 0.018-0.310 (and not 0.018-0.123 as in the toolkit);
4. Cryptosporidiosis:
a) (done, correct order restored) all parameters seem correct but on the outcome tree view when I click on "Complicated" it`s the uncomplicated numbers which show up and vice-versa;
b) (done, report updated) in the "disease report" view, Table 1, "Complicated", please delete "Age dep. (Table 3)" under 0.15%;
c) (done, refistribution table updated) distribution of beta transition (fatal cases) is wrong. Please find attached the correct age distribution tables of risk of dying (0.0042%).
5. (done partially, see notes) Giardiasis needs to be updated, see attached the final versions;
NOTE: Age dependent health states are not possible to be specified in the current version. Only transition probabilities can include redistribution.
Therefore health states of symptomatic infection are not updated.
Outcome tree updated to include fatal cases.
6. Hepatitis A:
a) (done, redistribution table added) please update the fatal cases: 0.1-0.3% to re-distribute according to Table 4 in the attached documents;
b) (done, disease report updated) "disease report" view: please correct the duration of symptomatic infections, it`s 0.038 (not 0.38) although it`s correct in the model parameters.
7. (done, see note) Hepatitis B and C (and the rest of the toolkit): please update the wording of Annual TP as we discussed in emails months ago ("Direct type" is difficult to understand);
NOTE: Parameter "redistribute" has been renamed to "Age-group redistribution".
Parameter "Direct type" has been renamed to "Lifetime transition probability" and "Cumulative type" has been renamed to "Annual transition probability". Text describing transition probability types in the transition probability dialog has been adjusted to reflect the renaming.
8. (done, parameter and disease report updated) HIV: in the "persistent HIV infection" the split is 5-15% of "rapid" and "Long-term" progressors whilst the remaining "Typical progressors" are set to 60-90%. I just realised now that 15+15=30, not 40. Therefore, both in the model and in the text in the "Disease report" tab the share of "Typical progressors" should be changed to 70%;
9. (no problem found there) Influenza: please update the re-distribution table for fatal cases "beta" to the one in the disease report and attached in powerpoint;
10. IHID:
a) (done) In the "Disease Report" can you please substitute the sentence "Reported data indicates that meningitis and septicaemia occur together in 0-1% of cases, whereas meningitis alone occurs in 15-17% (15% in 2010, 17% in 2011) of cases, resulting in an overall risk of 15-18% of developing meningitis." with "Reported data indicates that meningitis and septicaemia occur together in 0-1% of cases, whereas meningitis alone occurs in 15-18% (15% in 2010, 18% in 2011) of cases, resulting in an overall risk of 15-18% of developing meningitis."
b) (done) In the "Disease Report" can you please substitute the sentence "Meningitis accounts for various long-term sequelae (each of which is multiplied by the risk of developing meningitis during the acute phase of the disease: 15-17%):" with "Meningitis accounts for various long-term sequelae (each of which is multiplied by the risk of developing meningitis during the acute phase of the disease: 15-18%):";
c) (done) In the "Disease Report" can you please substitute the header for Table 4 to "Age specific distribution per gender of the 15-18% risk of developing meningitis manifestation during the symptomatic infection (TESSy 2010-2011)"
11. (done) IMD: all the age-group specific re-distributions from Table 4 in your transition probabilities parameters for women are wrong, you copied in the male ones but females are slightly different. Please update according to the powerpoint I attached.
12. (done) IPD: re-distribution of "eta" is wrong and does not follow Table 4 like the other transition probabilities, please update.
13 Listeriosis:
a) (done) perinatal outcome tree, the value of fatal cases is wrong ("beta"), it`s 18.71%, (not 20%). Please update.
b) (done) Acquired: fatal cases occur only from "Complicated symptomatic infections" and the age-group specific case fatality is incorrect in the toolkit, please update according to Table 3 in the powerpoint attached.
PART 3: Comments received on: 03/09/2015
1. "View detailed results": section "Results table", for each table
a) (done) compute numbers per outcome tree specific population.
b) (done) add to headers "Specific Population"
c) (done) add column "DALY per 100,000 Total Population"
d) (done) hide row "Total Infected"
2. (done) "View detailed results": section "Results table", add table with results for the whole disease model (only if multiple outcome trees exist, otherwise do not display). It should contain rows: "Acute Total", "Sequelae Total", "All Health Outcomes Total".
3. (done) "View detailed results": section "Results charts", add bar chart with results for the whole disease model (only if multiple outcome trees exist, otherwise do not display).
4. "View detailed results": section "Results details",
a) (done) Change header "DALY Per 100,000" to "DALY per 100,000 Specific Population"
b) (done) Add tab "DALY per 100,000 Total Population"
4. (done) "View aggregated results": copy here design of section "Results details" from "View detailed results". Display results aggregated over all disease models.
5. (done) Change "Per" to "per" across the toolkit.
6. (done) We were also wondering if you think that "Stratum Specific Population" instead of "Specific Population" would not over-charge too much the heading. Stratum gives a clearer idea of what we`re talking about...
7. (not done, forgot what the issue was) Please also remember to re-establish interactivity in the "Aggregated results table" of "Aggregate results".
v 0.127 (02/09/2015)
Changed:
- Processing of samples generated during model run completely rewritten: proper aggregations at health outcome, acute/sequela, outcome tree and disease model.
Now "DALY Per Case" categorized results (Detailed view, bottom part, results per age and sex) are properly computed in case of disease models with multiple outcome trees (previously all results blank due to infinity calculated).
- Detailed view: small adjustments in naming of colums to make them consistent across the toolkit ("DALY Per Case", etc.)
v 0.126 (31/08/2015)
Disease model updates:
- HAP OT updated according to "Final report_HAP_HAI.docx" (version 27/08/2015)
- CR-BSI removed
- P-BSI updated according to "Final report_P-BSI_HAI.docx" (version 27/08/2015)
- DSSI-CABG implemented
NOTES:
a) DW of "Symptomatic infection" is in the Power-Point presentation is different than in the Word document. Word version implemented.
b) sum of transitions from "Sever sepsis" is greater than 100%
v 0.125 (03/08/2015)
Disease model updates:
- Chlamydia Female OT updated according to "Final Report_Chlamydia.docx" (version 30/03/2015)
New:
- Aggregated view: Scaling of bubbles updated to ensure better visual effect. Scaling is not dependent on the number of points any more.
- Aggregated view: Table with selection of models to be displayed is now always equal to the height of the chart to the left (including the legend).
- Aggregated view: Aggregated results table - totals line added (tooltips and confidence bounds are not available).
- Aggregated view: Ranking of diseases chart - displays data according to the selection column of "Aggregated results table"
- Aggregated view: Ranking of diseases chart - tooltips are displayed when data item is hovered.
- Aggregated view: Ranking of diseases chart - labels on the x-axis are rotated in order to save space.
Fixes:
- Aggregated view: Ranking of diseases chart - last item on was displayed only partially. Now it is fully visible.
v 0.124 (27/07/2015)
Disease model updates:
- HAP: new implementation.
NOTES:
a) DW for "Renal failure" is "0.487-0.030" (in the tool it has been reversed)
b) sum of transitions from "Severe sepsis" is greater than 100%
- CR-BSI: new implementation.
NOTES:
a) DW for "Renal failure" is "0.487-0.030" (in the tool it has been reversed)
b) sum of transitions from "Complicated" is greater than 100%
c) Proportion of "Complicated/Uncomplicated" mentioned in Figure 1 of the disease report differs from those listed in Table 1 of the same report.
- UTI: new implementation.
NOTES:
a) DW for "Renal failure" is "0.487-0.030" (in the tool it has been reversed)
b) sum of transitions from "Urosepsis" is greater than 100%
- Clostridium Difficile: new implementation.
v 0.123 (26/07/2015)
Disease model updates:
P-BSI: new implementation.
NOTES:
a) sum of transitions from "Symptomatic - Complicated" is greater than 100%
b) DW for "Renal failure" is "0.487-0.030" (in the tool it has been reversed)
Neonatal Sepsis: new implementation.
v 0.122 (13/07/2015)
Changed:
- Dynamic walkthrough implemented. Styling consistent with the static pages of the tutorial.
v 0.121 (02/07/2015)
Changed:
- Tutorial includes more images and allows navigation with links to "previous" and "next" slide.
Fixed:
- Flow chart and dynamic walkthrough had some interoperability issues wrt the dark background show.
v 0.120 (29/06/2015)
New:
- Disease reports converted to html, cleaned up and included in the toolkit.
v 0.119 (24/06/2015)
New:
- Time discounting implemented.
v 0.118 (28/05/2015)
New:
- Tutorial flow charts implemented.
v 0.117 (27/04/2015)
Fixed:
- Importing "redistribution" table of transition probabilities from saved model files.
Changed:
- Better notifications when saving models.
v 0.116 (24/04/2015)
Fixed:
- Toxoplasmosis: reference data (missing "Age" input factor)
- Data Grid: shows "congenital" age categories if a "congenital" and "non-congenital" disease are created and the selection changes.
- Exporting of models did not include header (name) for transition probability and redistribution table.
v 0.115 (07/04/2015)
Fixed:
- Calculation of "Incidence Per 100,000" for the aggregated results view.
- OT of Chlamydia Men: Reactive Arthritis "Severe" was mapped to "Mild"
- Tooltip in the results per age category (detailed results view) was always showing results of the first model.
Disease model updates:
- All: word "after" replaced with "following" aligning it with the disease reports.
- Chlamydia (email from Alessandro 30/03/2015)
Women OT:
DW of Pelvic Inflammatory Disease changed to RandUniform(0.018, 0.123).
Transition probability "eta" changed to 0.02%.
Transition probability "zeta" changed to 0.07% over all age categories.
DW of Chronic pelvic pain changed to RandUniform(0.018, 0.123).
DW of Tubo-ovarian abscess changed to 0.8% and extended to all age categories.
- Gonorrhoea (email form Alessandro 30/03/2015)
Women OT:
Symptomatic infection Severe: DW changed RandUniform(0.002, 0.03) to RandUniform(0.005, 0.03)
Men OT:
Symptomatic infection Severe: DW changed RandPert(0.002, 0.01, 0.03) to RandUniform(0.005, 0.03)
Transition from Asymptomatic to Epididymitis removed
- Hepatitis B (email from Alessandro 30/03/2015)
No changes
- Hepatitis C (email from Alessandro 30/03/2015)
Remission from chronic hepatitis added together with transition mu.
Transitions delta_1 and delta_2: Probability RandUniform(0.55, 0.69) extended to age category 15-19 (previously stopped at 10-14).
Transition kappa_2: when clicked the title in the openede dialog was "kappa_1".
- HIV (email from Alessandro 30/03/2015)
AIDS terminal phase: DW changed from RandPert(0.515, 0.549, 0.572) to RandPert(0.518, 0.574, 0.635).
- Syphilis (email from Alessandro 30/03/2015)
No changes.
- Tuberculosis (email from Alessandro 30/03/2015)
Entirely new outcome tree, all new transition probabilities and disability weights.
v 0.114 (12/03/2015)
New:
- "Age dependent" transitions changed to "Redistribution". Such transition probabilities are split now into two tables: Probability and Redistribution.
Changed:
- Demographic data for countries updated (email from Alessandro 11/03/2015)
Fixed:
- Table aggregations (last row) did not show correct values if data pastes into table from external table or through "Fill..." option.
v 0.113 (05/03/2015)
Fixed:
- Data copied with "Paste table from clipboard" was not correctly set.
v 0.112 (03/03/2015)
Fixed:
- Changes to transition probability meta information made through the interface were not propagated to the calculation engine.
- Using options "Fill table with this formula" or "Paste table from clipboard" were resulting in removing all meta information rendering the table unusable.
New:
- Tutorial workflow according to the new design (request from Alessandro, email 27/02/2015)
v 0.111 (22/02/2015)
Changes:
- Button "Main page" removed.
Disease model updates:
- Poliomyelitis (email from Alessandro 12/02/2015)
No changes
- Diphtheria (email from Alessandro 12/02/2015)
No changes
- Influenza (email from Alessandro 18/02/2015)
No changes
- Invasive Haemophilus Influenzae (email from Alessandro 20/02/2015)
Updated age dependent probabilities of gamma, delta, epsilon, zeta, eta, theta, iota, kappa according to table 4.
- Invasive Meningococcal Disease (email from Alessandro 20/02/2015)
No changes
- Invasive Pneumococcal Disease (email from Alessandro 20/02/2015)
No changes
- Mumps (email from Alessandro 12/02/2015)
No changes
- Measles (email from Alessandro 12/02/2015)
No changes
- Pertussis (email from Alessandro 12/02/2015)
No changes
- Poliomyelitis (email from Alessandro 12/02/2015)
No changes
- Rubella (email from Alessandro 12/02/2015)
No changes
- Tetanus (email from Alessandro 12/02/2015)
No changes
v 0.110 (02/02/2015)
New:
- Items "Croatia" and "EU + EEA" added in the list of countries
- Prototype of the workflow in view "Tutorial"
- Disease report framework implemented. Disease report for "Tick Borne Encephalitis" implemented as a prototype.
Changed:
- Item "Custom Population" set as the first one in the list of countries
TODO:
[DONE] Put ?custom population? as first option;
[DONE] The tutorial should be more evident: I suggest that you change the name of the tab ?Workflow? (and delete that text) and call it ?Tutorial?;
[DONE] One the use clicks on ?Tutorial? on the menu on the left, instead of all that text a workflow appears with the same boxes used in the dynamic tutorial;
[DONE] The first box would have ?Start Tutorial? on it and clicking this starts the dynamic tutorial you`ve already implemented;
- If the use wants to jump directly to another phase of the tutorial he/she can do it by clicking on the workflow.
[DONE] Add "Croatia" to the country list
v 0.109 (25/01/2015)
New:
- Implementation of logic for the tutorial
- Item "Custom Population" added to the list of countries with no age distribution pre-initialized.
Removed:
- Item "London" removed from the list of countries
v 0.108 (23/01/2015)
New:
- Additional age category in Listeriosis.
- "Disease report" placeholder tab added in "Edit model data" view.
Changed:
- All parameters of "congenital" diseases contain all age categories. This includes "Age distribution" and "Life expectancy".
Removed:
- "References" tab removed
v 0.107 (13/01/2015)
New:
- Additional age category in disease models containing congenital outcome tree.
v 0.106 (19/11/2014)
Disease model updates:
- Q Fever (email from Alessandro 13/11/2014)
"Chronic Q Fever" DW and duration updated.
- Rabies (email from Alessandro 13/11/2014)
No changes
- Tick Borne Encephalitis (email from Alessandro 13/11/2014)
Transition "alpha" updated. "Symptomatic infection" duration, "Paralysis" DW, "Residual Paresis" DW, "Chronic post-encephalitic TBE syndrome" DW updated.
v 0.105 (11/11/2014)
New:
- added support for duration parameter of cumulative risk transition being specified as formula (rather than numeric).
Disease model updates:
- Influenza (email from Alessandro 10/11/2014)
Fixed "age distribution" in transition "gamma"
- Toxoplasmosis (email from Alessandro 10/11/2014)
Updated OT for Congenital
v 0.104 (06/11/2014)
Fixed:
- Aggregated results table was showing incorrect results (DALY per case, YLD per 100,000, YLL per 100,000, DALY per 100,000).
v 0.103 (04/11/2014)
Disease model updates:
- Pertusis:
OT changed and parameters updated according to email from Alessandro (04/11/2014)
- Influenza:
Transition beta updated according to email from Alessandro (04/11/2014)
v 0.102 (02/11/2014)
Experimental build. Allowes mixed sources of cases for health state (from parent health outcome and from transitions entering directly the health state).
v 0.101 (02/11/2014)
Disease model updates:
- Cryptosporidiosis (email from Alessandro 01/11/2014)
Updated OT and DWs according to "Final report_Cryptosporidiosis.docx".
- Tuberculosis (email from Alessandro 30/10/2014)
Updated OT and DWs according to "Final Report_Tuberculosis.docx".
The OT in the documents contains an error in the transition probability from "MDR TB" to "Fatal cases". It reads "0.12-0.039%", but should be "12.8-14.2%".
Changed:
- Aggregated results view:
Bar chart "Ranking of diseases according to burden" shows now "DALY per 100,000" instead of "DALY per year".
v 0.100 (31/10/2014)
Disease model updates:
- Chlamydia (email from Alessandro 21/10/2014)
Age dependent transitions eta and zeta implemented and outcome tree naming conventions copied directly from source OT (Final Report_Chlamydia.docx).
Bear in mind, that the age dependence (or redistribution, as it should rather be called) assumes about 14.28% of all cases per age category between 15 and 49 (7 categories in total).
- Hepatitis B (email from Alessandro 03/09/2014)
Outcome tree naming conventions copied directly from source OT (Final report_HBV.docx).
- Hepatitis C (email from Alessandro 03/09/2014)
Outcome tree naming conventions copied directly from source OT (Final report_HCV.docx).
- HIV (email from Alessandro 03/09/2014)
New transition from "AIDS early symptomatic" to "Permanent ARV treatment" and updated DW and transition probabilities.
- Syphilis (email from Alessandro 29/10/2014)
Duration of Neuro-Syphilis changed to RandUniform(0.027, 0.038). Fixed program crash when "Fatal cases" clicked. Updated naming in OT.
- Gonorrhoea (email from Alessandro 21/10/2014)
Age dependent transitions delta and eta and duration of Symptomatic infection (Women).
- Rabies (email from Alessandro 28/09/2014)
Updated OT (removed Asymptomatic) and DWs.
- Tick Borne Encephalitis (email from Alessandro 28/09/2014)
Reviewed and confirmed settings. No changes wrt v. 0.98.
- Diphtheria (email from Alessandro 28/09/2014)
Reviewed and confirmed settings. No changes wrt v. 0.98.
- Invasive Haemophilus Influenzae Disease (email from Alessandro 10/10/2014)
Add recovery for "Asymptomatic infection", fixing spelling errors, reviewed and confirmed settings.
Table 4 has been rescaled so that sums of percentages per each sex category is 1 (51.19% and 48.85% in "Final Report_IHID.docx").
- Invasive Meningococcal Disease (email from Alessandro 10/10/2014)
Add recovery for "Asymptomatic infection", fixing spelling errors, fixed delta transition (from RandUniform(0.0096, 0.101) to RandUniform(0.0096, 0.0101))
and epsilon transition (no age dependence applied before).
Table 4 has been rescaled so that sums of percentages per each sex category is 1 (47.28% and 52.71% in "Final Report_IMD.docx").
- Invasive Pneumococcal Disease (email from Alessandro 28/09/2014)
Add recovery for "Asymptomatic infection", fixing spelling errors.
Table 4 has been rescaled so that sums of percentages per each sex category is 1 (44.06% and 55.96% in "Final report_IPD.docx").
- Measles (email from Alessandro 28/09/2014)
Fixing spelling errors, transition delta fixed (from 0.0001 to 0.00001), transition iota fixed (table 3).
- Mumps (email from Alessandro 23/10/2014)
Updated OT and DWs according to "Final report_Mumps.docx". Transition beta implemented as age dependent, however with the current method - split equally between age categories.
- Pertussis (email from Alessandro 28/09/2014)
Updated OT and DWs according to "Final Report_Pertussis.docx". Transition beta implemented as age dependent, however with the current method - split equally between age categories.
- Poliomyelitis (email from Alessandro 31/10/2014)
Updated OT and DWs according to "Final Report_Pertussis.docx".
- Rubella (email from Alessandro 28/09/2014)
Updated OT and DWs according to "Final report_Rubella.docx". This document specifies probability of 5% of permanent disability due to Thyroid gland dysfunction for age 13-19.
Age categories in the toolkit are 10-14 and 15-19 therefore 2.5% is specified for age category 10-14 and 5% for age category 15-19.
- Tetanus (email from Alessandro 28/09/2014)
Updated OT and DWs according to "Final Report_Tetanus.docx".
- vCJD (email from Alessandro 10/10/2014)
Updated OT and DWs according to "Final report_vCJD.docx".
- Listeriosis (email from Alessandro 10/10/2014)
Updated OT and DWs according to "Final report_Listeriosis.docx".
- Giardiasis (email from Alessandro 10/10/2014)
Updated OT and DWs according to "Final report_Giardiasis.docx". Currently the toolkit does not support age dependent proportions, thus those are not implemented (parked for later).
- Hepatitis A (email from Alessandro 10/10/2014)
Updated OT and DWs according to "Final report_HAV.docx".
- Influenza (email from Alessandro 07/10/2014)
Reviewed and confirmed settings. No changes wrt v. 0.98.
- Salmonellosis (email from Alessandro 29/10/2014)
Updated OT and DWs according to "Final Report_Salmonellosis.docx".
- Campylobacteriosis (email from Alessandro 29/10/2014)
Updated OT and DWs according to "Final Report_Campylobacteriosis.docx". Age dependent proportions incorporated into transitions epsilon and theta.
- STEC/VTEC (email from Alessandro 30/10/2014)
Name changed from "VTEC/STEC" to "STEC/VTECT". Updated OT and DWs according to "Final report_STECVTEC.docx".
- Toxoplasmosis (email from Alessandro 30/10/2014)
Updated OT and DWs according to "Final Report_Toxoplasmosis.docx".
- Shigellosis (email from Alessandro 29/10/2014)
Updated OT and DWs according to "Final Report_Shigellosis.docx".
NOTE: "Age dependent" is used in all documents for two distinct situations:
a) simply denote that parameter has different value depending on age (like transition from "Symptomatic infection - Complicated" to "Fatal cases")
b) transition completely redistributes cases among age categories (like transition form "Symptomatic infection" to "Hemolytic Uremic syndrome")
This is confusing. Notion of "age dependent" transition has been used by the BCoDE consortium only in relation to situation "b".
- Legionnaires' disease (email from Alessandro 30/10/2014)
Name changed to "Legionnaires' disease". Updated OT and DWs according to "Final Report_Legionnaires'disease.docx".
NOTES:
Mumps, Giardiasis - age dependent proportions currently not supported.
v 0.99 (28/10/2014)
Fixed:
- Correctly aggregated death cases and YLL per health outcome, both if transitions are leaving that health outcome directly, as well as its internal health states.
v 0.98 (12/10/2014)
Disease model updates:
- Diphtheria (email from Alessandro 28/09/2014)
- Influenza (email from Alessandro 07/10/2014)
- Invasive Haemophilus Influenzae (email from Alessandro 30/09/2014)
- Invasive Meningococcal Disease (email from Alessandro 30/09/2014)
- Invasive Pneumococcal Disease (email from Alessandro 30/09/2014)
- Measles (email from Alessandro 28/09/2014)
- Tick Borne Encephalitis (email from Alessandro 28/09/2014)
v 0.97 (28/09/2014)
Disease model updates:
- Syphilis (email from Alessandro 03/09/2014)
NOTE: Duration of Neurosyphilis is different in the report (0.038 - 0.027) than in the outcome tree slide (10). 10 years implemented.
- Gonhorrea (email from Alessandro 03/09/2014)
v 0.96 (21/09/2014)
Disease model updates:
- Chlamydia (email from Alessandro 03/09/2014)
- Hepatitis B (email from Alessandro 03/09/2014)
- Hepatitis C (email from Alessandro 03/09/2014)
- HIV (email from Alessandro 03/09/2014)
Changed:
- Internal updates leading to performance improvements (about 60% shorter simulation time).
Notes:
1. Chlamydia, Women, Tubo-ovarian abscess: disability weight set to 0 for age category "1-4", like it was in the original OT.
2. Hepatitis C, Remission from chronic hepatitis: There is no motion of transition to Recovery in the methodology. All cases that have not transitioned further are assumed to be recoveries by default.
3. HIV: transition alpha not specified. Transition from "Infection" to "Acute Illness" must always be specifed per methodology. It is used to estimate the number of all cases from acute cases. Alpha set to 1, DW and duration for acute illnes set to 0.
v 0.95 (14/03/2014)
Parameter updates (emails Alies and Excel checking files from Marie-Josee, CIB comments to v. 0.86, no changes to disability weights):
- Tuberculosis: Transition beta_1 changed to RandPert(0, 0.03, 0.074)
- Gonorrhoea Infants: Transition epsilon changed to RandUniform(0.3, 0.35)
- Gonorrhoea Men: Transition gamma changed to 0.1
- Chlamydia Men: Duration of reactive arthritis changed to 0.3
- Chlamydia Women:
DW of tubo-ovarian abscess changed to 0 for age categories 0-4
Transition eta and zeta left non-zero only for age categories 15-49
Transition iota changed to 0.06
Transition theta changed to 0.03
- Syphilis Adults: Transition delta changed to RandUniform(0.0075, 0.0188)
- Listeriosis Perinatal (changes according to 20140202_Checking Listeria.xls, Marie-Josee, 04/02/2014 on CIB):
Health state "Septicemia" removed
Transition gamma incorporates "1 - beta" (permanent disability only on non-fatal meningitis)
- Listeriosis Acquired (changes according to 20140202_Checking Listeria.xls, Marie-Josee, 04/02/2014 on CIB):
Health states "Septicemia" and "Pneumonia" correctly labelled now
Transition gamma incorporates "1 - beta_1" (permanent disability only on non-fatal meningitis)
- Cryptosporidiosis: Set severe as 0.02%, mild as remaining cases (it was the other way around before)
- Toxoplasmosis Congenital:
Proportion of Severe set to RandPert(0.014, 0.024, 0.04)
Updates to the labelling of health outcomes in the OT
Duration of all Acute health states but "Severe" and "Post-1-year..." changed to 1
- Toxoplasmosis Acquired:
Removed health outcome "Fatal cases"
Duration of healh state "Chorioretinitis" changed to 1
- Campylobacteriosis: Duration of Acute illness changed from 0.017918 to 0.017863.
- Hepatitis A: transition beta updated according to DR (ages 0-29)
- Shigellosis: transition theta changed from "RandPert(0.012, 0.066, 0.98)" to "RandPert(0.012, 0.066, 0.098)"
- Pertussis: durations of health states in "Acute illness" updated according to "DR_Pertussis_20140311_no_results.doc"
v 0.94 (27/02/2014)
Fixed:
- Tooltips in the aggregated view results plots where showing incorrect results.
v 0.93 (23/02/2014)
Changed:
- Axis labels fixed in "DALY comparison" chart ("View aggregated results")
- Data displayed in "View aggregated results" changed according to the following specification:
Graph 1:
x-axis incidence per 100,000
y-axis: mortality per 100,000
bubble size: DALY per 100,000
Graph 2:
x-axis incidence per 100,000
y-axis: DALY per case
bubble size: DALY per 100,000
Disease models updates:
- Rubella: mapping of "Congenital" and "Non-congenital" outcome trees to age/sex categories has been reversed.
- Gonnorhoea: mapping of outcome trees to age/sex categories has been changed ("Infants" only to age 0).
v 0.92 (20/02/2014)
Parameter updates (source email Alessandro 20/02/2014):
- Chlamydia Men: duration of "Reactive arthritis" changed to "RandUniform(0.13, 0.28)"
- Campylobacteriosis: duration of "ReA" changed to "RandUniform(0.13, 0.28)"
- Shigellosis: duration of "ReA" changed to "RandUniform(0.13, 0.28)"
- Salmonellosis: duration of "ReA" changed to "RandUniform(0.13, 0.28)"
- Chlamydia Infants: duration of "Nasopharyngeal infection" changed to "0.5"
- Gonorrhoea: duration of "Acute illness - Uncomplicated" changed to "0"
- Gonorrhoea: disability weight of "Ophthalmia nenatorum" changed to "RandPert(0.011, 0.015, 0.019)"
- Gonorrhoea: duration of "Ophthalmia nenatorum" changed to "0.625"
- Hepatitis A: duration of "Acute illness" changed to "0.039671"
- Hepatitis B: duration of "Chronic hepatitis" changed to "RandUniform(4.5, 33.24)"
- Hepatitis B: duration of "Hepatocellular carcinoma" changed to age/sex dependent table (varying between 0.72 and 4.48)
- Hepatitis B: duration of "Compensated liver cirrhosis" changed to age/sex dependent table (varying between 6 and 10.4)
- Hepatitis B: duration of "Decompensated liver cirrhosis" changed to 1.4286 for all age categories
- Hepatitis C: duration of "Decompensated liver cirrhosis" changed to 3.472 for all age categories
- Tick-borne encephalitis: duration of "Acute illness" changed to "RandPert(0.00274, 0.11, 0.192)"
v 0.91 (16/02/2014)
New disability weights:
- Poliomyelitis
- Rubella
- Pertussis
- Invasive Meningococcal disease
- Invasive Pneumococcal disease
- Tuberculosis
- Syphilis
- Legionnaire's disease
- HIV
- Tetanus
- Chlamydia
- Gonorrhoea
- Mumps
- Salmonellosis
- VTEC/STEC
- Invasive Haemophilus Influenzae
- Diphtheria
- Rabies
- Listeriosis
- Tick-Borne Encephalitis
- Toxoplasmosis
- vCJD
Disease models updates:
- Poliomyelitis: OT changed according to email of Scott from 21/01/2014 and consistency rules applied.
- Rubella: OT changed according to email of Scott from 22/01/2014 and consistency rules applied.
- Pertussis: Consistency rules applied and durations updated (see note below)
- Invasive Meningococcal disease: Consistency rules applied
- Invasive Pneumococcal disease: Parameters updates according to email from Scott 22/01/2014; fixed program crashed when transition "delta" clicked.
- Syphilis: Parameters updates - email from Dietrich 19/12/2013, parameter values from "New DWs_AC&EC-2.xlsx", consistency rules applied
- Tuberculosis: Parameters updates - email from Dietrich 19/12/2013, parameter values from "New DWs_AC&EC-2.xlsx", consistency rules applied
- Legionnaire's disease: Parameters updates - email from Dietrich 19/12/2013, parameter values from "New DWs_AC&EC-2.xlsx", consistency rules applied
- HIV: Parameters updates - email from Dietrich 19/12/2013, parameter values from "New DWs_AC&EC-2.xlsx", consistency rules applied
- Tetanus: Parameters updates - email from Dietrich 19/12/2013, parameter values from "New DWs_AC&EC-2.xlsx", consistency rules applied
- Chlamydia: Parameters updates - email from Dietrich 19/12/2013, parameter values from "New DWs_AC&EC-2.xlsx", consistency rules applied
- Gonorrhoea: Parameters updates - email from Dietrich 19/12/2013, parameter values from "New DWs_AC&EC-2.xlsx", consistency rules applied
- Mumps: Parameters updates - email from Scott 22/01/2014, parameter values from "New DWs_AC&EC-2.xlsx", consistency rules applied
- Salmonellosis: Parameters updates from "DR_Salmonella_20140205.doc", parameter values from "New DWs_AC&EC-2.xlsx", consistency rules applied
- VTEC/STEC: Parameters updates from "DR_VTEC-STEC_20140205.doc", parameter values from "New DWs_AC&EC-2.xlsx", age dependent transitions from "Netherlands STEC 0157 2011-09-21.xls", consistency rules applied
- Invasive Haemophilus Influenzae: parameter values from "New DWs_AC&EC-2.xlsx", consistency rules applied
- Diphtheria: parameter values from "New DWs_AC&EC-2.xlsx", consistency rules applied
- Rabies: OT updated according to "DR_Rabies_20130925_no_results.doc", parameter values from "New DWs_AC&EC-2.xlsx", consistency rules applied
- Listeriosis: OT simplified, parameters based on "DR_Listeriosis_20140207.doc" and "New DWs_AC&EC-2.xlsx", consistency rules applied
- Tick-Borne Encephalitis: Parameters based on "DR_TBE_20110920.doc" and "New DWs_AC&EC-2.xlsx", consistency rules applied
- Toxoplasmosis: Parameters based on "DR_Toxoplasmosis_20140204.doc" and "New DWs_AC&EC-2.xlsx", consistency rules applied
- vCJD: Parameters values from "New DWs_AC&EC-2.xlsx", consistency rules applied
Note:
- Poliomyelitis: Scott says "Post-polio syndrome is a long-term sequela that occurs 30-35 years after infection in approximately 25-30% of patients with the paralytic form". Currently there is no 30-35 years delay between "Acute illness" and "Post-polio syndromes"
- Pertussis: durations have been recomputed from descriptions rather than copied directly from the table in the disease report. Compared to the OT in the disease report there are also fatal cases from "Otitis media" and "Seizures" as requested by Scott in "Pertussis_toolkit_changes_20140108.doc"
- Legionnaire's disease: PTSD is kept as part of the OT although a comment in the disability weights files says: "experts consider this as not part of the OT". OT cannot be simplified (beta_2 is different than beta_3 thus no simplification of fatal cases; all sequela follow Moderate and Severe only thus no single transition from Acute illness)
- Chlamydia women: model exported by Dietrich has transition probability Pert(0.0002, 0.0002, 0.4) for eta (agrees with DR), incorporated into the toolkit.
- Salmonellosis: newest DR (DR_VTEC-STEC_20140205.doc) recalculates durations from annual to period profiles, incorporated into the toolkit
- VTEC/STEC: newest DR (DR_VTEC-STEC_20140205.doc) recalculates durations from annual to period profiles, incorporated into the toolkit; duration of ESRD Severe kept at 1 (no new value found in DR, same for Shigellosis); transition gamma is set age-dependent per Excel model (no mention in the DR)
- Hepatitis C: health outcome "Remission of chronic infection" removed
- Rabies: two health states of "Acute illness" introduced: Furious form and Paralytic form (per DR "DR_Rabies_20130925_no_results.doc")
- Listeriosis perinatal: Health state "Meningitis" set as 100% of Acute illness cases per DR "DR_Listeriosis_20140207.doc"
- Toxoplasmosis congenital: Transition eta is implemented as cumulative probability RandPert(0.01, 0.02, 0.03) for age category 0 with duration 20 years ie formula is 1-(1-RandPert(0.01, 0.02, 0.03))^20.
Transition alpha is RandUniform(0.11, 0.25)
v 0.90 (14/02/2014)
New disability weights:
- Campylobacterios
- Cryptosporidiosis
- Giardiasis
- Influenza
- Hepatitis A
- Hepatitis B
- Measles
- Shigellosis
- Q Fever
Disease models updates:
- Campylobacterios: model simplified
- Shigellosis: model simplified, consistency rules applied
- Q Fever: model simplified
v 0.89 (10/02/2014)
New:
- Export uncertainty intervals to Excel together with the average results
v 0.88 (09/02/2014)
New:
- Display "YLD Per 100,000" and "YLL Per 100,000" in the detailed results table
- Display "YLD Per 100,000" and "YLL Per 100,000" in the aggregated results table
- Display uncertainty intervals in the aggregated results table
- Export result tables to Excel (right-click, select "Copy table to Excel", paste in Excel). Formatting is preserved, but numbers are copied with full precision.
- Two reference data files files are delivered. One with Standardized Life Expectancy ("referenceData.SLE.dat"), and one with the previously used Life Expectancy ("referenceData.dat"). The one
named as "referenceData.dat" is loaded by the toolkit, so make sure that the one you would to use is named like that.
Fixes:
- Numerous fixes to exporting of charts and tables. Now there is an option to export every single result item from the detailed and aggregated results view.
Disease models updates:
- Campylobacteriosis - fixed calculation for "GBS long-term" by an explicit specification of transition probabilities "1 - zeta_1" and "1 - zeta_2".
v 0.87 (05/02/2014)
Changed:
- Life expectancy has been set to "Standardized LE table"
- Subscripts in transition probability names were not displayed correctly in transition probability pop-ups
OT consistency rules implemented:
- Transition probabilities are always displayed lower case (it was not the case in the pop-up dialogs before).
- Transitions with names including index, for instance "beta_1" are now displayed with indices as subscipts.
- Acute illness health outcome is always named "Acute illness".
- Asymptomatic health outcome is always named "Asymptomatic acute infection".
- Death health outcomes are named "Fatal cases ([name of the previous health outcome])".
- Transitions leaving health outcome, not a health state, originates from the health outcome title.
- Health states are titled "after [title of the previous health state/outcome]".
- Health outcome representing long term illness are titled "[title] long-term".
Disease models updates:
- Hepatitis B - OT labelling updated
- Influenza - OT simplified and labelling updated
- Measles - OT updated with labelling
- Campylobacteriosis - OT updated with labelling, parameters updated
- Hepatatis A - Parameters updated, OT labelling updated
- Cryptosporidiosis - OT simplified, Parameters updated, OT labelling updated
- Giardiasis - OT simplified, OT labelling updated
v 0.86 (19/01/2014)
New:
- Highlight source and target health state/outcome when a transition is hovered with a mouse.
Disease models updates:
- Polio: New model added based on "DR_Polio_20130930.doc".
- Hepatitis C: OT updated to make it in line with the OT of Hepatitis B
- Influenza: OT updated according to file DR_Influenza_20131129.doc
- Tick Borne Encephalitis: OT updated according to file DR_TBE_20110920.doc
- Q Fever: OT updated per personal communication with Scott on 16/01/2014
v 0.85 (16/01/2014)
Disease models updates:
- Mumps: OT changed according to file Mumps_toolkit_changes_20130523.doc
- Pertussis: OT changed according to file Pertussis_toolkit_changes_20140108.doc
v 0.84 (14/01/2014)
New:
- Close all dialogs on ESC
Changed:
- Rename "Export disease models" to "Save disease models" and "Import disease models" to "BCoDE_Pathogens - the different steps.xlsx"
Disease models updates:
- Shigellosis - OT changed according to Marie-Josee's request: Gonococcal_infections_OT.pptx
- Rubella - OT changed according to update report: Rubella_toolkit_changes_20130523.doc
v 0.83 (08/12/2013)
New:
- Probability distributions added: Beta, Gamma, LogNormal. Mean, variance and weblink displayed for all distributions.
Changed:
- Parameter "Annual Profile" removed (reference data, calculations and interface)
Disease models updates:
- Gonnorhoea - OT for Men and Women changed according to Dietrich's request: Gonococcal_infections_OT.pptx
v 0.82 (04/12/2013)
New:
- Uncertainty bounds displayed in the results table when mouse hovers over a cell.
Disease models updates:
- Q Fever: durations in "Post infectous fatigue syndrom" corrected (1.5 - mild, 10 - severe)
- HIV: OT changed according to "BCoDE_Pathogens_OT_layout_check_Dietrich_update.xlsx" (Dietrich)
- Legionellosis: OT changed according to "BCoDE_Pathogens_OT_layout_check_Dietrich_update.xlsx" (Dietrich)
- Chlamydia: Parameter values changed according to "Toolkit testing 10-10-2013 SM.docx" (Scott)
v 0.81 (24/11/2013)
New:
- Health outcome to health outcome/state transitions are possible now (see Gonorrhoea for an example). In such cases remaining life expactancy
transfered to the child health outcome/state will be taken from the first health state of the parent health outcome.
Disease models updates:
- Gonorrhoea: changes according to "BCoDE_Pathogens_OT_layout_check_Dietrich_update.xlsx"
v 0.80 (17/11/2013)
Disease models updates:
- Hepatitis B: changes according to "BCoDE_Pathogens_OT_layout_check_Dietrich_update.xlsx"
- Tetanus: OT updated according to "BCoDE_Pathogens_OT_layout_check_Dietrich_update.xlsx"
- Chlamydia: OT updated according to "BCoDE_Pathogens_OT_layout_check_Dietrich_update.xlsx"
v 0.79 (13/11/2013)
Fixed:
- loading of multiple models from a single Excel file results in the incorrect entries in the list of created models
Changed:
- added progress on loading models
v 0.78 (10/11/2013)
Disease models updates:
- Campylobacteriosis
- Legionellosis
- Tuberculosis
v 0.77 (05/11/2013)
Fixed:
- Cryptosporidiosis model fixed. No more software crash.
Disease models updates:
- Toxoplasmosis: changed according to file "BCoDE_Pathogens - the different steps", email of Marie-Josee from 01/11/2013
Mapping to age categories changed according to the email of Marie-Josee from 31/10/2013
- Listeriosis: removed health state "stilbirth" according to file "BCoDE_Pathogens - the different steps", email of Marie-Josee from 01/11/2013
v 0.76 (31/10/2013)
Fixed:
- Changes to the type of transition probability made in the interface were not propagated to the calculation engine.
v 0.75 (23/10/2013)
Disease model updates:
- Q Fever: OT and parameters updated according to file "Toolkit testing 10-10-2013 SM.docx", email of Scott from 10/10/2013
Disease models final updates:
- Hepatatis A: parameters updated according to file "HAV_v71_withChanges.xls", email of Marie-Josee from 10/10/2013
- Cryptosporidiosis: parameters updated according to file "Crypto_v71_withChanges.xls", email of Marie-Josee from 10/10/2013
- Giardiasis: parameters updated according to file "Giardia_v71_withChanges.xls", email of Marie-Josee from 10/10/2013
- Rabies: parameters updated according to file "Toolkit testing 10-10-2013 SM.docx", email of Scott from 10/10/2013
Disease models fixes:
- Diphtheria: Program close when clicking health outcome "Permanent arrhythmias"
v 0.74 (14/10/2013)
Fixed:
- improper initialization of health states flagged as holding remaining cases
v 0.73 (12/10/2013)
Disease models:
- Diphtheria model updated
- Invasive Haemophilius Influenzae model updated
- Invasive Meningococcal Disease model updated
- Invasive Pneumococcal Disease model updated
- Measels model updated
Changed:
- If health states covers remaining cases within a health outcome, then "Meta" view is displayed by default with remaining cases indicated checked, instead of "Stratified" view.
v 0.72 (10/10/2013)
Fixed:
- Totals of input tables was not always correctly updated after manual editing of cells.
- Crash of the calculations for Influenza model.
- Display of "Incidence per 100,000" in detailed results view.
Disease models:
- Chlamydia model updated
- HIV model updated
TODO:
- Calculations crash for Hepatatis A model if number of iterations is 100,000.
v 0.71 (09/10/2013)
Changed:
- Transition probability type (Direct or Cumulative) can be set in the interface (meta information tab of input table).
- Values in simplified view of input tables are no longer treated as percentage ("%") but as ratios
Fixed:
- Syphilis and Legionellosis models crash the program when some elements in OT are clicked.
- Pasting numbers from Excel with thousands separators.
v 0.70 (07/10/2013)
Disease models updates:
Legionellosis:
- Toolkit: updated to the latest outcome tree (Netherlands Legionellosis 2011-08-11_DP.xls)
Tuberculosis:
- Toolkit: updated to the latest outcome tree (Tuberculosis_draft_20130529.xlsm)
Syphilis:
- Toolkit: updated to the latest outcome tree (Syphilis_toolkit_changes_20130717.doc)
Chlamydia:
- Not fully updated: "Death due to tubo-ovarian abscess" and "Death due to ectopic pregnancy" in "Women" model are specified in the update file. This was not the case before. On the other hand, death cases after "Tubal infertility" are in the model and not mentioned in the upadte file.
Gonnorhoea:
- Not fully updated: Update file specified no "Ophthalmia neonatorum" in the "Infants" outcome tree. However, parameters in the same file suggest that this health outcome exists. This is contradictory.
HIV:
- Not updated: "Persistent latent infection" will have 6 health states after the proposed change (3 three proposed health states for each parent health outcome, "symptomatic" and "asymptomatic" - see Q fever for an example).
TODO:
- Transition type should be specified in "modelData-...", not in disease data.
- "Duration" in transition corresponds to the cumulative type, not "age dependent". Make sure this is made explicit in the toolkit.
v 0.69 (04/10/2013)
Fixes:
- show totals in the tables (both input and output table)
- change of "Age Dependent" and "Duration" meta parameter of transition probability was not effective
- health state covering remaining cases may not be correctly detected by the engine (last health state when ordered by name would be assumed to the one covering remaining cases).
- Numeric data in input tables (stratified view) was implicitly converted to string containing "," (comma) before sending to the computational engine. This results in computational errors.
Changed:
- do no show meta information for output tables
Disease models notes:
Campylobacteriosis:
- Toolkit: updated to the latest outcome tree (Campylobacter_OT.pdf), but parameters must be checked (currently copied for the previous OT)
- Toolkit: transition "beta" is specified as age dependent now
- Excel: model "Netherlands Campylobacteriosis 2012-04-11.xls" does not subtract duration of previous health states in YLL Sequela 3, but this model is not up-to-date anymore.
Cryptosporidiosis:
- Toolkit: updated to the latest outcome tree (Crypto_OT_20130107.pdf), but parameters must be checked (currently copied for the previous OT)
Giardiasis:
- Toolkit: updated to the latest outcome tree (Giardia_OT_20130107.pdf), but parameters must be checked (currently copied for the previous OT)
Listeriosis:
- Toolkit: updated to the latest outcome tree (Listeriosis_OT_20130107.pdf)
Salmonella:
- Toolkit: updated to the latest outcome tree (Salmonella_OT.pdf)
VETC:
- Toolkit: updated to the latest outcome tree (VETC_OT_20130107.pdf)
Chlamydia:
- Excel model for infants in YLD Sequela 3 takes incidence of sequela 2 (formula in columns refers to column C in YLD Sequela 2) instead of incidence of sequela 3 (column E).
v 0.68 (11/09/2013)
New:
- Toxoplasmosis and vCJD disease models implemented
- Random seed can be set (Tools -> Options -> Random seed)
- One health state within a health outcome can have empty proportion supplied. It will be set to 1 - sum of proportions of remaining health states.
- New parameter of transition probability introduced, "Duration". For transition probability type "Cumulative" this parameter can be used to overwrite the number of years (by default it's remaining life expectancy).
- Popups displayed when clicking an element of outcome trees are managed now. Clicking twice on the same health state will not cause opening multiple popups any more. Popups are closed if models are deleted.
- All input parameters of health states and transition probabilities are editable. They are also exported and imported when saving and loading models, respectively.
- Display tables have been redesigned to feature 3 tabs: stratified, simplified, meta information (description, weblink, extra parameters)
- Very deep cleaning action on old and obsolete code in the engine.
Fixes:
- Incorrectly specified model for "Cryptosporidiosis" - results computed and popups not displayed for fatal cases.
v 0.67 (19/07/2013)
New
- Completely rewritten displaying of results table. Now they feature "Detailed" view (old grid view), and a "Simplified"
view. Simplified view allows to specify input random distribution from a drop-down. The simplified view selection has to
be copied to the Detailed view (click "Copy to Detailed") in order to be accessible in the run.
Changed:
- Importing reference data reintroduced
Fixed:
- Changes 1 - 10 of the change list
- No asymptomatic results displayed in the popup window
v 0.66 (22/06/2013)
Fixed:
- Totals in grids are not computed correctly if cells contain numbers with comma separated decimals, like "23,243.00" (this was treated as "23" when aggregating).
v 0.65 (12/06/2013)
Fixed:
- Pasting data to tables results in software crash. More strict check applied now.
- Model selection and refresh of outcome trees in "Edit model data" view not working. Changes to parameters are now
applied properly and model selection correctly reflected in the displayed parameters.
New:
- Long formulas truncated in the tables are displayed in tooltip and hover over it.
v 0.64 (02/06/2013)
New:
- Input parameter checking when entered through the interface.
v 0.63 (27/05/2013)
New:
- Added chart "Ranking of diseases according to burden" in view "View aggregated results"
v 0.62 (20/02/2013)
Fixes:
- Running models for Luxembourg and Liechtenstein results in run-time error.
- Selection of all countries in "Create models" view does not work with the "Select All" (top) checkbox.
- Selection of models bubble charts in "View aggregated results" does not work.
- Various problems with "Fill table with formula", "Copy table to clipboard", "Paste table from clipboard" commands of
Multiplication Factors and Age Distribution tables.
- Empty/wrong results for multi-outcome tree disease models (Listeriosis, Gonorrhoea, Chlamydia).
- Tooltips in DALY bar charts per age/sex category always display results from the first run.
Model reconciliation:
- Hepatitis B
- transition probability "gamma" updated from 0.0075 to RandUniform(0.005, 0.01) for all age/sex categories.
- NL and Germany Excel model overestimate YLD of Chronic Hepatitis for age above 45 (Durations 2A and 2B are checked against
the remaining life expectancy separately instead of as a total, resulting in overstatment of both durations)
- NL Excel model has incorrect formula in column L of sheet "Notification Corrections" (read cell D298 instead of D299).
- Durations and disability weights differ betwen NL and Germany. Toolkit implements NL data as reference.
v 0.61 (30/01/2013)
New:
- "Country data" can be specified per model now. Thus, this data has been moved to "Edit model data" view (tab "Population data").
Both "Life expectancy" and "Age distribution" data is editable, just like other model parameters (tab "Model parameter").
Click "Apply changes" to apply new values in calculations.
- Redesigned health states dialogs (opened when health outcome/state is clicked in outcome tree). Only "Parameters" tab
is visible in no results exist for the model (model not run yet). If results are available, then a new tab appears ("Results").
- New editable parameter per age/sex category introduced: "Proportion of cases covered". It is currently not editable in the interface
but can be set in reference data (file "modelData-generic.xls"). If not specified in the health states section of this file, then
it is assumed that this health state covers 100% of all cases of the corresponding health outcome.
- "Reference" section added.
- Interface remodelling and cleaning
- "About" dialog redesigned to include license information on used external libraries (propoer copyright handling)
Fixed:
- populated case data for Salmonellosis in the reference data Excel file.
- axis in the aggregated results view: X-axis of the second chart is "DALY per 100,000". Size of the bubbles
is proportional to DALY results.
v 0.60 (05/12/2012)
New:
- Annual profile duration interpreted properly - not deducted from the remaining life expectancy.
- Help text in "Set model parameters" extended to show how to enter formulas in input parameters tables.
Fixed:
- Country data not displayed in "View country data" tab.
- Transition probabilities arrows not displayed in the "Edit diease data" tab.
- Saving and loading of models reimplemented and enabled again.
v 0.59 (25/11/2012)
New:
- Formula parser implemented
- Age/sex dependent multiplication factors allowed
Changed:
- All models have been adopted to use the new reference data format
v 0.58 (04/10/2012)
New:
- Formula parser implemented
- Age/sex dependent multiplication factors allowed
v 0.57 (20/08/2012)
New:
- Implemented diseases:
a) Legionellosis
b) Gonorrhoea (awaiting confirmation of outcome tree mapping)
c) Syphilis
d) Mumps
e) Pertussis (YLL for Pneumonia slightly smaller than in the Excel model, due to subtraction of duration of
Pneumonia from the remaining life expectancy. This will be fixed when annual profile disability weights are properly interpreted in the toolkit).
f) Diphtheria
g) Rabies (same as Pertussis)
h) Rubella
i) Tetanuss
j) Listeriosis (currently with constant proportions of cases in health states, until a more general solution is implemented)
k) Q Fever
l) Thick Borne Encephalitis (again, annual profile incorrect interpretation, but differences not significant).
- Beta distribution added as a possible random transition probability
Changed:
- Hepatitis A, disability weights updated according to the latest changes of Marie-Josee.
- Syphilis:
a) misplaced labels of transitions Delta and Gamma in the outcome tree (not really important).
b) duration of Acute Illness and Neurosyphilis is not subtracted from the remaining life expectancy at YLL Neurosyphilis.
- Diphtheria:
a) YLD Sequela 3 - formula in column C, Female, links to column C instead of E of YLD Sequela 2.
- Poliomyelitis:
a) Excel model missing on ViaDesk.
- Tetanus:
a) YLL Sequela 3 - formula in column C, Female, links to column C of YLD Acute Illness instead of column E of YLD Sequela 2.
b) Results Summary does not include Cephalic tetanus in the totals
- Toxoplasmosis:
a) Excel model missing on ViaDesk.
- Listeriosis:
a) Transition "Gamma" for Perinatal is linked to 113, instead of 249
- vCJD:
a) Excel model missing on ViaDesk.
- Q Fever:
a) misplaced labels of transitions Delta, Epsilon, Zeta in the outcome tree (not really important).
b) YLL Sequlea 3 - formula in column E referenced "Notification Corrections" instead of YLD Acute Illness.
- Tick-Borne Encephalitis
a) Results summary table, "Residual Paraesis" and "Post-encephalitic TBE", "Cases" and "YLD per year" have incorrect
formulas. For instance, they should reference YLD Sequela 3!E5 and YLD Sequela 4!E5, respectively.
v 0.56 (19/08/2012)
New:
- Possibility to specify time between infection and death. It is subtracted from the remaining life expectancy at YLL calculation. Applied in Tuberculosis disease model.
- Implemented diseases:
a) Tuberculosis
b) Invasive Meningococcal
c) Invasive Haemophilus Influenzae
Fixed:
- Group all acute health outcomes of Invasive Pneumococcal Disease in the "Acute" section of the results summary table in "Detailed results" view.
Changed:
- Make the model drop down box in the detailed results view wider to accommodate longer model names.
- Fix colouring of health states in the "Edit models" view.
v 0.55 (09/08/2012)
Changed:
- Adjustments in the Campylobacteriosis outcome tree according to Marie-Josee's requests.
New:
- Implemented diseases:
a) Invasive Pneumococcal
- Invasive Pneumococcal
a) sheet "YLD Sequela 2", column C, Female: reference to $F$22 instead of 'OutcomeTree'$F$22
b) sheet "YLD Sequela 3", column C, Female: reference to $F$20 instead of 'OutcomeTree'$F$20
c) sheet "YLD Sequela 3", column C, All: reference to column E of 'YLD Invasive', instead of column C
- Tuberculosis:
a) sheet "YLL Acute Illness", column G, All: formula "=A9+'YLD Acute Illness'!G9" in cell G9, and "='YLD Acute Illness'!G[i]" in the remaning ones. Which one is correct?
b) all YLL sheets - duration of acute TB is not subtracted (0.25 year)
v 0.54 (31/07/2012)
New:
- Implemented diseases:
a) Hepatitis C
b) HIV
Changed:
- Detailed results layout adjusted to make more explicit split between health outcomes results.
- Use the same bounds for the X-axis of the DALY charts in the "Detailed results" view.
- Hepatitis C
a) sheet "YLD Acute Illness", column C: incorrectly referencing all infected cased for Female starting from age category 1-4 up.
b) sheet "YLD Sequela 2", column C: incorrectly referencing only symptomatic cases, it should link to all infected cases if it's supposed to be consistent with Hepatitis B outcome tree.
c) sheet "YLD Sequela 3", column G: incorrect formula in column G (Ci*Di instead of Ci*Fi) for both Male and Female
d) sheet "YLD Sequela 3", column F in Female: incorrect formula referencing Male incidenence and remainining life expectancy
f) sheet "YLD Sequela 4", column F: incorrect formula in the denominator (sum of zeta + eta instead of zeta + theta) for Male
g) sheet "YLD Sequela 4", column F: incorrect formula in the numerator and denominator (referencing Male transition probability) for Female
h) sheet "YLD Sequela 4", column G: incorrect formula in column G (Ci*Di instead of Ci*Fi) for Male and Female
i) sheet "YLD Sequela 5", column D and F: based on trans. probs theta and eta, instead of theta and zeta for cases following from Compensated liver cirrhosis
j) sheet "YLD Sequela 5", column D and F: based on trans. probs eta, iota, theta, instead of eta and iota for cases following from Decompensated liver cirrhosis
k) sheet "YLL Sequela 4", column G: formula referencing column D instead of F
- HIV
a) sheet "Outcome Tree", transition probability "Alpha": formula fixed on C39
b) duration of sequela is not checked against remaining life expectancy, leading to overestimation of YLD.
- Tuberculosis
a) In all disease models and all discussions with the BCoDE team, transition probability "alpha" is the one that gives
proportion of symptomatic cases among all infected cases. This proability is used as input for calculations in YLD Acute Illness
sheet as "Percent developing acute ilness".
Tuberculosis model defines "alpha" but never uses it in the YLD Acute illness, only later indirectly in YLD Sequela 1.
YLD Acute Illness has two health states defined (fine), but none of the transition probabilities is alpha. They are
not even listed in "Outcome trees" sheet, but hard coded in "YLD Acute Illness".
b) After initial two health states in "YLD Acute Illness" cases in the following health outcomes are aggregated and
"Multi-drug resistant TB" and "Extensively-drug resistant TB" have only a single health state. This is the first time
I see such a construction.
I realize that there is no guideline on building disease models in Excel and modellers can in principle define any
way of handling computations. However, I thought that there is at least a desire to keep the models coherent. Otherwise any
attempts to build a software capable of accomodating all models will simply fail. The TB model creates totally new
calculation logic.
v 0.53 (19/07/2012)
Fixed:
- Displaying of health outcome data in "Edit disease model" view for Campylobacteriosis
New:
- Implemented diseases:
a) Cryptosporidiosis
b) Giardiasis
c) Hepatitis A
d) Shigella
- Added London population data
- Allow two parents of a health outcome, but only if health outcome type is "Acute". This extension allows to accomodate "Tuberculosis".
Changed:
- Calculation of average number of infected cases (before model run). Check "Total average case-based data" in "All infections" health outcome in the outcome tree.
- Random number generating engine is improved resulting in better efficiency (speed and randomness).
v 0.52 (02/07/2012)
Changed:
- Label "population" changed to "cases" in the detailed results table
- Long health outcomes names are fully displayed in the detailed results table (together with label of the last row "All Health Outcomes Total")
New:
- Possibility to specify hidden (dummy) health outcomes. These health outcomes are not displayed in the detailed results view (tables and charts).
This is used already in VTEC/STEC (10 years delay), Influenza (sepsis, ards, otitis), Measles (pneumonia, otitis, encepahilitits, postinfectious encephalomyelitis)
Fixed:
- Displaying aggregated results
v 0.51 (19/06/2012)
New:
- Allow selection only of the implemented diseases.
- Interface look'n'feel adjustments to make it more user-friendly and explicit in showing what's editable input, and
what's a fixed parameter.
Fixed:
- Outcome trees were not shown after certain actions executed in sequence.
v. 0.50 (10/06/2012)
New:
- Support for multiple outcome trees per disease. Previously disease model = outcome tree, now disease model is a collection
of outcome trees. Each outcome tree has an ID and is mapped to a specific age/sex category. Specified case count
data is then processed through appropriate outcome tree. All diseases have been converted to the new definition
of a disease model, and Chlamydia is the first model utilizing 3 outcome trees.
Fixed:
- VTEC/STEC model has been redesigned to allow the exact same calculation as in the Excel model, but by complying
with the requirements of the toolkit. A dummy health outcome has been added to introduce delay between HUS and ESRD.
It is also used to split the HUS cases between "ESRD long-term" and "ESRD fatal". Transition probability "omnicron"
has been introduced, but it is 1 (all "ESRD Fatal" cases will be transfered to YLL calculation).
v. 0.48 (16/05/2012)
Fixed:
- Measles: "omicron" transition probability name spelling correction, "nu" transition probability changed from 0% to 100%.
- Salmonellosis: adjusted, tested; takes only severe cases of symptomatic, but with constant proportion of 6.32% of all symptomatic cases.
In order to make this proportion random I will have to either introduce a "dummy" state in between with transition probability Pert(5.35%, 6.24%, 7.61%)
or make generalization in the computational engine and allow passing an extra ratio parameter that can be of random type.
v. 0.47 (15/05/2012)
New:
- all Chlamydia models reconciled (after some fixing of the Excel models*)
- Measles and Influenza adjusted and reconciled (after some fixing of the Excel models*)
Fixed:
- do not show "-1" as duration, if model is not run then show "Rem. life exp.", if run then show actual remaining life expectancy
v. 0.46 (13/05/2012)
New:
- Chlomydia implemented as three separate models (Men, Women, Infants)
Todo:
- Chlomydia Men Excel model has errors:
a) YLD Sequela 3 (Reiter's syndrome) is connected to "Symptomatic", instead of "(Sexually acquired) reactive arthritis"
b) YLD Sequela 3 (Reiter's syndrome): formula for duration is wrong in cells G10 - G27 (should be "=VLOOKUP(A10,'Disability Weights, Durations'!$H$15:$J$16,2,TRUE)" in G10)
- Chlomydia Women Excel model has errors in:
a) alpha transition probability is 0 because it refers wrong cell (D39 instead of D44 for Female)
b) YLD Sequela 2 (Tubo-ovarian abscess) is connected to "Symptomatic" instead of "Pelvic Inflammatory Disease"
c) YLD Sequela 3 (Chronic pelvic pain syndrome) is connected to "Symptomatic" instead of "Pelvic Inflammatory Disease"
d) YLD Sequela 4 (Ectopic pregnancy) is connected to "Symptomatic" instead of "Pelvic Inflammatory Disease"
e) Power-Point outcome tree different from the Excel outcome tree (Symptomatic and Asymptomatic PID)
f) YLL Sequela 2 is connected to Tubo-ovarian abscess. This sequla should not have YLL according to the outcome tree.
g) YLL Sequela 4 is connected to Ectopic pregnancy. This sequla should not have YLL according to the outcome tree.
h) There is no YLL for "Tubal infetility" and "Pelvic Inflammatory Disease"
- Chlomydia Infants Excel model has errors in:
a) alpha transition probability is 0 because it refers wrong cell (D39 instead of D44 for Female)
v. 0.45 (09/05/2012)
New:
- Campylobacteriosis:
* changed "GBS" to "GBS Clinical Phase"
* updated outcome tree (according to the outcome trees Power-Point presentation)
- Hepatitis B:
* updated outcome tree (according to the outcome trees Power-Point presentation)
* all calculations fully reconcile with the (fixed) Excel model
* all health states made explicitly visible - all results are available for view on the health state level now
v. 0.44 (06/05/2012)
New:
- implemented facilities for storing program settings
- added initial settings dialog (just one settings so far - default number of samples per run)
- reorganized top toolbar (File menu added for importing/exporting models)
- added confirmation on software exit
- removed zooming and panning of country selection map, Malta enlarged and Cyprus is not cropped any more. Selecting
a country on the map is made visible in the country table below (scroll to selected country).
- added showing full table description and weblink when mouse is over the text. Useful when original text is too long
to fit in the field and is cropped.
- added Campylobacteriosis disease model
- completely rewritten health outcome/health state/transition probability internal logic to allow accomodating
more disease model structures
Fixed:
- fixed spelling erorrs in disease names
- fixed broken creating models for Czech Republic
- fixed loading duration as severity
- fixed wrong rounding of displayed numbers when "fixed" format used (x.xx)
- fixed incorrect placing of some data in export files
- semi-fix for missing row in country and disease tables if they are scrolled, user navigates to a different page,
and comes back to "Create models" view. Tables are scrolled always to the top to force them to refresh. No
other trick worked unfortunatelly. Ideally, scroll position would be remembered. Currently this is not possible
in html.
Todo:
- add "Recovery" nodes in the existing outcome trees
- reconcile numbers for the existing outcome trees (Campylobacteriosis checked, fine)