Data query - Githubissues

VirginiaChiocchia commented 8 years ago

Can you please help with the following issues:

In the allocation report the field "Reallocated" have missing values in some cases. Why? Does missing values mean they were not allocated at all (considering nearly all of them have the allocated transplant hospital missing too)? If so, can I then exclude these cases? However, one case with missing Reallocated have the allocated Transplant hospital. How should I classify this?
In the Donor report Alcohol abuse takes values: 0, 1, 2, None. What are the codes for this variable? I checked on the Data Models but cannot find the codes for this variable anywhere.

Many thanks, Virginia

mertenssarah commented 8 years ago

@VirginiaChiocchia I should be able to help with the second question about the reallocation issue. Which case is it? Then I can check the paper forms.

VirginiaChiocchia commented 8 years ago

@mertenssarah The cases with missing reallocation values are the following: WP446903L WP445903L WP456001R WP451004L WP453003L WP453002R WP443002R WP457005R WP454001R

For all of these the Transplant Hospital is also missing apart from WP456001R where despite the missing value for reallocation the transplant hospital appear to be Universitair Medisch Centrum Groningen, Netherlands.

Thank you for your help.

Virginia

mertenssarah commented 8 years ago

@VirginiaChiocchia

See my answers below:

WP446903L: was not transplanted WP445903L: not allocated, not transplanted WP456001R: went to groningen and was transplanted in a consented patient. WP451004L: Went to Leiden where it was transplanted in a patient who could not give consent due to mental state of the patient WP453003L: Went to AMC WP453002R: not transplanted: Kidney was not allocated. I can't seem to change this in the database in order to close the form. @marshalc Can you have a look? WP443002R: was not accepted anywhere so not transplanted: Kidney was not allocated. I can't seem to change this in the database in order to close the form. @marshalc Can you have a look? WP457005R: Went to Nijmegen (Transplanted in consented patient) WP454001R: Went to Nijmegen: but was discarded (not transplanted): changed this in database but can't close the form

VirginiaChiocchia commented 8 years ago

Thank you for clarifying these. Please make sure the relevant allocation fields (Reallocated and Transplant Hospital are updated on the database).

@mertenssarah Since I have these info about not transplanted kidneys (reasons) and "no recipients" (whether for consent and allocation reason) on a separate dataset I would take them from there. However, I do not have the reasons why there is no recipient (unless for the cases listed above). Therefore, if you and Ina would like to have the number of reallocated non consented/ not allocated etc reported at the DMC meeting, I will have to give you the list of cases so that you can add the reasons for all them. Hope that's ok.

mertenssarah commented 8 years ago

@VirginiaChiocchia I will update the database once the database is working faster. It took me 1h and a half just to check these IDs. Just give me a list and I'll update them! No problem.

VirginiaChiocchia commented 8 years ago

@mertenssarah Hi Sarah, This is the list of kidneys that has Recipient=No

WP441901L WP441901R WP444901L WP444901R WP456901L WP457901L WP445903L WP445903R WP451905L WP451905R WP452901L WP443902R WP446903R WP441906L WP441906R WP456904L WP446904R WP456906L WP456906R WP453904R WP452903L WP451909L WP441001L WP443002R WP453002R WP453003L WP456001R WP451004L WP451006R WP445001L WP441005L WP441005R WP457005L WP457005R WP454001L WP454001R

Also, there is a discrepancy for WP446903L. This is reported as Not transplantable but it has recipient, organ and perfusion/intervention data and eventually reported as Operation concluded successfully. Does anyone know what happened with this kidney?

mertenssarah commented 8 years ago

@VirginiaChiocchia I will check these IDs by tomorrow noon!

Anything else I need to check for you?

mertenssarah commented 8 years ago

WP441901L: not transplanted WP441901R: was transplanted in Erasme, TT arrived too late in hospital and no data was collected during transplantation. I'm trying to get as much data as possible retrospectively WP444901L: not transplanted WP444901R: not transplanted WP456901L: not transplanted WP457901L: VU Amsterdam: patient was consented later WP445903L: not transplanted WP445903R: not transplanted WP451905L: not transplanted WP451905R: went to groningen: no data available, not sure why. WP452901L: not transplanted, reason mentioned in this form is wrong WP443902R: went to Austria WP446903R: not transplanted WP441906L: went to Rotterdam and was transplanted in a consented patient WP441906R: went to Austria WP456904L: not transplanted WP446904R: went to Austria WP456906L: not transplanted WP456906R: not transplanted WP453904R: went to Austria WP452903L: not transplanted (WP452903R wasn't transplanted either but there is data in the form.. will need to check this!) WP451909L: not transplanted WP441001L: went to Austria WP443002R: not transplanted ( @marshalc this kidney was not allocated, but I can't change this in the database myself) WP453002R: not transplanted ( @marshalc same thing as above: not allocated but I can't change this in the database myself) WP453003L: went to AMC: patient was consented later: transplantation form not completed WP456001R: went to Groningen WP451004L: went to Leiden but got transplanted in a patient who couldn't give consent due to the mental state of this patient WP451006R: went to Austria WP445001L: went to Hopital Erasme: no data in form WP441005L: not transplanted WP441005R: not transplanted WP457005L: went to Rotterdam: was transplanted in a consented patient (no data in form) WP457005R: went to Nijmegen: was transplanted in a consented patient (no data in form) WP454001L: Went to Rotterdam but was transplanted in a patient who didn't give consent WP454001R: not transplanted WP446903L: I don't find this ID back in the database as being transplanted.

VirginiaChiocchia commented 8 years ago

@mertenssarah Thanks for these. For this occasion I can change this data on my datasets but please update this on the database for the next data lock. I need clarification on some wording for the purpose of the report:

for cases when you indicate "not transplanted" does this mean the kidney was not transplanted because not "good enough" (i.e. discards) or because of other reasons such as no consent (i.e. withdrawals)? In other words, does 'not transplanted' mean Recipient should be 'No' or only 'Organ transplantable' should be 'No'?
'went to Austria' is an exclusion for the trial? i.e. go to ineligible/non-consented patients?
'WP457901L: VU Amsterdam: patient was consented later' So, is this kidney still included in the trial?
'WP453003L: went to AMC: patient was consented later: transplantation form not completed' As above, is this still included in the trial?
'went to Hopital Erasme: no data in form' I presume this is included in the trial but they did not enter data yet, right?

I will change the relevant data for those 2 cases that were not transplanted but data was entered.

mertenssarah commented 8 years ago

for cases when you indicate "not transplanted" does this mean the kidney was not transplanted because not "good enough" (i.e. discards) or because of other reasons such as no consent (i.e. withdrawals)? In other words, does 'not transplanted' mean Recipient should be 'No' or only 'Organ transplantable' should be 'No'? Answer: not transplanted means not transplanted because not good enough: discarded kidneys or sometimes not even allocated to a transplant centre

'went to Austria' is an exclusion for the trial? i.e. go to ineligible/non-consented patients? Austria doesn't participate into our trial so it went to ineligible/non-consented patient

'WP457901L: VU Amsterdam: patient was consented later' So, is this kidney still included in the trial? this kidney is in the trial.

'WP453003L: went to AMC: patient was consented later: transplantation form not completed' As above, is this still included in the trial? Yes

'went to Hopital Erasme: no data in form' I presume this is included in the trial but they did not enter data yet, right? yes

VirginiaChiocchia commented 8 years ago

In the extracted datasets for kidneys WP445903L and WP445903R (both listed above as not transplanted) Recipient is equal to No. However, when asked if organ is transplantable (before Recipient Y/N) only WP445903L is reported as No and the reason being "Carcinoma of the kidneys". Should I change this to No for WP445903R too?

Similar issue for WP441005L and WP441005R. Both listed as not transplanted above and Recipient equal No. But when asked if organ is transplantable only WP441005L had No with reason being "too much damage on arterie". Should I change this to No for WP441005R too?

mertenssarah commented 8 years ago

For WP445903 L and R are not transplantable due to the carcinoma in one of the kidneys

WP441005L: was not transplantable and WP441005R didn't get allocated so was not transplanted because of this reason.

VirginiaChiocchia commented 8 years ago

So, 'organ transplantable' should be 'No' for both WP445903 L and R but I would leave this field as 'Yes' for WP441005R. Is this correct?

mertenssarah commented 8 years ago

Correct!

marshalc commented 8 years ago

Ok, much of this may be moot. The work request by @VirginiaChiocchia for changes to the contents of the reports was done prior to my accident, but was pending release. That release has now happened, so the reports (including the SAE ones) can now be downloaded from: [https://cope.nds.ox.ac.uk/en-gb/wp4/administrator/]()

I'll review any further issues on my return (currently scheduled for Tuesday 21st June)

VirginiaChiocchia commented 8 years ago

Thank you releasing the data. However, the link above redirect to this page, not to the downloads. Due to the little time left before the DMC meeting I will probably not be able to do data cleaning and rerun any reports on these data but I will look at it and send any feedback. The DMC reports have been prepared based on the previous data extraction.

AllyBradley commented 8 years ago

The text link is correct however you do not appear to have had a user account and never accessed the live system. An account has now been created for you and details sent by email.

ouhft / COPE

Data query #113