review mapping of disturbance week numbers

[gregcaporaso]

I applied @jrrideout's script (#17) to map the disturbance week numbers to match the WeeksSinceStart column, and there are now two new sheets in @DDomogala3's disturbance list spreadsheet: Detailed disturbances (mapped #8dd097d470) and Summarized disturbances (mapped #8dd097d470).

There are three PersonalIDs in the disturbance list that are not in the mapping file. These are: 104, 251, and 046. @floresg, does that sound right to you? These are now marked with a ?? in the cell.

Cells marked with a single ? cannot be mapped unambiguously as the week number from @DDomogala3's spreadsheet doesn't show up in the mapping file.

@floresg, would you be willing to review and see if the places where the ? and ?? show up make sense, and if they arise because of missing samples (e.g., samples didn't amplify) or errors in data entry?

[floresg]

Baby is asleep so I can get a little work done. Most of those mismatched samples make sense ­ they either did not turn in enough kits to have all their samples sequence so many only have week.1 samples. Others have ambiguous week values in the mapping file and can't be assigned to the correct week. There are only 3 personalIDs that I am unsure why the are failing ­ these are NAU107, NAU150 and NAU160. I think NAU107 may be related to an extra comma in Dan's disturbance list while I am still investigating the other 2. See the attached spreadsheet for why PersonalIDs are not matched.

From: Greg Caporaso notifications@github.com Reply-To: gregcaporaso/student-microbiome-project <reply+i-9042798-98c40ca62475f6722bf1bba927722d574e710154-2468519@reply.gith ub.com> Date: Wednesday, December 5, 2012 8:57 PM To: gregcaporaso/student-microbiome-project student-microbiome-project@noreply.github.com Cc: Gilberto Flores flores.gilbert.e@gmail.com Subject: [student-microbiome-project] review mapping of disturbance week numbers (#21)

I applied @jrrideout https://github.com/jrrideout 's script (#17 https://github.com/gregcaporaso/student-microbiome-project/issues/17 ) to map the disturbance week numbers to match the WeeksSinceStart column, and there are now two new sheets in @DDomogala3 https://github.com/DDomogala3 's disturbance list https://docs.google.com/spreadsheet/ccc?key=0AszoyIf-SUHrdHAxSFRtTUVtUHU5R3 EwNDdaMGZ5LWc#gid=4 spreadsheet: Detailed disturbances (mapped

8dd097d470) and Summarized disturbances (mapped #8dd097d470).

There are three PersonalIDs in the disturbance list that are not in the mapping file https://docs.google.com/spreadsheet/ccc?key=0AvglGXLayhG7dDFUZ3JVVkFrTFFjMW JDWTZheVVROVE#gid=0 . These are: 104, 251, and 046. @floresg https://github.com/floresg , does that sound right to you? These are now marked with a ?? in the cell.

Cells marked with a single ? cannot be mapped unambiguously as the week number from @DDomogala3 https://github.com/DDomogala3 's spreadsheet doesn't show up in the mapping file.

@floresg https://github.com/floresg , would you be willing to review and see if the places where the ? and ?? show up make sense, and if they arise because of missing samples (e.g., samples didn't amplify) or errors in data entry?

‹ Reply to this email directly or view it on GitHub https://github.com/gregcaporaso/student-microbiome-project/issues/21 .

[gregcaporaso]

The attachment doesn't come through - can you email it to me?

[DDomogala3]

@gregcaporaso, @floresg Ok I looked at NAU150 and NAU160 and it does look like I made some errors. NAU150 has no disturbance reported for week 10(before being mapped to weekssince start). NAU 160 does not have a disturbance mapped to week 10 before weekssincestart either, to weekssince start) but does have a diahreae disturbance at week 8 that doesn't seem to be reported.

[gregcaporaso]

OK, thanks! Can one of you guys fix this in the disturbance sheets? Both the original and the mapped-to-WeeksSinceStart would be ideal (in case we ever need to re-run the mapping).

[DDomogala3]

@gregcaporaso I am still proofreading the disturbance list.