added nosocomial death analysis section

[kya2]

I added nosocomial death analysis section with the new MLL community_hcf designation.

[thibautjombart]

Thanks for this. The report is currently failing for me:

/// compiling report: 'temporal_trends_2019-10-17'


processing file: temporal_trends_2019-10-17.Rmd
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label: setup (with options) 
List of 1
 $ include: logi FALSE

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label: read_scripts

Global cleaning rules have been imported from:
 'dictionary/cleaning_rules.xlsx'
and stored into: 'cleaning_rules'.

You can use these to clean data with linelist's function:
'clean_data(... , wordlists = cleaning_rules)'.
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label: load_data
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label: add_top_zones
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label: contacts_overall
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label: contacts_sub_coordination
Quitting from lines 347-437 (temporal_trends_2019-10-17.Rmd) 
Error: Column `month_report` is unknown
In addition: Warning messages:
1: New theme missing the following elements: axis.ticks.length.x, axis.ticks.length.x.top, axis.ticks.length.x.bottom, axis.ticks.length.y, axis.ticks.length.y.left, axis.ticks.length.y.right 
2: a tie among values (butembo, katwa, kayna, kyondo) was broken by choosing the first value 

[eeg31]

likewise I've submitted a new pull request with Aminata's updates to this report

[thibautjombart]

Again, sorry for a fast review:

• I can confirm the new version compiles fine with the current data (Tues 17 Dec 2019) and looks fine (beautiful!) on my laptop
• new code looks good
• one caveat to check out (not necessarily wrong per say, but need checking): the denominator for the proportions is sometimes the whole dataset, sometimes the number of non-missing observations

[thibautjombart]

note: the denominator here excludes unknown place of death; this is not the case later

[thibautjombart]

here the denominator is the total

[thibautjombart]

same as above: denominator is the total

[thibautjombart]

same as above, denominator is the total (including unknown)

[jarvisc1]

Removing review request from history.