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clean_maindata.log
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----------------------------------------------------------------------------------------------------------------------------------
name: <unnamed>
log: E:\users\amy.mason\Pipeline_27_07_2016\clean_maindata.log
log type: text
opened on: 25 Jul 2016, 10:43:07
.
. noi di "Run by AMM on $S_DATE $S_TIME"
Run by AMM on 25 Jul 2016 10:43:07
.
.
.
.
.
. use "E:\users\amy.mason\staph_carriage\Datasets\raw_input.dta", clear
.
. bysort patid: gen first=(_n==1)
.
. summ first
Variable | Obs Mean Std. Dev. Min Max
-------------+---------------------------------------------------------
first | 13,767 .1000218 .30004 0 1
.
. noi di " starting with " _N " records from " r(sum) " paticipants"
starting with 13767 records from 1377 paticipants
.
. drop first
.
.
.
. *******************************************************************
.
.
.
. * drop people who were recruited in hospital / non nasal swabs
.
. noi di _n(5) _dup(80) "=" _n "(2) DROP NON-NASAL/ NON-GP RECRUITMENT PEOPLE" _n _dup(80) "="
================================================================================
(2) DROP NON-NASAL/ NON-GP RECRUITMENT PEOPLE
================================================================================
.
. * merge with group records
.
. merge m:1 patid using "E:\users\amy.mason\staph_carriage\Datasets\groups", update
Result # of obs.
-----------------------------------------
not matched 0
matched 13,767
not updated 13,767 (_merge==3)
missing updated 0 (_merge==4)
nonmissing conflict 0 (_merge==5)
-----------------------------------------
. tab StudyGroup
StudyGroup | Freq. Percent Cum.
------------------------------+-----------------------------------
C3 GP | 11,065 80.37 80.37
D1a MAU disease | 87 0.63 81.01
D1b Surgery | 657 4.77 85.78
D2 Sterile site | 704 5.11 90.89
D3a Skin and soft tissue (GP) | 41 0.30 91.19
Multisite | 1,158 8.41 99.60
Vaccine | 55 0.40 100.00
------------------------------+-----------------------------------
Total | 13,767 100.00
.
. * upload lab data
.
.
.
. cd E:\users\amy.mason\Pipeline\Amy_work
E:\users\amy.mason\Pipeline\Amy_work
.
.
.
. use "E:\users\amy.mason\Pipeline\Amy_work\lab_compare_all_wide.dta", clear
.
.
.
. cd E:\users\amy.mason\Pipeline_27_07_2016\
E:\users\amy.mason\Pipeline_27_07_2016
.
.
.
.
.
. * get wetlab counts
.
. reshape long
(note: j = ciprofloxacin clindamycin erythromycin eta etb etd fusidicacid gentamicin meca mecc methicillin mupirocin penicillin pv
> l rifampicin sea seb sec sed see seg seh sei sej selr sep seu tetracycline trimethoprim tsst1 vancomycin)
Data wide -> long
-----------------------------------------------------------------------------
Number of obs. 1379 -> 42749
Number of variables 126 -> 7
j variable (31 values) -> site
xij variables:
goldstandardciprofloxacin goldstandardclindamycin ... goldstandardvancomycin->goldstandard
genefinderciprofloxacin genefinderclindamycin ... genefindervancomycin->genefinder
typewriterciprofloxacin typewriterclindamycin ... typewritervancomycin->typewriter
zamciprofloxacin zamclindamycin ... zamvancomycin->zam
-----------------------------------------------------------------------------
.
.
.
. * add type to discriminate graphs at later stage
.
. gen type =""
(42,749 missing values generated)
.
. replace type ="Phenotype" if inlist(site, "ciprofloxacin", "fusidicacid", "clindamycin", "erythromycin")
variable type was str1 now str9
(5,516 real changes made)
.
. replace type ="Phenotype" if inlist(site, "gentamicin", "mupirocin", "penicillin","rifampicin")
(5,516 real changes made)
.
. replace type ="Phenotype" if inlist(site,"tetracycline", "trimethoprim", "vancomycin", "methicillin")
(5,516 real changes made)
.
.
.
. keep if type!=""
(26,201 observations deleted)
.
. *keep if type==""
.
.
.
. gen anti=(strlen(site)>5)
.
.
.
. contract anti site gold gene typew zam
.
. gen result = gene + typew + zam
.
.
.
. * note order is GENEFINDER THEN TYPEWRITER THEN MYKROBE
.
. drop gene typew zam
.
. replace result = "missing" if result==""
(0 real changes made)
.
. replace gold = "missing" if gold==""
(0 real changes made)
.
.
.
.
.
. reshape wide _freq, i(site gold) j(result) string
(note: j = RRR RRS RSR RSS SSR SSS)
Data long -> wide
-----------------------------------------------------------------------------
Number of obs. 107 -> 44
Number of variables 5 -> 9
j variable (6 values) result -> (dropped)
xij variables:
_freq -> _freqRRR _freqRRS ... _freqSSS
-----------------------------------------------------------------------------
.
. rename _freq* *
.
.
.
. egen combor = rowtotal(RRR RSR)
.
. replace combor=0 if combor==.
(0 real changes made)
.
. egen combos= rowtotal(SSR SSS)
.
. replace combos=0 if combos==.
(0 real changes made)
.
.
.
. drop R* S*
.
.
.
. keep if inlist(gold, "R", "S")
(21 observations deleted)
.
.
.
.
.
. reshape wide combo*, i(site) j(gold) string
(note: j = R S)
Data long -> wide
-----------------------------------------------------------------------------
Number of obs. 23 -> 12
Number of variables 5 -> 6
j variable (2 values) goldstandard -> (dropped)
xij variables:
combor -> comborR comborS
combos -> combosR combosS
-----------------------------------------------------------------------------
.
.
.
. rename combo* *
.
.
.
. *** generate sensitivity and specificity
.
. ***** NOTE: [ called GOLD] is format of these variables
.
.
.
. replace sS = 0 if sS==.
(0 real changes made)
.
. replace rS = 0 if rS==.
(0 real changes made)
.
. replace sR = 0 if sR==.
(1 real change made)
.
. replace rR = 0 if rR==.
(1 real change made)
.
.
.
.
.
. for any lsens usens lspec uspec lme ume lvme uvme:gen X=.
-> gen lsens=.
(12 missing values generated)
-> gen usens=.
(12 missing values generated)
-> gen lspec=.
(12 missing values generated)
-> gen uspec=.
(12 missing values generated)
-> gen lme=.
(12 missing values generated)
-> gen ume=.
(12 missing values generated)
-> gen lvme=.
(12 missing values generated)
-> gen uvme=.
(12 missing values generated)
.
.
.
. gen TP= rR
.
. gen FP = rS
.
. gen TN = sS
.
. gen FN = sR
.
. use "E:\users\amy.mason\staph_carriage\Datasets\raw_input.dta", clear
.
. bysort patid: gen first=(_n==1)
.
. summ first
Variable | Obs Mean Std. Dev. Min Max
-------------+---------------------------------------------------------
first | 13,767 .1000218 .30004 0 1
.
. noi di " starting with " _N " records from " r(sum) " paticipants"
starting with 13767 records from 1377 paticipants
.
. drop first
. list if strpos(spatype, "t1236")
+---------------------------------------------------------------------------------+
| SwabID patid Sent Received Result DateTa~n spatype timepo~t |
|---------------------------------------------------------------------------------|
1005. | 176 144 23feb2009 23feb2009 MSSA . t1236 0 |
+---------------------------------------------------------------------------------+
. list if strpos(spatype, "t570")
+----------------------------------------------------------------------------------+
| SwabID patid Sent Received Result DateTaken spatype timepo~t |
|----------------------------------------------------------------------------------|
640. | 357 97 31mar2009 06apr2009 MSSA 02apr2009 t570 2 |
642. | 202 97 04mar2009 16mar2009 MSSA 09mar2009 t570 1 |
647. | 119 97 11feb2009 11feb2009 MSSA . t570 0 |
+----------------------------------------------------------------------------------+
. list if strpos(spatype, "t6798")
+---------------------------------------------------------------------------------+
| SwabID patid Sent Received Result DateTa~n spatype timepo~t |
|---------------------------------------------------------------------------------|
2959. | 474 611 20apr2009 20apr2009 MSSA . t6798 0 |
+---------------------------------------------------------------------------------+
. list if strpos(spatype, "t6801")
+---------------------------------------------------------------------------------+
| SwabID patid Sent Received Result DateTa~n spatype timepo~t |
|---------------------------------------------------------------------------------|
230. | 33 31 13jan2009 13jan2009 MSSA . t6801 0 |
+---------------------------------------------------------------------------------+
. list if patid==31
+-------------------------------------------------------------------------------------+
| SwabID patid Sent Received Result DateTaken spatype timepo~t |
|-------------------------------------------------------------------------------------|
229. | 1388 31 01sep2009 . . 8 |
230. | 33 31 13jan2009 13jan2009 MSSA . t6801 0 |
231. | 889 31 09jul2009 . . 6 |
232. | 81 31 04feb2009 16mar2009 No growth 15feb2009 1 |
233. | 2041 31 11nov2009 . . 10 |
|-------------------------------------------------------------------------------------|
234. | 196 31 04mar2009 16mar2009 No growth . 2 |
235. | 2793 31 11jan2010 25jan2010 No growth 17jan2010 12 |
236. | 533 31 08may2009 . . 4 |
+-------------------------------------------------------------------------------------+
. list if patid==611
+-------------------------------------------------------------------------------------+
| SwabID patid Sent Received Result DateTaken spatype timepo~t |
|-------------------------------------------------------------------------------------|
2955. | 3219 611 12feb2010 22feb2010 MSSA 16feb2010 t089 10 |
2956. | 573 611 14may2009 01jun2009 MSSA 25may2009 t089 1 |
2957. | 1603 611 06oct2009 09nov2009 MSSA 30oct2009 t089 6 |
2958. | 5583 611 13oct2010 02nov2010 No growth 31oct2010 18 |
2959. | 474 611 20apr2009 20apr2009 MSSA . t6798 0 |
|-------------------------------------------------------------------------------------|
2960. | 4964 611 11aug2010 24aug2010 No growth 16aug2010 16 |
2961. | 1222 611 14aug2009 15sep2009 MSSA 06sep2009 t089 4 |
2962. | 3659 611 09apr2010 28apr2010 No growth 20apr2010 12 |
2963. | 6151 611 07dec2010 20dec2010 No growth 13dec2010 20 |
2964. | 4365 611 11jun2010 30jun2010 No growth . 14 |
|-------------------------------------------------------------------------------------|
2965. | 728 611 11jun2009 29jun2009 MSSA 21jun2009 t089 2 |
2966. | 2595 611 09dec2009 04jan2010 MSSA 11dec2009 t089 8 |
2967. | 7354 611 12apr2011 03may2011 MSSA 22apr2011 t089 24 |
2968. | 6752 611 08feb2011 28feb2011 No growth 21feb2011 22 |
+-------------------------------------------------------------------------------------+
.
. * upload lab data
.
.
.
. cd E:\users\amy.mason\Pipeline\Amy_work
E:\users\amy.mason\Pipeline\Amy_work
.
.
.
. use "E:\users\amy.mason\Pipeline\Amy_work\lab_compare_all_wide.dta", clear
.
.
.
. cd E:\users\amy.mason\Pipeline_27_07_2016\
E:\users\amy.mason\Pipeline_27_07_2016
.
.
.
.
.
. * get wetlab counts
.
. reshape long
(note: j = ciprofloxacin clindamycin erythromycin eta etb etd fusidicacid gentamicin meca mecc methicillin mupirocin penicillin pv
> l rifampicin sea seb sec sed see seg seh sei sej selr sep seu tetracycline trimethoprim tsst1 vancomycin)
Data wide -> long
-----------------------------------------------------------------------------
Number of obs. 1379 -> 42749
Number of variables 126 -> 7
j variable (31 values) -> site
xij variables:
goldstandardciprofloxacin goldstandardclindamycin ... goldstandardvancomycin->goldstandard
genefinderciprofloxacin genefinderclindamycin ... genefindervancomycin->genefinder
typewriterciprofloxacin typewriterclindamycin ... typewritervancomycin->typewriter
zamciprofloxacin zamclindamycin ... zamvancomycin->zam
-----------------------------------------------------------------------------
.
.
.
. * add type to discriminate graphs at later stage
.
. gen type =""
(42,749 missing values generated)
.
. replace type ="Phenotype" if inlist(site, "ciprofloxacin", "fusidicacid", "clindamycin", "erythromycin")
variable type was str1 now str9
(5,516 real changes made)
.
. replace type ="Phenotype" if inlist(site, "gentamicin", "mupirocin", "penicillin","rifampicin")
(5,516 real changes made)
.
. replace type ="Phenotype" if inlist(site,"tetracycline", "trimethoprim", "vancomycin", "methicillin")
(5,516 real changes made)
.
.
.
. keep if type!=""
(26,201 observations deleted)
.
. *keep if type==""
.
.
.
. gen anti=(strlen(site)>5)
.
.
.
. contract anti site gold gene typew zam
.
. gen result = gene + typew + zam
.
.
.
. * note order is GENEFINDER THEN TYPEWRITER THEN MYKROBE
.
. drop gene typew zam
.
. replace result = "missing" if result==""
(0 real changes made)
.
. replace gold = "missing" if gold==""
(0 real changes made)
.
.
.
.
.
. reshape wide _freq, i(site gold) j(result) string
(note: j = RRR RRS RSR RSS SSR SSS)
Data long -> wide
-----------------------------------------------------------------------------
Number of obs. 107 -> 44
Number of variables 5 -> 9
j variable (6 values) result -> (dropped)
xij variables:
_freq -> _freqRRR _freqRRS ... _freqSSS
-----------------------------------------------------------------------------
.
. rename _freq* *
.
.
.
. egen combor = rowtotal(RRR RSR)
.
. replace combor=0 if combor==.
(0 real changes made)
.
. egen combos= rowtotal(SSR SSS)
.
. replace combos=0 if combos==.
(0 real changes made)
.
.
.
. drop R* S*
.
.
.
. keep if inlist(gold, "R", "S")
(21 observations deleted)
.
.
.
.
.
. reshape wide combo*, i(site) j(gold) string
(note: j = R S)
Data long -> wide
-----------------------------------------------------------------------------
Number of obs. 23 -> 12
Number of variables 5 -> 6
j variable (2 values) goldstandard -> (dropped)
xij variables:
combor -> comborR comborS
combos -> combosR combosS
-----------------------------------------------------------------------------
.
.
.
. rename combo* *
.
.
.
. *** generate sensitivity and specificity
.
. ***** NOTE: [ called GOLD] is format of these variables
.
.
.
. replace sS = 0 if sS==.
(0 real changes made)
.
. replace rS = 0 if rS==.
(0 real changes made)
.
. replace sR = 0 if sR==.
(1 real change made)
.
. replace rR = 0 if rR==.
(1 real change made)
.
.
.
.
.
. for any lsens usens lspec uspec lme ume lvme uvme:gen X=.
-> gen lsens=.
(12 missing values generated)
-> gen usens=.
(12 missing values generated)
-> gen lspec=.
(12 missing values generated)
-> gen uspec=.
(12 missing values generated)
-> gen lme=.
(12 missing values generated)
-> gen ume=.
(12 missing values generated)
-> gen lvme=.
(12 missing values generated)
-> gen uvme=.
(12 missing values generated)
.
.
.
. gen TP= rR
.
. gen FP = rS
.
. gen TN = sS
.
. gen FN = sR
.
. * upload lab data
.
.
.
. cd E:\users\amy.mason\Pipeline\Amy_work
E:\users\amy.mason\Pipeline\Amy_work
.
.
.
. use "E:\users\amy.mason\Pipeline\Amy_work\lab_compare_all_wide.dta", clear
.
.
.
. cd E:\users\amy.mason\Pipeline_27_07_2016\
E:\users\amy.mason\Pipeline_27_07_2016
.
.
.
.
.
. * get wetlab counts
.
. reshape long
(note: j = ciprofloxacin clindamycin erythromycin eta etb etd fusidicacid gentamicin meca mecc methicillin mupirocin penicillin pv
> l rifampicin sea seb sec sed see seg seh sei sej selr sep seu tetracycline trimethoprim tsst1 vancomycin)
Data wide -> long
-----------------------------------------------------------------------------
Number of obs. 1379 -> 42749
Number of variables 126 -> 7
j variable (31 values) -> site
xij variables:
goldstandardciprofloxacin goldstandardclindamycin ... goldstandardvancomycin->goldstandard
genefinderciprofloxacin genefinderclindamycin ... genefindervancomycin->genefinder
typewriterciprofloxacin typewriterclindamycin ... typewritervancomycin->typewriter
zamciprofloxacin zamclindamycin ... zamvancomycin->zam
-----------------------------------------------------------------------------
.
.
.
. * add type to discriminate graphs at later stage
.
. gen type =""
(42,749 missing values generated)
.
. replace type ="Phenotype" if inlist(site, "ciprofloxacin", "fusidicacid", "clindamycin", "erythromycin")
variable type was str1 now str9
(5,516 real changes made)
.
. replace type ="Phenotype" if inlist(site, "gentamicin", "mupirocin", "penicillin","rifampicin")
(5,516 real changes made)
.
. replace type ="Phenotype" if inlist(site,"tetracycline", "trimethoprim", "vancomycin", "methicillin")
(5,516 real changes made)
.
.
.
. keep if type!=""
(26,201 observations deleted)
.
. *keep if type==""
. keep if strpos(site, "mup")
(15,169 observations deleted)
.
. gen anti=(strlen(site)>5)
.
.
.
. contract anti site gold gene typew zam
.
. gen result = gene + typew + zam
. drop gene typew zam
.
. replace result = "missing" if result==""
(0 real changes made)
.
. replace gold = "missing" if gold==""
(0 real changes made)
.
. reshape wide _freq, i(site gold) j(result) string
(note: j = RRR RSR SSS)
Data long -> wide
-----------------------------------------------------------------------------
Number of obs. 7 -> 4
Number of variables 5 -> 6
j variable (3 values) result -> (dropped)
xij variables:
_freq -> _freqRRR _freqRSR _freqSSS
-----------------------------------------------------------------------------
.
. rename _freq* *
.
. keep if inlist(gold, "R", "S")
(2 observations deleted)
.
.
.
.
.
. reshape wide combo*, i(site) j(gold) string
variable combo* not found
r(111);
.
.
.
. rename combo* *
variable combo* not found
r(111);
.
. egen combor = rowtotal(RRR RSR)
.
. replace combor=0 if combor==.
(0 real changes made)
.
. egen combos= rowtotal(SSR SSS)
variable SSR not found
r(111);
.
. replace combos=0 if combos==.
variable combos not found
r(111);
.
.
.
. drop R* S*
.
.
.
. cd E:\users\amy.mason\Pipeline\Amy_work
E:\users\amy.mason\Pipeline\Amy_work
.
.
.
. use "E:\users\amy.mason\Pipeline\Amy_work\lab_compare_all_wide.dta", clear
.
.
.
. cd E:\users\amy.mason\Pipeline_27_07_2016\
E:\users\amy.mason\Pipeline_27_07_2016
.
.
.
.
.
. * get wetlab counts
.
. reshape long
(note: j = ciprofloxacin clindamycin erythromycin eta etb etd fusidicacid gentamicin meca mecc methicillin mupirocin penicillin pv
> l rifampicin sea seb sec sed see seg seh sei sej selr sep seu tetracycline trimethoprim tsst1 vancomycin)
Data wide -> long
-----------------------------------------------------------------------------
Number of obs. 1379 -> 42749
Number of variables 126 -> 7
j variable (31 values) -> site
xij variables:
goldstandardciprofloxacin goldstandardclindamycin ... goldstandardvancomycin->goldstandard
genefinderciprofloxacin genefinderclindamycin ... genefindervancomycin->genefinder
typewriterciprofloxacin typewriterclindamycin ... typewritervancomycin->typewriter
zamciprofloxacin zamclindamycin ... zamvancomycin->zam
-----------------------------------------------------------------------------
.
.
.
. * add type to discriminate graphs at later stage
.
. gen type =""
(42,749 missing values generated)
.
. replace type ="Phenotype" if inlist(site, "ciprofloxacin", "fusidicacid", "clindamycin", "erythromycin")
variable type was str1 now str9
(5,516 real changes made)
.
. replace type ="Phenotype" if inlist(site, "gentamicin", "mupirocin", "penicillin","rifampicin")
(5,516 real changes made)
.
. replace type ="Phenotype" if inlist(site,"tetracycline", "trimethoprim", "vancomycin", "methicillin")
(5,516 real changes made)
.
.
.
. keep if type!=""
(26,201 observations deleted)
.
. *keep if type==""
.
.
.
. gen anti=(strlen(site)>5)
.
.
.
. contract anti site gold gene typew zam
.
. gen result = gene + typew + zam
.
.
.
. * note order is GENEFINDER THEN TYPEWRITER THEN MYKROBE
.
. drop gene typew zam
.
. replace result = "missing" if result==""
(0 real changes made)
.
. replace gold = "missing" if gold==""
(0 real changes made)
.
.
.
.
.
. reshape wide _freq, i(site gold) j(result) string
(note: j = RRR RRS RSR RSS SSR SSS)
Data long -> wide
-----------------------------------------------------------------------------
Number of obs. 107 -> 44
Number of variables 5 -> 9
j variable (6 values) result -> (dropped)
xij variables:
_freq -> _freqRRR _freqRRS ... _freqSSS
-----------------------------------------------------------------------------
.
. rename _freq* *
.
.
.
. egen combor = rowtotal(RRR RSR)
.
. replace combor=0 if combor==.
(0 real changes made)
.
. egen combos= rowtotal(SSR SSS)
.
. replace combos=0 if combos==.
(0 real changes made)
.
.
.
. drop R* S*
.
.
.
. keep if inlist(gold, "R", "S")
(21 observations deleted)
.
.
.
.
.
. reshape wide combo*, i(site) j(gold) string
(note: j = R S)
Data long -> wide
-----------------------------------------------------------------------------
Number of obs. 23 -> 12
Number of variables 5 -> 6
j variable (2 values) goldstandard -> (dropped)
xij variables:
combor -> comborR comborS
combos -> combosR combosS
-----------------------------------------------------------------------------
.
.
.
. rename combo* *
.
.
.
. *** generate sensitivity and specificity