Merge branch 'load-match-cohorts' of https://github.com/opensafely/po…

…st-covid-thrombosis-research into load-match-cohorts

analysis/000_cr_define_covariates.do

@@ -19,7 +19,7 @@
 
 
 di "STARTING COUNT FROM IMPORT:"
-noi count
+noi safecount
 
 * Age: Exclude children and implausibly old people
 qui summ age // Should be no missing ages

analysis/101_cr_pneumonia_matches.do

@@ -111,10 +111,17 @@ noi di "Matching Report:"
 noi di "****************************************"
 
 forvalues reportMatch = 1/`numMatch' {
-   qui count if matchedto_`reportMatch' != -999
+   qui safecount if matchedto_`reportMatch' != -999
+   if `r(N)'!=. {
 	local perC = round(100*`r(N)'/ `totaltomatch', 0.1)
 noi di "Out of `totaltomatch' patients, `r(N)' (`perC' %) received `reportMatch' match"
 }
+else `r(N)'==. {
+	local perC = round(100*5/ `totaltomatch', 0.1)
+noi di "Out of `totaltomatch' patients, <5 (`perC' %) received `reportMatch' match"
+
+}
+
 
 	global numMatches `r(N)'	
 

analysis/102_cr_matched_cohort_pneumonia.do

@@ -61,11 +61,11 @@ keep if eligibleMatchFound == 1
 drop matchedFlag eligibleMatchFound
 
 bysort setid patient: gen duplicatePatid = _n
-count if duplicatePatid > 1
+safecount if duplicatePatid > 1
 drop if duplicatePatid > 1
 drop duplicatePatid
 
 sort setid
 order setid patient_id indexdate flag 
 save "data/cr_matched_cohort_pneumonia_`outcome'", replace 
-}
+}

analysis/103_cr_control_2019_matches.do

@@ -133,11 +133,19 @@ noi di "****************************************"
 noi di "Matching Report:"
 noi di "****************************************"
 
+
 forvalues reportMatch = 1/`numMatch' {
-   qui count if matchedto_`reportMatch' != -999
+   qui safecount if matchedto_`reportMatch' != -999
+   if `r(N)'!=. {
 	local perC = round(100*`r(N)'/ `totaltomatch', 0.1)
 noi di "Out of `totaltomatch' patients, `r(N)' (`perC' %) received `reportMatch' match"
 }
+else `r(N)'==. {
+	local perC = round(100*5/ `totaltomatch', 0.1)
+noi di "Out of `totaltomatch' patients, <5 (`perC' %) received `reportMatch' match"
+
+}
+
 
 global numMatches `r(N)'	
 

analysis/104_cr_matched_cohort_control_2019.do

@@ -58,7 +58,7 @@ keep if eligibleMatchFound == 1
 drop matchedFlag eligibleMatchFound
 
 bysort setid patient: gen duplicatePatid = _n
-count if duplicatePatid > 1
+safecount if duplicatePatid > 1
 drop if duplicatePatid > 1
 drop duplicatePatid
 
@@ -75,4 +75,4 @@ order setid patient_id indexdate flag
 
 
 save "data/cr_matched_cohort_control_2019_`outcome'", replace 
-}
+}

analysis/105_cr_control_2020_matches.do

@@ -131,10 +131,17 @@ noi di "****************************************"
 noi di "Matching Report:"
 noi di "****************************************"
 
+
 forvalues reportMatch = 1/`numMatch' {
-   qui count if matchedto_`reportMatch' != -999
+   qui safecount if matchedto_`reportMatch' != -999
+   if `r(N)'!=. {
 	local perC = round(100*`r(N)'/ `totaltomatch', 0.1)
 noi di "Out of `totaltomatch' patients, `r(N)' (`perC' %) received `reportMatch' match"
+}
+else `r(N)'==. {
+	local perC = round(100*5/ `totaltomatch', 0.1)
+noi di "Out of `totaltomatch' patients, <5 (`perC' %) received `reportMatch' match"
+
 }
 
 global numMatches `r(N)'	

analysis/106_cr_matched_cohort_control_2020.do

@@ -58,7 +58,7 @@ keep if eligibleMatchFound == 1
 drop matchedFlag eligibleMatchFound
 
 bysort setid patient: gen duplicatePatid = _n
-count if duplicatePatid > 1
+safecount if duplicatePatid > 1
 drop if duplicatePatid > 1
 drop duplicatePatid
 
@@ -75,4 +75,4 @@ order setid patient_id indexdate flag
 
 
 save "data/cr_matched_cohort_`outcome'", replace 
-}
+}

analysis/ado/safecount.ado

@@ -0,0 +1,34 @@
+cap prog drop safecount
+prog define safecount, byable(recall) rclass
+
+marksample touse
+local if " if `touse'"
+
+local ifpos = strpos("`0'", "if ")
+local inpos = strpos("`0'", "in ")
+
+if `inpos'==1 & `ifpos'>0 {
+	noi di in red "if cannot be combined with in"
+	error 999
+	}
+
+if `ifpos'>0{
+ local if "`0' & `touse'"
+ local if "`if' & `touse'"
+}
+
+if `inpos'==1{
+local in = substr("`0'", `inpos',.)
+}
+
+qui cou `if' `in'
+if (r(N)>5 | r(N)==0) {
+count `if' `in'
+scalar count = r(N)
+}
+else {
+scalar count = .
+noi di in yellow _n "** COUNT <=5 **"
+}
+return scalar N = count
+end

analysis/ado/safetab.ado

@@ -0,0 +1,46 @@
+cap prog drop safetab
+prog define safetab, byable(recall)
+
+marksample touse
+local if " if `touse'"
+local commapos = strpos("`0'", ",")
+local commaposm1 = `commapos'-1
+
+if `commapos'>0 {
+	local main = substr("`0'", 1, `commaposm1')
+	local options = substr("`0'", `commapos', .)
+	}
+else local main `0'
+
+local ifpos = strpos("`main'", " if ")
+local ifposm1 = `ifpos'-1
+
+local inpos = strpos("`main'", " in ")
+local inposm1 = `inpos'-1
+
+if `inpos'>0 & `ifpos'>0 {
+	noi di in red "if cannot be combined with in"
+	error 999
+	}
+
+if `ifpos'>0{
+local if = substr("`main'", `ifpos', .)
+local if "`if' & `touse'"
+local main = substr("`main'", 1, `ifposm1')
+}
+
+if `inpos'>0{
+local in = substr("`main'", `inpos',.)
+local main = substr("`main'", 1, `inposm1')
+}
+
+qui tab `main' `if' `in', matcell(T)
+m: T=st_matrix("T")
+m: T=(T:+(10:*(T:==0)))
+m: st_numscalar("checkmin", min(T) )
+
+
+if checkmin>5 tab `main' `if' `in' `options'
+else noi di _n "**TABLE OF `main' REDACTED DUE TO SMALL N**" _n
+
+end