fix NA values in survey_hiv_indicators column std_error

data-raw/survey.R

@@ -896,6 +896,8 @@ survey_hiv_indicators <- calc_survey_hiv_indicators(
   survey_biomarker,
   demo_area_hierarchy)
 
+filter(survey_hiv_indicators, is.na(std_error))
+survey_hiv_indicators$std_error[is.na(survey_hiv_indicators$std_error)] <- 0.0
 
 #' ## Save datasets
 #'

inst/extdata/demo_survey_hiv_indicators.csv

@@ -15908,7 +15908,7 @@ art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,both,Y045_049,177,240,1
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,both,Y050_054,129,162,120.54389037448695,0.7748599566807669,0.03905360222942496,0.6893738079387397,0.8422048964212699
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,both,Y055_059,88,109,80.85309273638147,0.7695115138884412,0.044489222350464,0.6712678191657072,0.8451667482868456
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,both,Y060_064,60,70,54.212237875912976,0.8091266443320001,0.055209812341668336,0.6778028857662217,0.8952003952540727
-art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,both,Y000_000,1,1,1,0,NA,NA,NA
+art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,both,Y000_000,1,1,1,0,0,NA,NA
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,both,Y001_004,18,19,14.001704889638258,0.6569553204935843,0.12727378529840955,0.3876681553116353,0.8527877522680566
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,male,Y015_049,296,559,413.7810042594462,0.6025270373779054,0.024935000059006975,0.5527871489046333,0.6502351252266833
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,male,Y015_064,330,715,527.9651856480385,0.6349933905516871,0.021412824012724166,0.5920935512814668,0.6758514631593975
@@ -15957,7 +15957,7 @@ art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,female,Y045_049,109,134
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,female,Y050_054,79,92,67.26084291939691,0.7383353798552105,0.055047935218396404,0.6174825784892003,0.8314295014319167
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,female,Y055_059,54,58,40.980527410570545,0.8062973593393401,0.05865815216628626,0.6659698999459963,0.8968073503551113
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,female,Y060_064,31,35,28.865378277878452,0.8141291563780553,0.06993925587137714,0.6390399789700845,0.9155166554304044
-art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,female,Y000_000,1,1,1,0,NA,NA,NA
+art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,female,Y000_000,1,1,1,0,0,NA,NA
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,female,Y001_004,8,8,7.125023177711781,0.450821665090431,0.2012542756391103,0.14300300695794438,0.8015270629465587
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_1_demo,Northern,all,both,Y015_049,47,149,129.9167754259742,0.7095078187744512,0.03299395227896437,0.6408924544039271,0.7697233867575317
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_1_demo,Northern,all,both,Y015_064,51,182,159.15510760305264,0.7271995528723063,0.02939191051171283,0.6659832380873617,0.7808877744617115
@@ -16123,7 +16123,7 @@ art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,both,Y045_049,99,14
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,both,Y050_054,76,95,71.33216353389295,0.7654317997684672,0.053298704879957075,0.6458560365159409,0.8537741512108593
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,both,Y055_059,41,48,35.16776879176661,0.8105785751619565,0.06359671606174175,0.6551955289951933,0.9059869905198982
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,both,Y060_064,44,53,42.27859686695561,0.792880355818035,0.06496072924156025,0.6380880359822956,0.8926093745184708
-art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,both,Y000_000,1,1,1,0,NA,NA,NA
+art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,both,Y000_000,1,1,1,0,0,NA,NA
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,both,Y001_004,12,13,9.677498093333027,0.7020247557532454,0.14279478706913773,0.3820267319420337,0.8997879904178266
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,male,Y015_049,158,341,251.73162445844568,0.6280110059125654,0.030301399848660867,0.5669630915577909,0.6852307049151976
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,male,Y015_064,168,428,313.8365771888916,0.6539088283950566,0.02607980646571124,0.6011844780229604,0.703105168512981
@@ -16172,7 +16172,7 @@ art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,female,Y045_049,63,
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,female,Y050_054,47,54,40.356276767680704,0.7222581019604578,0.07329535690746976,0.5596057497573013,0.841818114403322
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,female,Y055_059,25,28,19.107157416862716,0.8298465119087445,0.08015581744009995,0.6158394863709681,0.9368584888491283
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,female,Y060_064,24,27,23.262461904120887,0.8269290431469299,0.07485386157110663,0.6315585086832759,0.9301584463389765
-art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,female,Y000_000,1,1,1,0,NA,NA,NA
+art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,female,Y000_000,1,1,1,0,0,NA,NA
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,female,Y001_004,4,4,3.8214178328274997,0.5808147855433148,0.26283549126771677,0.14310356057744214,0.9199734694284686
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_1_demo,Northern,all,both,Y015_049,47,149,129.9167754259742,0.7095078187744512,0.03299395227896437,0.6408924544039271,0.7697233867575317
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_1_demo,Northern,all,both,Y015_064,51,182,159.15510760305264,0.7271995528723063,0.02939191051171283,0.6659832380873617,0.7808877744617115
@@ -16478,7 +16478,7 @@ art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,both,Y045_049,62,
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,both,Y050_054,47,55,40.25105198063331,0.7702540336506881,0.07587604290389445,0.5913080679347493,0.8859594244748754
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,both,Y055_059,25,30,23.643309698961644,0.7846071237709136,0.07818954658150766,0.5952991473553306,0.900206663772158
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,both,Y060_064,30,35,28.54222819769796,0.8417338681594824,0.06840839294112025,0.6603221468549171,0.9356943668513962
-art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,both,Y000_000,1,1,1,0,NA,NA,NA
+art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,both,Y000_000,1,1,1,0,0,NA,NA
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,both,Y001_004,6,6,5.062361470955532,0.7076824180773964,0.19608419347533246,0.2741558784349028,0.9394569697215944
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,male,Y015_049,102,240,185.62103250738627,0.631185482012857,0.033752889182644234,0.5629456597244568,0.6945517399000651
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,male,Y015_064,108,297,226.17645181697776,0.6553808467814354,0.03136168114855262,0.5916094824478016,0.7140079994019548
@@ -16527,7 +16527,7 @@ art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,female,Y045_049,4
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,female,Y050_054,27,30,22.310384504820178,0.7684727946846136,0.09428056599320409,0.5401951442385823,0.9036354199787159
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,female,Y055_059,14,17,12.967302486273946,0.8146617204899899,0.114543273456242,0.49842815021013287,0.9510826093278688
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,female,Y060_064,14,16,14.218776381233273,0.8129599303256666,0.1010522740650321,0.5416087994590735,0.9411381575613841
-art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,female,Y000_000,1,1,1,0,NA,NA,NA
+art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,female,Y000_000,1,1,1,0,0,NA,NA
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,female,Y001_004,1,1,1,1,0,NA,NA
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_1_demo,Chitipa,all,both,Y015_049,4,14,13.079921524097607,0.5697500395361266,0.09690420400556586,0.37896083604068515,0.7418534116545574
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_1_demo,Chitipa,all,both,Y015_064,4,15,13.962417971284841,0.5901693603411527,0.08628538364704366,0.41713662645085964,0.7434294300508175
@@ -17659,7 +17659,7 @@ art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,both,Y045_049,38,5
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,both,Y050_054,31,37,28.971021157532107,0.7578903195187772,0.08478863112371024,0.5586003626082315,0.8856250953721512
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,both,Y055_059,13,17,16.826643640957975,0.8229920644290639,0.08414212343243836,0.5998121049243477,0.9351616233325795
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,both,Y060_064,14,16,12.37343064787388,0.53422764153731,0.15381061635737578,0.25456619661424157,0.7939097299536315
-art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,both,Y000_000,1,1,1,0,NA,NA,NA
+art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,both,Y000_000,1,1,1,0,0,NA,NA
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,both,Y001_004,3,3,2.9685669356661766,0.659421354577168,0.28378121752100083,0.1399316946654481,0.9584050086609006
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,male,Y015_049,63,151,117.2254133741664,0.5505924779260516,0.04582465796283461,0.4601074311530433,0.6378488857573587
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,male,Y015_064,65,184,140.99689221636893,0.5792052685775926,0.041926727264350025,0.49558802246015765,0.6585123948797179
@@ -17708,7 +17708,7 @@ art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,female,Y045_049,24
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,female,Y050_054,17,20,13.489097261708068,0.7636912670847119,0.12379844197501175,0.4572321114467524,0.9253622959017467
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,female,Y055_059,8,11,10.932092422559974,0.8292373699270147,0.10712500257861728,0.5243518087060408,0.9553395968870257
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,female,Y060_064,6,6,4.784013791501877,0.21706432603953751,0.15478125384609845,0.04445038412399939,0.62297608074363
-art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,female,Y000_000,1,1,1,0,NA,NA,NA
+art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,female,Y000_000,1,1,1,0,0,NA,NA
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_24_demo,Mwanza,all,both,Y015_049,3,17,16.253566102685422,0.6179858275360864,0.08388896390947519,0.4463448442931162,0.7644918446869419
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_24_demo,Mwanza,all,both,Y015_064,3,17,16.253566102685422,0.6179858275360864,0.08388479202422319,0.446353403492301,0.7644856086993684
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_24_demo,Mwanza,all,both,Y000_064,3,17,16.253566102685422,0.6179858275360864,0.08388413010421227,0.4463547615156104,0.7644846192740784
@@ -19393,7 +19393,7 @@ art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,both,Y045_049
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,both,Y050_054,28,33,30.399052972451507,0.7622677140135403,0.07993068973760899,0.5746015825273446,0.883875625599874
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,both,Y055_059,13,17,16.826643640957975,0.8229920644290639,0.08414212343243836,0.5998121049243477,0.9351616233325795
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,both,Y060_064,13,15,13.87136677542012,0.6513141948956539,0.14392886886733905,0.35039100923771527,0.8661064521174505
-art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,both,Y000_000,1,1,1,0,NA,NA,NA
+art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,both,Y000_000,1,1,1,0,0,NA,NA
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,both,Y001_004,3,3,2.9685669356661766,0.659421354577168,0.28378121752100083,0.1399316946654481,0.9584050086609006
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,male,Y015_049,58,139,123.04362621121932,0.5208130984522058,0.04070545064155076,0.4411790635998353,0.5994032623510778
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,male,Y015_064,60,172,150.80269737778997,0.559343474613215,0.03769542445367252,0.4846920031573383,0.6314045665576387
@@ -19442,7 +19442,7 @@ art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,female,Y045_0
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,female,Y050_054,14,16,14.88670670542045,0.7800976185085934,0.10332952234736598,0.5214019678908002,0.9203278928842241
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,female,Y055_059,8,11,10.932092422559974,0.8292373699270147,0.10712500257861728,0.5243518087060408,0.9553395968870257
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,female,Y060_064,5,5,4.677033003604339,0.3292526499520002,0.20756938876381897,0.07217768246736284,0.7559450080669983
-art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,female,Y000_000,1,1,1,0,NA,NA,NA
+art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,female,Y000_000,1,1,1,0,0,NA,NA
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_30_demo,Thyolo,all,both,Y015_049,12,69,65.55932519254539,0.7074743010501984,0.04501746203468915,0.6122572491293277,0.7874273225463437
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_30_demo,Thyolo,all,both,Y015_064,13,77,73.20869482890575,0.7334283435031405,0.045281767402567695,0.6360233145445926,0.8124529446325933
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_30_demo,Thyolo,all,both,Y000_064,13,79,68.51317841292828,0.7519647646915016,0.042277439899731754,0.6603489780726222,0.8254024596619344