code: minor updates for revisions

mishra-lab · Nov 24, 2021 · 5597d4c · 5597d4c
1 parent f03069a
commit 5597d4c
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Showing 3 changed files with 13 additions and 7 deletions.
diff --git a/code/analysis/meta.r b/code/analysis/meta.r
@@ -115,8 +115,9 @@ P = list(# stuff to plot
   ),
   dist = c('api.prev','api.inc','art.rbeta','act.n','age.n','hiv.n',
            'act.HRW.p','act.HRM.p','act.HRW.cr','act.HR.pr',
-           'api.prev.cat','api.phase','Risk','pt.def')
+           'api.prev.cat','api.phase','Risk','pt.def'),
   # TODO: api.inc, api.chi from XA
+  eff.sub = c('Sex','Risk','act.turn.any','pt.def')
 )
 D = list(# definitions
   api.prev     = 'HIV prevalence at $t_0$ (\\%)',
@@ -146,7 +147,7 @@ D = list(# definitions
   age.mix      = 'Type of age mixing',
 
   act.kp       = 'Activity groups \\& key populations',
-  Risk         = 'Summary of risk heterogeneity',
+  Risk         = 'Risk Stratification \\& ART cascade differences',
   Sex          = 'Sex stratification \\& any ART cascade differences',
   act.HRW.p    = 'Proportion of women in the highest female activity group',
   act.HRM.p    = 'Proportion of men in the client or highest activity male group',
@@ -174,9 +175,9 @@ R = list(# Rename stuff
     'HTC Behav. Change' = 'bc.any',
     'Sex Stratification' = 'act.def.sex',
     'Any ART Diff. by Sex' = 'diff.any.sex',
-    'Sex Strat. & ART' = 'Sex',
+    'Sex Stratif. & Cascade Diff.' = 'Sex',
     'Activity Turnover' = 'act.turn.any',
-    'Risk Definition' = 'Risk'),
+    'Risk Stratif. & Cascade Diff.' = 'Risk'),
   t.cat = list(
     '0-10'='0',
     '11-20'='10',

diff --git a/code/analysis/numeric.r b/code/analysis/numeric.r
@@ -234,13 +234,16 @@ numeric.api = function(XA){
         } else {
           tabstr = strfun('%.0f & %.0f & ( %.0f , %.0f ) & \\textsc{ref} & ',nums[1:4])
         }
+        save.tex(strfun('%.0f~(%.0f,~%.0f)',nums[5:7]),namefun(var,level,'eff'),dir=dir)
         save.tex(tabstr,namefun(var,level,'xtab'),dir=dir)
       }
     }
   }
   names(model) = c('IR','CIA')
   g = plot.effects(model,group='Outcome')
   save.plot(g,'effects',dir='api',w=6,h=10)
+  g = plot.effects(model,group='Outcome',subset=c(P$eff.sub,'(Intercept)'))
+  save.plot(g,'effects-subset',dir='api',w=6,h=4)
 }
 save.distr = function(x,name,dir='',d=2,funs=NULL,lt=NULL){
   fun.list = list(

diff --git a/code/analysis/plot.r b/code/analysis/plot.r
@@ -93,28 +93,30 @@ gen.effects = function(model,name=NULL,group=''){
     if (var=='(Intercept)'){ varlvls = var; i = TRUE; } else { i = FALSE; }
     E.var = coef[varlvls,c('Estimate','low','high')]
     lvl.ref = paste0('\n    REF = ',rename.lvl(lvls[is.na(E.var$Estimate)],var))
-    E.var$var = paste0(rename.lvl(var,'vars'),ifelse(i,'',lvl.ref))
+    E.var$var = var
     E.var$lvl = rename.lvl(lvls,var)
+    E.var$grp = paste0(rename.lvl(var,'vars'),ifelse(i,'',lvl.ref))
     return(E.var)
   }))
   E[[group]] = name
   E = E[!is.na(E$Estimate),]
   return(E)
 }
 
-plot.effects = function(model,group='.'){
+plot.effects = function(model,group='.',subset=NULL){
   if ('coefficients' %in% names(model)){
     E = gen.effects(model,name='',group=group)
   } else {
     E = do.call(rbind,lapply(names(model),function(name){
       gen.effects(model[[name]],name=name,group=group) }))
   }
+  if (!is.null(subset)){ E = E[E$var %in% subset,] }
   pos = position_dodge(width=.6)
   g = ggplot(E,aes_string(x='Estimate',y='lvl',xmin='low',xmax='high',color=group)) +
     geom_point(position=pos) +
     geom_linerange(position=pos) +
     scale_color_viridis(option='inferno',discrete=TRUE,begin=.3,end=.7) +
-    facet_grid(rows=vars(E$var),scales='free_y',space='free_y',switch='y') +
+    facet_grid(rows=vars(E$grp),scales='free_y',space='free_y',switch='y') +
     labs(x='Effect',y='Factor') +
     theme_light() +
     theme(legend.position='top',