fix vignette issue with knitr

vignettes/articles/web_only/u5mr-dhs-vignette.Rmd

@@ -94,20 +94,9 @@ The map files for this DHS can be freely downloaded from [https://spatialdata.dh
 mapfilename <- "data/shps/sdr_subnational_boundaries.shp"
 sf_use_s2(FALSE)
 geo <- read_sf(mapfilename)
-```
-
-```
-## Error: Cannot open "data/shps/sdr_subnational_boundaries.shp"; The file doesn't seem to exist.
-```
-
-```r
 Amat <- getAmat(geo, geo$REGNAME)
 ```
 
-```
-## Error in eval(expr, envir, enclos): object 'geo' not found
-```
-
 
 The `Amat` matrix encodes the spatial adjacency matrix of the 8 Admin-1 region groups, with column and row names matching the regions used in the map. This adjacency matrix will be used for the spatial smoothing model. It can also be created by hand if necessary. 
 
@@ -294,58 +283,20 @@ The syntax to fit subnational smoothing model is similar. Similar to the nationa
 ```r
 fit3 <- smoothDirect(data = direct, Amat = Amat, year_label = years, year_range = c(1985,
     2019), time.model = "rw2", type.st = 4, m = 1)
-```
-
-```
-## Error in eval(expr, envir, enclos): object 'Amat' not found
-```
-
-```r
 out3 <- getSmoothed(fit3)
 ```
 
-```
-## Error in eval(expr, envir, enclos): object 'fit3' not found
-```
-
 Similarly we can also estimate the Random Walk 2 random effects on the yearly scale. 
 
 
 
 ```r
 fit4 <- smoothDirect(data = direct, Amat = Amat, year_label = years, year_range = c(1985,
     2019), time.model = "rw2", type.st = 4, m = 5)
-```
-
-```
-## Error in eval(expr, envir, enclos): object 'Amat' not found
-```
-
-```r
 out4 <- getSmoothed(fit4)
-```
-
-```
-## Error in eval(expr, envir, enclos): object 'fit4' not found
-```
 
-```r
 g1 <- plot(out3) + ggtitle("Subnational period model") + ylim(c(0, 0.3))
-```
-
-```
-## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'plot': object 'out3' not found
-```
-
-```r
 g2 <- plot(out4) + ggtitle("Subnational yearly model") + ylim(c(0, 0.3))
-```
-
-```
-## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'plot': object 'out4' not found
-```
-
-```r
 g1 + g2
 ```
 
@@ -360,9 +311,7 @@ plot(out4, data.add = direct, option.add = list(point = "mean", by = "survey"))
     facet_wrap(~region, scales = "free")
 ```
 
-```
-## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'plot': object 'out4' not found
-```
+<img src="figure/unnamed-chunk-21-1.png" width="90%" />
 
 We can show the estimates over time on maps. We revert the color scale so that higher mortality are represented by darker colors. 
 
@@ -373,9 +322,7 @@ mapPlot(data = subset(out4, is.yearly == FALSE), geo = geo, variables = "years",
     direction = -1, legend.label = "U5MR", per1000 = TRUE)
 ```
 
-```
-## Error in eval(expr, envir, enclos): object 'geo' not found
-```
+<img src="figure/unnamed-chunk-22-1.png" width="90%" />
 
 In order to also illustrate uncertainties of the estimates when presented on maps, we can use hatching to indicate the width of the 94% posterior credible intervals.
 
@@ -386,9 +333,7 @@ hatchPlot(data = subset(out4, is.yearly == FALSE), geo = geo, variables = "years
     is.long = TRUE, direction = -1, legend.label = "U5MR", per1000 = TRUE, ncol = 4)
 ```
 
-```
-## Error in eval(expr, envir, enclos): object 'geo' not found
-```
+<img src="figure/unnamed-chunk-23-1.png" width="90%" />
 
 
 
@@ -413,18 +358,7 @@ for (model in c("rw1", "rw2")) {
         index <- index + 1
     }
 }
-```
-
-```
-## Error in eval(expr, envir, enclos): object 'Amat' not found
-```
-
-```r
 plot(est.list, plot.CI = TRUE) + facet_grid(st.model ~ st.u)
 ```
 
-```
-## Error in plot.window(...): need finite 'xlim' values
-```
-
 <img src="figure/unnamed-chunk-24-1.png" width="90%" />