adding default values to item x group pairs that don’t have a value (df %>% spread %>% gather seems strange)

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There is a new function complete in the development version of tidyr that does this. 

df1 %>% complete(itemid, groupid, fill = list(value = 0))
##    itemid groupid value
## 1       1     one     3
## 2       1     two     0
## 3       2     one     2
## 4       2     two     0
## 5       3     one     1
## 6       3     two     0
## 7       4     one     0
## 8       4     two     2
## 9       5     one     0
## 10      5     two     3
## 11      6     one    22
## 12      6     two     1

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