R Under development (unstable) (2024-10-01 r87205 ucrt) -- "Unsuffered Consequences"
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> ## Copyright 2013-2020 Stefan Widgren and Maria Noremark,
> ## National Veterinary Institute, Sweden
> ##
> ## Licensed under the EUPL, Version 1.1 or - as soon they
> ## will be approved by the European Commission - subsequent
> ## versions of the EUPL (the "Licence");
> ## You may not use this work except in compliance with the
> ## Licence.
> ## You may obtain a copy of the Licence at:
> ##
> ## http://ec.europa.eu/idabc/eupl
> ##
> ## Unless required by applicable law or agreed to in
> ## writing, software distributed under the Licence is
> ## distributed on an "AS IS" basis,
> ## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either
> ## express or implied.
> ## See the Licence for the specific language governing
> ## permissions and limitations under the Licence.
> 
> library(EpiContactTrace)
> data(transfers)
> 
> ##
> ## Check shortest paths
> ##
> 
> ##
> ## Case 1
> ##
> sp_1 <- ShortestPaths(transfers, root = 2645, tEnd = "2005-10-31", days = 90)
> sp_2 <- ShortestPaths(Trace(movements = transfers,
+                             root = 2645,
+                             tEnd = "2005-10-31",
+                             days = 90))
> in_1 <- sp_1[sp_1$direction == "in", c("source", "distance")]
> in_2 <- sp_2[sp_2$direction == "in", c("source", "distance")]
> in_1 <- in_1[order(in_1$source, in_1$distance), ]
> in_2 <- in_2[order(in_2$source, in_2$distance), ]
> rownames(in_1) <- NULL
> rownames(in_2) <- NULL
> stopifnot(identical(in_1, in_2))
> out_1 <- sp_1[sp_1$direction == "out", c("destination", "distance")]
> out_2 <- sp_2[sp_2$direction == "out", c("destination", "distance")]
> out_1 <- out_1[order(out_1$destination, out_1$distance), ]
> out_2 <- out_2[order(out_2$destination, out_2$distance), ]
> rownames(out_1) <- NULL
> rownames(out_2) <- NULL
> stopifnot(identical(out_1, out_2))
> 
> ##
> ## Case 2
> ##
> sp_in_exp <- data.frame(
+     root = c("100", "100", "100", "100", "100"),
+     source = c("54", "262", "356", "357", "358"),
+     distance = c(1L, 1L, 1L, 1L, 1L),
+     stringsAsFactors = FALSE)
> 
> sp_in <- ShortestPaths(Trace(movements = transfers,
+                              root = 100,
+                              tEnd = "2005-10-31",
+                              days = 90))
> sp_in <- sp_in[sp_in$direction == "in", c("root", "source", "distance")]
> sp_in <- sp_in[order(as.numeric(sp_in$source)), ]
> rownames(sp_in) <- NULL
> stopifnot(identical(sp_in, sp_in_exp))
> 
> sp_out_exp <- data.frame(
+     root = c("100", "100", "100", "100", "100", "100",
+         "100", "100", "100", "100", "100", "100", "100", "100"),
+     destination = c("101", "357", "358", "2508", "8239", "8243",
+         "8327", "8356", "8388", "8420", "8991", "9003", "9087", "9110"),
+     distance = c(1L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 3L),
+     stringsAsFactors = FALSE)
> 
> sp_out <- ShortestPaths(Trace(movements = transfers,
+                               root = 100,
+                               tEnd = "2005-10-31",
+                               days = 90))
> sp_out <- sp_out[sp_out$direction == "out",
+                  c("root", "destination", "distance")]
> sp_out <- sp_out[order(as.numeric(sp_out$destination)), ]
> rownames(sp_out) <- NULL
> stopifnot(identical(sp_out, sp_out_exp))
> 
> proc.time()
   user  system elapsed 
   2.79    0.18    2.92