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R3744/TransitionTime.R
76bc7dbf8fd7HCV_reinfection

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TransitionTime.R
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#####################################################################
### specifies which transitions are "time to transition"
#####################################################################
#template for time to transition logic
timeToTrans <- matrix(data = FALSE, nrow = statesNum, ncol = statesNum)
####################################################################
# specifies which transitions are "time to transition"
for (i in 1:5)
{
timeToTrans [i, i + 5] = TRUE # progress horizantally
}
for(i in 1:49)
{
if (i > 15 && i < 26)
{
if (i %% blocks_size == 0)
timeToTrans [i, blocks_size * blocks_nb] = TRUE # spontaneous recovery for state F4 at any block
else
timeToTrans [i, blocks_size * (blocks_size - floor(i/ blocks_size)) + i] = TRUE # Spontaneous recovery
}# end of if (i > 15 && i < 26)
########################################
if (i < 16)
{
if (i %% blocks_size == 0)
timeToTrans [i, blocks_size * blocks_nb] = TRUE # spontaneous recovery for state F4 at any block
else
{
timeToTrans [i, blocks_size * (blocks_size - floor(i/ blocks_size)) + i] = TRUE # Spontaneous recovery
}
}
}
for (i in 11:25)
timeToTrans [i, i + 5] = TRUE
##########################################
#spontaneous recovery in DC, HCC and LT
for (i in 31:35)
timeToTrans [i, 36] = TRUE
for (i in 37:41)
timeToTrans [i, 42] = TRUE
for (i in 43: 47)
timeToTrans [i, 48] = TRUE
############################################
for (i in 0:2)
{
timeToTrans [35 + 6 * i, 36 + 6 * i] = TRUE #SVR
timeToTrans [33 + 6 * i, 34 + 6 * i] = TRUE # Scenario.treatment
timeToTrans [34 + 6 * i, 36 + 6 * i] = TRUE # SVR
timeToTrans [34 + 6 * i, 35 + 6 * i] = TRUE # second treatment
}
####################################################
timeToTrans[31, 32] = TRUE
timeToTrans[37,38] = TRUE
timeToTrans[43,44] = TRUE
#which(timeToTrans == TRUE, arr.ind = TRUE)
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