[1] "Working dir: /home/bobby/epicvs/epi/amei/inst/doc"
[1] "27-04-2010-10:34:39"
[1] "EXPRESSION:"
[1] "seed <- 12345"
[1] "DEPENDENCIES:"
list()
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-10:34:39"
[1] "EXPRESSION:"
[1] "set.seed(seed)"
[1] "DEPENDENCIES:"
                              seed 
"6ecc3cee4446acafa978aa7735cedf7f" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-10:34:39"
[1] "EXPRESSION:"
[1] "vac <- list(frac = 0, stop = 0)"
[1] "DEPENDENCIES:"
list()
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-10:34:39"
[1] "EXPRESSION:"
[1] "init.MCepi <- MCepi(init, true, vac, costs)"
[1] "DEPENDENCIES:"
                               vac 
"1cbb46ecad05db131f656701e52e6d24" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-10:34:40"
[1] "EXPRESSION:"
[1] "plot(init.MCepi)"
[1] "DEPENDENCIES:"
                        init.MCepi 
"d2c2299ce31834724f50f25965f8032e" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-10:34:40"
[1] "EXPRESSION:"
[1] "plot(init.MCepi, type = \"costs\")"
[1] "DEPENDENCIES:"
                        init.MCepi 
"d2c2299ce31834724f50f25965f8032e" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-10:34:40"
[1] "EXPRESSION:"
[1] "vacgrid <- list(fracs = seq(0, 1, 0.1), stops = seq(2, init$S0 -      75, 75))"
[1] "DEPENDENCIES:"
list()
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-10:34:41"
[1] "EXPRESSION:"
[1] "out.optvac <- optvac(init, true, vacgrid, costs)"
[1] "DEPENDENCIES:"
                           vacgrid 
"6136d4c9ffd47d46dc71c25ad39bafc6" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-10:34:43"
[1] "EXPRESSION:"
[1] "best <- getpolicy(out.optvac)"
[1] "DEPENDENCIES:"
                        out.optvac 
"703572c7a1912e609926dc6133372e0f" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-10:34:43"
[1] "EXPRESSION:"
[1] "worst <- getpolicy(out.optvac, which = \"worst\")"
[1] "DEPENDENCIES:"
                        out.optvac 
"703572c7a1912e609926dc6133372e0f" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-10:34:43"
[1] "EXPRESSION:"
[1] "rbind(best, worst)"
[1] "DEPENDENCIES:"
                              best 
"583dddd4cc4c97cb38b0a4704165e012" 
                             worst 
"87f5ec50cb1ea6c5f6be9b986eb60446" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-10:34:43"
[1] "EXPRESSION:"
[1] "plot(out.optvac)"
[1] "DEPENDENCIES:"
                        out.optvac 
"703572c7a1912e609926dc6133372e0f" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-10:34:43"
[1] "EXPRESSION:"
[1] "vac.opt <- best[3:4]"
[1] "DEPENDENCIES:"
                              best 
"583dddd4cc4c97cb38b0a4704165e012" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-10:34:43"
[1] "EXPRESSION:"
[1] "opt.MCepi <- MCepi(init, true, vac.opt, costs)"
[1] "DEPENDENCIES:"
                           vac.opt 
"a738dfbca45e6eb1c25331fdd739b72c" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-10:34:44"
[1] "EXPRESSION:"
[1] "plot(opt.MCepi)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-10:34:45"
[1] "EXPRESSION:"
[1] "plot(opt.MCepi, type = \"costs\")"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-10:34:45"
[1] "EXPRESSION:"
[1] "getvac(opt.MCepi)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-10:34:45"
[1] "EXPRESSION:"
[1] "T <- length(opt.MCepi$Median$C)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-10:34:45"
[1] "EXPRESSION:"
[1] "optC <- getcost(opt.MCepi)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-10:34:45"
[1] "EXPRESSION:"
[1] "initC <- getcost(init.MCepi)"
[1] "DEPENDENCIES:"
                        init.MCepi 
"d2c2299ce31834724f50f25965f8032e" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-10:34:45"
[1] "EXPRESSION:"
[1] "data.frame(rbind(initC, optC), row.names = c(\"init\", \"opt\"))"
[1] "DEPENDENCIES:"
                             initC 
"fa9b162bb4f585e9f39ba5af0ad2041a" 
                              optC 
"69ca0a605b3699aee6daff787d11edc6" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-10:34:45"
[1] "EXPRESSION:"
[1] "opt.MCepi"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-10:34:46"
[1] "EXPRESSION:"
[1] "out.man <- manage(init, epistep, vacgrid, costs)"
[1] "DEPENDENCIES:"
                           vacgrid 
"6136d4c9ffd47d46dc71c25ad39bafc6" 
[1] "computing..."
[1] "Working dir: /home/bobby/epicvs/epi/amei/inst/doc"
[1] "27-04-2010-10:44:58"
[1] "EXPRESSION:"
[1] "seed <- 12345"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_2/6ecc3cee4446acafa978aa7735cedf7f.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:44:58"
[1] "EXPRESSION:"
[1] "set.seed(seed)"
[1] "DEPENDENCIES:"
                              seed 
"6ecc3cee4446acafa978aa7735cedf7f" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_2/0e1b44a61a0ace2fb0163953bac48b05.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:44:58"
[1] "EXPRESSION:"
[1] "vac <- list(frac = 0, stop = 0)"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_4/1cbb46ecad05db131f656701e52e6d24.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:44:59"
[1] "EXPRESSION:"
[1] "init.MCepi <- MCepi(init, true, vac, costs)"
[1] "DEPENDENCIES:"
                               vac 
"1cbb46ecad05db131f656701e52e6d24" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_5/d2c2299ce31834724f50f25965f8032e.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:44:59"
[1] "EXPRESSION:"
[1] "plot(init.MCepi)"
[1] "DEPENDENCIES:"
                        init.MCepi 
"d2c2299ce31834724f50f25965f8032e" 
[1] "FOUND r_env_cache/2.10.1/epis_6/b74ab8610420b87e1dd6ddc17800bd12.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:44:59"
[1] "EXPRESSION:"
[1] "plot(init.MCepi, type = \"costs\")"
[1] "DEPENDENCIES:"
                        init.MCepi 
"d2c2299ce31834724f50f25965f8032e" 
[1] "FOUND r_env_cache/2.10.1/costs_7/aeef4fb5e80bd1f6c5eff1a31e6eaa8e.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:44:59"
[1] "EXPRESSION:"
[1] "vacgrid <- list(fracs = seq(0, 1, 0.1), stops = seq(2, init$S0 -      75, 75))"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_8/6136d4c9ffd47d46dc71c25ad39bafc6.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:44:59"
[1] "EXPRESSION:"
[1] "out.optvac <- optvac(init, true, vacgrid, costs)"
[1] "DEPENDENCIES:"
                           vacgrid 
"6136d4c9ffd47d46dc71c25ad39bafc6" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_9/703572c7a1912e609926dc6133372e0f.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:44:59"
[1] "EXPRESSION:"
[1] "best <- getpolicy(out.optvac)"
[1] "DEPENDENCIES:"
                        out.optvac 
"703572c7a1912e609926dc6133372e0f" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_10/583dddd4cc4c97cb38b0a4704165e012.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:44:59"
[1] "EXPRESSION:"
[1] "worst <- getpolicy(out.optvac, which = \"worst\")"
[1] "DEPENDENCIES:"
                        out.optvac 
"703572c7a1912e609926dc6133372e0f" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_10/87f5ec50cb1ea6c5f6be9b986eb60446.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:45:00"
[1] "EXPRESSION:"
[1] "rbind(best, worst)"
[1] "DEPENDENCIES:"
                              best 
"583dddd4cc4c97cb38b0a4704165e012" 
                             worst 
"87f5ec50cb1ea6c5f6be9b986eb60446" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_10/8fa614174ae97d23af9225efe6c77c3c.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:45:00"
[1] "EXPRESSION:"
[1] "plot(out.optvac)"
[1] "DEPENDENCIES:"
                        out.optvac 
"703572c7a1912e609926dc6133372e0f" 
[1] "FOUND r_env_cache/2.10.1/optvac_11/2dc3acf6a5d632b2ea1f6957c251bea5.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:45:00"
[1] "EXPRESSION:"
[1] "vac.opt <- best[3:4]"
[1] "DEPENDENCIES:"
                              best 
"583dddd4cc4c97cb38b0a4704165e012" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_12/a738dfbca45e6eb1c25331fdd739b72c.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:45:00"
[1] "EXPRESSION:"
[1] "opt.MCepi <- MCepi(init, true, vac.opt, costs)"
[1] "DEPENDENCIES:"
                           vac.opt 
"a738dfbca45e6eb1c25331fdd739b72c" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_12/5cc568d78b57af17d64152306621f5e3.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:45:00"
[1] "EXPRESSION:"
[1] "plot(opt.MCepi)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/episov_13/c37c3ac54c57d8dadd5665219d72124e.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:45:00"
[1] "EXPRESSION:"
[1] "plot(opt.MCepi, type = \"costs\")"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/costsov_14/67ad9a26d9c4ea35e49d26eb5812d70c.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:45:00"
[1] "EXPRESSION:"
[1] "getvac(opt.MCepi)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_15/9ecd6e44946d5ff837bb4dcffb3a8c24.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:45:01"
[1] "EXPRESSION:"
[1] "T <- length(opt.MCepi$Median$C)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_16/d8cce82ec58af71c935ab28e306340af.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:45:01"
[1] "EXPRESSION:"
[1] "optC <- getcost(opt.MCepi)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_16/69ca0a605b3699aee6daff787d11edc6.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:45:01"
[1] "EXPRESSION:"
[1] "initC <- getcost(init.MCepi)"
[1] "DEPENDENCIES:"
                        init.MCepi 
"d2c2299ce31834724f50f25965f8032e" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_16/fa9b162bb4f585e9f39ba5af0ad2041a.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:45:01"
[1] "EXPRESSION:"
[1] "data.frame(rbind(initC, optC), row.names = c(\"init\", \"opt\"))"
[1] "DEPENDENCIES:"
                             initC 
"fa9b162bb4f585e9f39ba5af0ad2041a" 
                              optC 
"69ca0a605b3699aee6daff787d11edc6" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_16/979f9bfd8f85d50efa97caf6b7e624ad.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:45:01"
[1] "EXPRESSION:"
[1] "opt.MCepi"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_17/b9a1029e977fa93cdc9e292d527f4532.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:45:01"
[1] "EXPRESSION:"
[1] "out.man <- manage(init, epistep, vacgrid, costs)"
[1] "DEPENDENCIES:"
                           vacgrid 
"6136d4c9ffd47d46dc71c25ad39bafc6" 
[1] "computing..."
[1] "Working dir: /home/bobby/epicvs/epi/amei/inst/doc"
[1] "27-04-2010-10:46:19"
[1] "EXPRESSION:"
[1] "seed <- 12345"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_2/6ecc3cee4446acafa978aa7735cedf7f.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:46:20"
[1] "EXPRESSION:"
[1] "set.seed(seed)"
[1] "DEPENDENCIES:"
                              seed 
"6ecc3cee4446acafa978aa7735cedf7f" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_2/0e1b44a61a0ace2fb0163953bac48b05.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:46:20"
[1] "EXPRESSION:"
[1] "vac <- list(frac = 0, stop = 0)"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_4/1cbb46ecad05db131f656701e52e6d24.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:46:20"
[1] "EXPRESSION:"
[1] "init.MCepi <- MCepi(init, true, vac, costs)"
[1] "DEPENDENCIES:"
                               vac 
"1cbb46ecad05db131f656701e52e6d24" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_5/d2c2299ce31834724f50f25965f8032e.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:46:20"
[1] "EXPRESSION:"
[1] "plot(init.MCepi)"
[1] "DEPENDENCIES:"
                        init.MCepi 
"d2c2299ce31834724f50f25965f8032e" 
[1] "FOUND r_env_cache/2.10.1/epis_6/b74ab8610420b87e1dd6ddc17800bd12.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:46:20"
[1] "EXPRESSION:"
[1] "plot(init.MCepi, type = \"costs\")"
[1] "DEPENDENCIES:"
                        init.MCepi 
"d2c2299ce31834724f50f25965f8032e" 
[1] "FOUND r_env_cache/2.10.1/costs_7/aeef4fb5e80bd1f6c5eff1a31e6eaa8e.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:46:20"
[1] "EXPRESSION:"
[1] "vacgrid <- list(fracs = seq(0, 1, 0.1), stops = seq(2, init$S0 -      75, 75))"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_8/6136d4c9ffd47d46dc71c25ad39bafc6.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:46:21"
[1] "EXPRESSION:"
[1] "out.optvac <- optvac(init, true, vacgrid, costs)"
[1] "DEPENDENCIES:"
                           vacgrid 
"6136d4c9ffd47d46dc71c25ad39bafc6" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_9/703572c7a1912e609926dc6133372e0f.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:46:21"
[1] "EXPRESSION:"
[1] "best <- getpolicy(out.optvac)"
[1] "DEPENDENCIES:"
                        out.optvac 
"703572c7a1912e609926dc6133372e0f" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_10/583dddd4cc4c97cb38b0a4704165e012.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:46:21"
[1] "EXPRESSION:"
[1] "worst <- getpolicy(out.optvac, which = \"worst\")"
[1] "DEPENDENCIES:"
                        out.optvac 
"703572c7a1912e609926dc6133372e0f" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_10/87f5ec50cb1ea6c5f6be9b986eb60446.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:46:21"
[1] "EXPRESSION:"
[1] "rbind(best, worst)"
[1] "DEPENDENCIES:"
                              best 
"583dddd4cc4c97cb38b0a4704165e012" 
                             worst 
"87f5ec50cb1ea6c5f6be9b986eb60446" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_10/8fa614174ae97d23af9225efe6c77c3c.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:46:21"
[1] "EXPRESSION:"
[1] "plot(out.optvac)"
[1] "DEPENDENCIES:"
                        out.optvac 
"703572c7a1912e609926dc6133372e0f" 
[1] "FOUND r_env_cache/2.10.1/optvac_11/2dc3acf6a5d632b2ea1f6957c251bea5.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:46:21"
[1] "EXPRESSION:"
[1] "vac.opt <- best[3:4]"
[1] "DEPENDENCIES:"
                              best 
"583dddd4cc4c97cb38b0a4704165e012" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_12/a738dfbca45e6eb1c25331fdd739b72c.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:46:21"
[1] "EXPRESSION:"
[1] "opt.MCepi <- MCepi(init, true, vac.opt, costs)"
[1] "DEPENDENCIES:"
                           vac.opt 
"a738dfbca45e6eb1c25331fdd739b72c" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_12/5cc568d78b57af17d64152306621f5e3.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:46:21"
[1] "EXPRESSION:"
[1] "plot(opt.MCepi)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/episov_13/c37c3ac54c57d8dadd5665219d72124e.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:46:22"
[1] "EXPRESSION:"
[1] "plot(opt.MCepi, type = \"costs\")"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/costsov_14/67ad9a26d9c4ea35e49d26eb5812d70c.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:46:22"
[1] "EXPRESSION:"
[1] "getvac(opt.MCepi)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_15/9ecd6e44946d5ff837bb4dcffb3a8c24.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:46:22"
[1] "EXPRESSION:"
[1] "T <- length(opt.MCepi$Median$C)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_16/d8cce82ec58af71c935ab28e306340af.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:46:22"
[1] "EXPRESSION:"
[1] "optC <- getcost(opt.MCepi)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_16/69ca0a605b3699aee6daff787d11edc6.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:46:22"
[1] "EXPRESSION:"
[1] "initC <- getcost(init.MCepi)"
[1] "DEPENDENCIES:"
                        init.MCepi 
"d2c2299ce31834724f50f25965f8032e" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_16/fa9b162bb4f585e9f39ba5af0ad2041a.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:46:22"
[1] "EXPRESSION:"
[1] "data.frame(rbind(initC, optC), row.names = c(\"init\", \"opt\"))"
[1] "DEPENDENCIES:"
                             initC 
"fa9b162bb4f585e9f39ba5af0ad2041a" 
                              optC 
"69ca0a605b3699aee6daff787d11edc6" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_16/979f9bfd8f85d50efa97caf6b7e624ad.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:46:22"
[1] "EXPRESSION:"
[1] "opt.MCepi"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_17/b9a1029e977fa93cdc9e292d527f4532.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:46:23"
[1] "EXPRESSION:"
[1] "out.man <- manage(init, epistep, vacgrid, costs)"
[1] "DEPENDENCIES:"
                           vacgrid 
"6136d4c9ffd47d46dc71c25ad39bafc6" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-10:46:39"
[1] "EXPRESSION:"
[1] "plot(out.man)"
[1] "DEPENDENCIES:"
                           out.man 
"2a30b4a74e393458fe94c705419aabcb" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-10:46:40"
[1] "EXPRESSION:"
[1] "plot(out.man, type = \"cost\")"
[1] "DEPENDENCIES:"
                           out.man 
"2a30b4a74e393458fe94c705419aabcb" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-10:46:40"
[1] "EXPRESSION:"
[1] "getcost(out.man)"
[1] "DEPENDENCIES:"
                           out.man 
"2a30b4a74e393458fe94c705419aabcb" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-10:46:40"
[1] "EXPRESSION:"
[1] "true <- as.list(formals(epistep)$true)"
[1] "DEPENDENCIES:"
list()
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-10:46:40"
[1] "EXPRESSION:"
[1] "plot(out.man, type = \"params\", true = true)"
[1] "DEPENDENCIES:"
                           out.man 
"2a30b4a74e393458fe94c705419aabcb" 
                              true 
"2c5c7c936a067cd9d8176d7f02176bbb" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-10:46:41"
[1] "EXPRESSION:"
[1] "out.man"
[1] "DEPENDENCIES:"
                           out.man 
"2a30b4a74e393458fe94c705419aabcb" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-10:46:41"
[1] "EXPRESSION:"
[1] "out.MCmanage <- MCmanage(init, epistep, vacgrid, costs)"
[1] "DEPENDENCIES:"
                           vacgrid 
"6136d4c9ffd47d46dc71c25ad39bafc6" 
[1] "computing..."
[1] "Working dir: /home/bobby/epicvs/epi/amei/inst/doc"
[1] "27-04-2010-10:58:32"
[1] "EXPRESSION:"
[1] "seed <- 12345"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_2/6ecc3cee4446acafa978aa7735cedf7f.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:58:33"
[1] "EXPRESSION:"
[1] "set.seed(seed)"
[1] "DEPENDENCIES:"
                              seed 
"6ecc3cee4446acafa978aa7735cedf7f" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_2/0e1b44a61a0ace2fb0163953bac48b05.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:58:33"
[1] "EXPRESSION:"
[1] "vac <- list(frac = 0, stop = 0)"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_4/1cbb46ecad05db131f656701e52e6d24.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:58:33"
[1] "EXPRESSION:"
[1] "init.MCepi <- MCepi(init, true, vac, costs)"
[1] "DEPENDENCIES:"
                               vac 
"1cbb46ecad05db131f656701e52e6d24" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_5/d2c2299ce31834724f50f25965f8032e.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:58:33"
[1] "EXPRESSION:"
[1] "plot(init.MCepi)"
[1] "DEPENDENCIES:"
                        init.MCepi 
"d2c2299ce31834724f50f25965f8032e" 
[1] "FOUND r_env_cache/2.10.1/epis_6/b74ab8610420b87e1dd6ddc17800bd12.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:58:33"
[1] "EXPRESSION:"
[1] "plot(init.MCepi, type = \"costs\")"
[1] "DEPENDENCIES:"
                        init.MCepi 
"d2c2299ce31834724f50f25965f8032e" 
[1] "FOUND r_env_cache/2.10.1/costs_7/aeef4fb5e80bd1f6c5eff1a31e6eaa8e.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:58:33"
[1] "EXPRESSION:"
[1] "vacgrid <- list(fracs = seq(0, 1, 0.1), stops = seq(2, init$S0 -      75, 75))"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_8/6136d4c9ffd47d46dc71c25ad39bafc6.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:58:34"
[1] "EXPRESSION:"
[1] "out.optvac <- optvac(init, true, vacgrid, costs)"
[1] "DEPENDENCIES:"
                           vacgrid 
"6136d4c9ffd47d46dc71c25ad39bafc6" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_9/703572c7a1912e609926dc6133372e0f.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:58:34"
[1] "EXPRESSION:"
[1] "best <- getpolicy(out.optvac)"
[1] "DEPENDENCIES:"
                        out.optvac 
"703572c7a1912e609926dc6133372e0f" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_10/583dddd4cc4c97cb38b0a4704165e012.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:58:34"
[1] "EXPRESSION:"
[1] "worst <- getpolicy(out.optvac, which = \"worst\")"
[1] "DEPENDENCIES:"
                        out.optvac 
"703572c7a1912e609926dc6133372e0f" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_10/87f5ec50cb1ea6c5f6be9b986eb60446.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:58:34"
[1] "EXPRESSION:"
[1] "rbind(best, worst)"
[1] "DEPENDENCIES:"
                              best 
"583dddd4cc4c97cb38b0a4704165e012" 
                             worst 
"87f5ec50cb1ea6c5f6be9b986eb60446" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_10/8fa614174ae97d23af9225efe6c77c3c.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:58:34"
[1] "EXPRESSION:"
[1] "plot(out.optvac)"
[1] "DEPENDENCIES:"
                        out.optvac 
"703572c7a1912e609926dc6133372e0f" 
[1] "FOUND r_env_cache/2.10.1/optvac_11/2dc3acf6a5d632b2ea1f6957c251bea5.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:58:34"
[1] "EXPRESSION:"
[1] "vac.opt <- best[3:4]"
[1] "DEPENDENCIES:"
                              best 
"583dddd4cc4c97cb38b0a4704165e012" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_12/a738dfbca45e6eb1c25331fdd739b72c.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:58:34"
[1] "EXPRESSION:"
[1] "opt.MCepi <- MCepi(init, true, vac.opt, costs)"
[1] "DEPENDENCIES:"
                           vac.opt 
"a738dfbca45e6eb1c25331fdd739b72c" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_12/5cc568d78b57af17d64152306621f5e3.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:58:35"
[1] "EXPRESSION:"
[1] "plot(opt.MCepi)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/episov_13/c37c3ac54c57d8dadd5665219d72124e.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:58:35"
[1] "EXPRESSION:"
[1] "plot(opt.MCepi, type = \"costs\")"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/costsov_14/67ad9a26d9c4ea35e49d26eb5812d70c.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:58:35"
[1] "EXPRESSION:"
[1] "getvac(opt.MCepi)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_15/9ecd6e44946d5ff837bb4dcffb3a8c24.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:58:35"
[1] "EXPRESSION:"
[1] "T <- length(opt.MCepi$Median$C)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_16/d8cce82ec58af71c935ab28e306340af.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:58:35"
[1] "EXPRESSION:"
[1] "optC <- getcost(opt.MCepi)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_16/69ca0a605b3699aee6daff787d11edc6.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:58:35"
[1] "EXPRESSION:"
[1] "initC <- getcost(init.MCepi)"
[1] "DEPENDENCIES:"
                        init.MCepi 
"d2c2299ce31834724f50f25965f8032e" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_16/fa9b162bb4f585e9f39ba5af0ad2041a.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:58:35"
[1] "EXPRESSION:"
[1] "data.frame(rbind(initC, optC), row.names = c(\"init\", \"opt\"))"
[1] "DEPENDENCIES:"
                             initC 
"fa9b162bb4f585e9f39ba5af0ad2041a" 
                              optC 
"69ca0a605b3699aee6daff787d11edc6" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_16/979f9bfd8f85d50efa97caf6b7e624ad.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:58:35"
[1] "EXPRESSION:"
[1] "opt.MCepi"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_17/b9a1029e977fa93cdc9e292d527f4532.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:58:36"
[1] "EXPRESSION:"
[1] "out.man <- manage(init, epistep, vacgrid, costs)"
[1] "DEPENDENCIES:"
                           vacgrid 
"6136d4c9ffd47d46dc71c25ad39bafc6" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_18/2a30b4a74e393458fe94c705419aabcb.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:58:36"
[1] "EXPRESSION:"
[1] "plot(out.man)"
[1] "DEPENDENCIES:"
                           out.man 
"2a30b4a74e393458fe94c705419aabcb" 
[1] "FOUND r_env_cache/2.10.1/epi_19/d3c12da9026a5783944c9cc53b947019.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:58:36"
[1] "EXPRESSION:"
[1] "plot(out.man, type = \"cost\")"
[1] "DEPENDENCIES:"
                           out.man 
"2a30b4a74e393458fe94c705419aabcb" 
[1] "FOUND r_env_cache/2.10.1/cost_20/6dab79cd4ff3adb9569925a20c9fd6a0.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:58:36"
[1] "EXPRESSION:"
[1] "getcost(out.man)"
[1] "DEPENDENCIES:"
                           out.man 
"2a30b4a74e393458fe94c705419aabcb" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_21/f4590fba5b744f74a3883a5103e7687b.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:58:36"
[1] "EXPRESSION:"
[1] "true <- as.list(formals(epistep)$true)"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/params_22/2c5c7c936a067cd9d8176d7f02176bbb.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:58:37"
[1] "EXPRESSION:"
[1] "plot(out.man, type = \"params\", true = true)"
[1] "DEPENDENCIES:"
                           out.man 
"2a30b4a74e393458fe94c705419aabcb" 
                              true 
"2c5c7c936a067cd9d8176d7f02176bbb" 
[1] "FOUND r_env_cache/2.10.1/params_22/7a1a1bde90c7c12796464a2062912cfb.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:58:37"
[1] "EXPRESSION:"
[1] "out.man"
[1] "DEPENDENCIES:"
                           out.man 
"2a30b4a74e393458fe94c705419aabcb" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_23/296b3699dae2fc01c52ffa0feca21226.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-10:58:37"
[1] "EXPRESSION:"
[1] "out.MCmanage <- MCmanage(init, epistep, vacgrid, costs)"
[1] "DEPENDENCIES:"
                           vacgrid 
"6136d4c9ffd47d46dc71c25ad39bafc6" 
[1] "computing..."
[1] "Working dir: /home/bobby/epicvs/epi/amei/inst/doc"
[1] "27-04-2010-11:33:44"
[1] "EXPRESSION:"
[1] "seed <- 12345"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_2/6ecc3cee4446acafa978aa7735cedf7f.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:33:44"
[1] "EXPRESSION:"
[1] "set.seed(seed)"
[1] "DEPENDENCIES:"
                              seed 
"6ecc3cee4446acafa978aa7735cedf7f" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_2/0e1b44a61a0ace2fb0163953bac48b05.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:33:44"
[1] "EXPRESSION:"
[1] "vac <- list(frac = 0, stop = 0)"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_4/1cbb46ecad05db131f656701e52e6d24.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:33:44"
[1] "EXPRESSION:"
[1] "init.MCepi <- MCepi(init, true, vac, costs)"
[1] "DEPENDENCIES:"
                               vac 
"1cbb46ecad05db131f656701e52e6d24" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_5/d2c2299ce31834724f50f25965f8032e.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:33:44"
[1] "EXPRESSION:"
[1] "plot(init.MCepi)"
[1] "DEPENDENCIES:"
                        init.MCepi 
"d2c2299ce31834724f50f25965f8032e" 
[1] "FOUND r_env_cache/2.10.1/epis_6/b74ab8610420b87e1dd6ddc17800bd12.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:33:44"
[1] "EXPRESSION:"
[1] "plot(init.MCepi, type = \"costs\")"
[1] "DEPENDENCIES:"
                        init.MCepi 
"d2c2299ce31834724f50f25965f8032e" 
[1] "FOUND r_env_cache/2.10.1/costs_7/aeef4fb5e80bd1f6c5eff1a31e6eaa8e.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:33:45"
[1] "EXPRESSION:"
[1] "vacgrid <- list(fracs = seq(0, 1, 0.1), stops = seq(2, init$S0 -      75, 75))"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_8/6136d4c9ffd47d46dc71c25ad39bafc6.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:33:45"
[1] "EXPRESSION:"
[1] "out.optvac <- optvac(init, true, vacgrid, costs)"
[1] "DEPENDENCIES:"
                           vacgrid 
"6136d4c9ffd47d46dc71c25ad39bafc6" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_9/703572c7a1912e609926dc6133372e0f.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:33:45"
[1] "EXPRESSION:"
[1] "best <- getpolicy(out.optvac)"
[1] "DEPENDENCIES:"
                        out.optvac 
"703572c7a1912e609926dc6133372e0f" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_10/583dddd4cc4c97cb38b0a4704165e012.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:33:45"
[1] "EXPRESSION:"
[1] "worst <- getpolicy(out.optvac, which = \"worst\")"
[1] "DEPENDENCIES:"
                        out.optvac 
"703572c7a1912e609926dc6133372e0f" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_10/87f5ec50cb1ea6c5f6be9b986eb60446.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:33:45"
[1] "EXPRESSION:"
[1] "rbind(best, worst)"
[1] "DEPENDENCIES:"
                              best 
"583dddd4cc4c97cb38b0a4704165e012" 
                             worst 
"87f5ec50cb1ea6c5f6be9b986eb60446" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_10/8fa614174ae97d23af9225efe6c77c3c.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:33:45"
[1] "EXPRESSION:"
[1] "plot(out.optvac)"
[1] "DEPENDENCIES:"
                        out.optvac 
"703572c7a1912e609926dc6133372e0f" 
[1] "FOUND r_env_cache/2.10.1/optvac_11/2dc3acf6a5d632b2ea1f6957c251bea5.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:33:45"
[1] "EXPRESSION:"
[1] "vac.opt <- best[3:4]"
[1] "DEPENDENCIES:"
                              best 
"583dddd4cc4c97cb38b0a4704165e012" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_12/a738dfbca45e6eb1c25331fdd739b72c.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:33:46"
[1] "EXPRESSION:"
[1] "opt.MCepi <- MCepi(init, true, vac.opt, costs)"
[1] "DEPENDENCIES:"
                           vac.opt 
"a738dfbca45e6eb1c25331fdd739b72c" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_12/5cc568d78b57af17d64152306621f5e3.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:33:46"
[1] "EXPRESSION:"
[1] "plot(opt.MCepi)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/episov_13/c37c3ac54c57d8dadd5665219d72124e.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:33:46"
[1] "EXPRESSION:"
[1] "plot(opt.MCepi, type = \"costs\")"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/costsov_14/67ad9a26d9c4ea35e49d26eb5812d70c.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:33:46"
[1] "EXPRESSION:"
[1] "getvac(opt.MCepi)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_15/9ecd6e44946d5ff837bb4dcffb3a8c24.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:33:46"
[1] "EXPRESSION:"
[1] "T <- length(opt.MCepi$Median$C)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_16/d8cce82ec58af71c935ab28e306340af.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:33:46"
[1] "EXPRESSION:"
[1] "optC <- getcost(opt.MCepi)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_16/69ca0a605b3699aee6daff787d11edc6.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:33:46"
[1] "EXPRESSION:"
[1] "initC <- getcost(init.MCepi)"
[1] "DEPENDENCIES:"
                        init.MCepi 
"d2c2299ce31834724f50f25965f8032e" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_16/fa9b162bb4f585e9f39ba5af0ad2041a.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:33:47"
[1] "EXPRESSION:"
[1] "data.frame(rbind(initC, optC), row.names = c(\"init\", \"opt\"))"
[1] "DEPENDENCIES:"
                             initC 
"fa9b162bb4f585e9f39ba5af0ad2041a" 
                              optC 
"69ca0a605b3699aee6daff787d11edc6" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_16/979f9bfd8f85d50efa97caf6b7e624ad.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:33:47"
[1] "EXPRESSION:"
[1] "opt.MCepi"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_17/b9a1029e977fa93cdc9e292d527f4532.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:33:47"
[1] "EXPRESSION:"
[1] "out.man <- manage(init, epistep, vacgrid, costs)"
[1] "DEPENDENCIES:"
                           vacgrid 
"6136d4c9ffd47d46dc71c25ad39bafc6" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_18/2a30b4a74e393458fe94c705419aabcb.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:33:47"
[1] "EXPRESSION:"
[1] "plot(out.man)"
[1] "DEPENDENCIES:"
                           out.man 
"2a30b4a74e393458fe94c705419aabcb" 
[1] "FOUND r_env_cache/2.10.1/epi_19/d3c12da9026a5783944c9cc53b947019.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:33:47"
[1] "EXPRESSION:"
[1] "plot(out.man, type = \"cost\")"
[1] "DEPENDENCIES:"
                           out.man 
"2a30b4a74e393458fe94c705419aabcb" 
[1] "FOUND r_env_cache/2.10.1/cost_20/6dab79cd4ff3adb9569925a20c9fd6a0.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:33:47"
[1] "EXPRESSION:"
[1] "getcost(out.man)"
[1] "DEPENDENCIES:"
                           out.man 
"2a30b4a74e393458fe94c705419aabcb" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_21/f4590fba5b744f74a3883a5103e7687b.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:33:47"
[1] "EXPRESSION:"
[1] "true <- as.list(formals(epistep)$true)"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/params_22/2c5c7c936a067cd9d8176d7f02176bbb.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:33:48"
[1] "EXPRESSION:"
[1] "plot(out.man, type = \"params\", true = true)"
[1] "DEPENDENCIES:"
                           out.man 
"2a30b4a74e393458fe94c705419aabcb" 
                              true 
"2c5c7c936a067cd9d8176d7f02176bbb" 
[1] "FOUND r_env_cache/2.10.1/params_22/7a1a1bde90c7c12796464a2062912cfb.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:33:48"
[1] "EXPRESSION:"
[1] "out.man"
[1] "DEPENDENCIES:"
                           out.man 
"2a30b4a74e393458fe94c705419aabcb" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_23/296b3699dae2fc01c52ffa0feca21226.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:33:48"
[1] "EXPRESSION:"
[1] "out.MCmanage <- MCmanage(init, epistep, vacgrid, costs)"
[1] "DEPENDENCIES:"
                           vacgrid 
"6136d4c9ffd47d46dc71c25ad39bafc6" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:41:57"
[1] "EXPRESSION:"
[1] "plot(out.MCmanage)"
[1] "DEPENDENCIES:"
                      out.MCmanage 
"35ff202aa6b7c15b03cbdc4a7c4d2d84" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:41:57"
[1] "EXPRESSION:"
[1] "plot(out.MCmanage, type = \"costs\")"
[1] "DEPENDENCIES:"
                      out.MCmanage 
"35ff202aa6b7c15b03cbdc4a7c4d2d84" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:41:58"
[1] "EXPRESSION:"
[1] "getvac(out.MCmanage)"
[1] "DEPENDENCIES:"
                      out.MCmanage 
"35ff202aa6b7c15b03cbdc4a7c4d2d84" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:41:58"
[1] "EXPRESSION:"
[1] "plot(out.MCmanage, type = \"fracs\")"
[1] "DEPENDENCIES:"
                      out.MCmanage 
"35ff202aa6b7c15b03cbdc4a7c4d2d84" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:41:58"
[1] "EXPRESSION:"
[1] "plot(out.MCmanage, type = \"stops\")"
[1] "DEPENDENCIES:"
                      out.MCmanage 
"35ff202aa6b7c15b03cbdc4a7c4d2d84" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:41:58"
[1] "EXPRESSION:"
[1] "cinit <- getcost(init.MCepi)"
[1] "DEPENDENCIES:"
                        init.MCepi 
"d2c2299ce31834724f50f25965f8032e" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:41:58"
[1] "EXPRESSION:"
[1] "copt <- getcost(opt.MCepi)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:41:58"
[1] "EXPRESSION:"
[1] "cman <- getcost(out.MCmanage)"
[1] "DEPENDENCIES:"
                      out.MCmanage 
"35ff202aa6b7c15b03cbdc4a7c4d2d84" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:41:58"
[1] "EXPRESSION:"
[1] "data.frame(rbind(cinit, copt, cman), row.names = c(\"init\", \"opt\",      \"man\"))"
[1] "DEPENDENCIES:"
                             cinit 
"6a5df1ae4f745e23c4e414a55c844ecd" 
                              cman 
"da79f1f00c18f6bdcec34c4773fd2291" 
                              copt 
"0ff5ff348651505aae21159f4869ce83" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:41:58"
[1] "EXPRESSION:"
[1] "bad <- list(b = 0.001, k = 10, nu = 0.9, mu = 0)"
[1] "DEPENDENCIES:"
list()
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:41:59"
[1] "EXPRESSION:"
[1] "costs.bad <- optvac(init, bad, vacgrid, costs)"
[1] "DEPENDENCIES:"
                               bad 
"9c60d43cfb84255e4258278d51b0e163" 
                           vacgrid 
"6136d4c9ffd47d46dc71c25ad39bafc6" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:42:03"
[1] "EXPRESSION:"
[1] "pol.bad <- getpolicy(costs.bad)"
[1] "DEPENDENCIES:"
                         costs.bad 
"f5eaac04a8459d9a65561438406302f5" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:42:03"
[1] "EXPRESSION:"
[1] "pol.bad"
[1] "DEPENDENCIES:"
                           pol.bad 
"72de5d681de4dd9ac1fcfe772b6b5982" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:42:03"
[1] "EXPRESSION:"
[1] "bad.MCepi <- MCepi(init, true, pol.bad[3:4], costs)"
[1] "DEPENDENCIES:"
                           pol.bad 
"72de5d681de4dd9ac1fcfe772b6b5982" 
                              true 
"2c5c7c936a067cd9d8176d7f02176bbb" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:42:04"
[1] "EXPRESSION:"
[1] "cbad <- getcost(bad.MCepi)"
[1] "DEPENDENCIES:"
                         bad.MCepi 
"4730ccca406b6ff64ef3164f02e2fc72" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:42:04"
[1] "EXPRESSION:"
[1] "cbad"
[1] "DEPENDENCIES:"
                              cbad 
"7249343746cd92f08b02a6a984f1d3b0" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:42:05"
[1] "EXPRESSION:"
[1] "alt.epistep <- function(SIR, last = list(rem = 0, rec = 0, infect = 0,      dead = 0, Z = 0), true = list(a = 0.05, mu = 0.05, nu = 0.1,      m = 0.4, rho = 200, C = 500)) {     Z <- last$Z     fz <- Z/(Z + true$C)     pi <- 1 - exp(-true$a * fz)     infect <- rbinom(1, SIR$S, pi)     pr <- 1 - exp(-true$nu)     rec <- rbinom(1, SIR$I, pr)     pd <- 1 - exp(-true$mu)     dead <- rbinom(1, SIR$I - rec, pd)     pz <- 1 - exp(-true$m)     dz <- rbinom(1, Z, pz)     bz <- round(SIR$I * true$rho)     Z <- Z - dz + bz     return(list(rem = (rec + dead), rec = rec, infect = infect,          dead = dead, Z = Z)) }"
[1] "DEPENDENCIES:"
list()
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:42:05"
[1] "EXPRESSION:"
[1] "init1 <- list(S0 = 150, I0 = 1, R0 = 0, D0 = 0)"
[1] "DEPENDENCIES:"
list()
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:42:05"
[1] "EXPRESSION:"
[1] "true <- list(a = 0.065, mu = 0, nu = 0.3, m = 0.99, rho = 500,      C = 500)"
[1] "DEPENDENCIES:"
                              true 
"2c5c7c936a067cd9d8176d7f02176bbb" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:42:05"
[1] "EXPRESSION:"
[1] "alt.epistep1 <- alt.epistep"
[1] "DEPENDENCIES:"
                       alt.epistep 
"b25520b22b54e43a73301f938286625b" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:42:05"
[1] "EXPRESSION:"
[1] "formals(alt.epistep1)$true <- true"
[1] "DEPENDENCIES:"
                              true 
"3504ed0a1cf5b1134bfd6cbb16d4981c" 
                      alt.epistep1 
"ad6e28167b57f771336df0843c44ab59" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:42:05"
[1] "EXPRESSION:"
[1] "out.alt <- manage(init1, alt.epistep1, NULL, NULL, T = 80)"
[1] "DEPENDENCIES:"
                      alt.epistep1 
"fc92fadd441d749d1baaf8f65b2226ef" 
                             init1 
"16ddc62509622bea432730a764d1cf3c" 
[1] "computing..."
[1] "Working dir: /home/bobby/epicvs/epi/amei/inst/doc"
[1] "27-04-2010-11:52:24"
[1] "EXPRESSION:"
[1] "seed <- 12345"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_2/6ecc3cee4446acafa978aa7735cedf7f.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:24"
[1] "EXPRESSION:"
[1] "set.seed(seed)"
[1] "DEPENDENCIES:"
                              seed 
"6ecc3cee4446acafa978aa7735cedf7f" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_2/0e1b44a61a0ace2fb0163953bac48b05.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:24"
[1] "EXPRESSION:"
[1] "vac <- list(frac = 0, stop = 0)"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_4/1cbb46ecad05db131f656701e52e6d24.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:24"
[1] "EXPRESSION:"
[1] "init.MCepi <- MCepi(init, true, vac, costs)"
[1] "DEPENDENCIES:"
                               vac 
"1cbb46ecad05db131f656701e52e6d24" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_5/d2c2299ce31834724f50f25965f8032e.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:24"
[1] "EXPRESSION:"
[1] "plot(init.MCepi)"
[1] "DEPENDENCIES:"
                        init.MCepi 
"d2c2299ce31834724f50f25965f8032e" 
[1] "FOUND r_env_cache/2.10.1/epis_6/b74ab8610420b87e1dd6ddc17800bd12.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:25"
[1] "EXPRESSION:"
[1] "plot(init.MCepi, type = \"costs\")"
[1] "DEPENDENCIES:"
                        init.MCepi 
"d2c2299ce31834724f50f25965f8032e" 
[1] "FOUND r_env_cache/2.10.1/costs_7/aeef4fb5e80bd1f6c5eff1a31e6eaa8e.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:25"
[1] "EXPRESSION:"
[1] "vacgrid <- list(fracs = seq(0, 1, 0.1), stops = seq(2, init$S0 -      75, 75))"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_8/6136d4c9ffd47d46dc71c25ad39bafc6.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:25"
[1] "EXPRESSION:"
[1] "out.optvac <- optvac(init, true, vacgrid, costs)"
[1] "DEPENDENCIES:"
                           vacgrid 
"6136d4c9ffd47d46dc71c25ad39bafc6" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_9/703572c7a1912e609926dc6133372e0f.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:25"
[1] "EXPRESSION:"
[1] "best <- getpolicy(out.optvac)"
[1] "DEPENDENCIES:"
                        out.optvac 
"703572c7a1912e609926dc6133372e0f" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_10/583dddd4cc4c97cb38b0a4704165e012.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:26"
[1] "EXPRESSION:"
[1] "worst <- getpolicy(out.optvac, which = \"worst\")"
[1] "DEPENDENCIES:"
                        out.optvac 
"703572c7a1912e609926dc6133372e0f" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_10/87f5ec50cb1ea6c5f6be9b986eb60446.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:26"
[1] "EXPRESSION:"
[1] "rbind(best, worst)"
[1] "DEPENDENCIES:"
                              best 
"583dddd4cc4c97cb38b0a4704165e012" 
                             worst 
"87f5ec50cb1ea6c5f6be9b986eb60446" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_10/8fa614174ae97d23af9225efe6c77c3c.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:26"
[1] "EXPRESSION:"
[1] "plot(out.optvac)"
[1] "DEPENDENCIES:"
                        out.optvac 
"703572c7a1912e609926dc6133372e0f" 
[1] "FOUND r_env_cache/2.10.1/optvac_11/2dc3acf6a5d632b2ea1f6957c251bea5.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:26"
[1] "EXPRESSION:"
[1] "vac.opt <- best[3:4]"
[1] "DEPENDENCIES:"
                              best 
"583dddd4cc4c97cb38b0a4704165e012" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_12/a738dfbca45e6eb1c25331fdd739b72c.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:26"
[1] "EXPRESSION:"
[1] "opt.MCepi <- MCepi(init, true, vac.opt, costs)"
[1] "DEPENDENCIES:"
                           vac.opt 
"a738dfbca45e6eb1c25331fdd739b72c" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_12/5cc568d78b57af17d64152306621f5e3.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:26"
[1] "EXPRESSION:"
[1] "plot(opt.MCepi)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/episov_13/c37c3ac54c57d8dadd5665219d72124e.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:26"
[1] "EXPRESSION:"
[1] "plot(opt.MCepi, type = \"costs\")"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/costsov_14/67ad9a26d9c4ea35e49d26eb5812d70c.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:27"
[1] "EXPRESSION:"
[1] "getvac(opt.MCepi)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_15/9ecd6e44946d5ff837bb4dcffb3a8c24.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:27"
[1] "EXPRESSION:"
[1] "T <- length(opt.MCepi$Median$C)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_16/d8cce82ec58af71c935ab28e306340af.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:27"
[1] "EXPRESSION:"
[1] "optC <- getcost(opt.MCepi)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_16/69ca0a605b3699aee6daff787d11edc6.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:27"
[1] "EXPRESSION:"
[1] "initC <- getcost(init.MCepi)"
[1] "DEPENDENCIES:"
                        init.MCepi 
"d2c2299ce31834724f50f25965f8032e" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_16/fa9b162bb4f585e9f39ba5af0ad2041a.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:27"
[1] "EXPRESSION:"
[1] "data.frame(rbind(initC, optC), row.names = c(\"init\", \"opt\"))"
[1] "DEPENDENCIES:"
                             initC 
"fa9b162bb4f585e9f39ba5af0ad2041a" 
                              optC 
"69ca0a605b3699aee6daff787d11edc6" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_16/979f9bfd8f85d50efa97caf6b7e624ad.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:27"
[1] "EXPRESSION:"
[1] "opt.MCepi"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_17/b9a1029e977fa93cdc9e292d527f4532.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:27"
[1] "EXPRESSION:"
[1] "out.man <- manage(init, epistep, vacgrid, costs)"
[1] "DEPENDENCIES:"
                           vacgrid 
"6136d4c9ffd47d46dc71c25ad39bafc6" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_18/2a30b4a74e393458fe94c705419aabcb.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:28"
[1] "EXPRESSION:"
[1] "plot(out.man)"
[1] "DEPENDENCIES:"
                           out.man 
"2a30b4a74e393458fe94c705419aabcb" 
[1] "FOUND r_env_cache/2.10.1/epi_19/d3c12da9026a5783944c9cc53b947019.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:28"
[1] "EXPRESSION:"
[1] "plot(out.man, type = \"cost\")"
[1] "DEPENDENCIES:"
                           out.man 
"2a30b4a74e393458fe94c705419aabcb" 
[1] "FOUND r_env_cache/2.10.1/cost_20/6dab79cd4ff3adb9569925a20c9fd6a0.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:28"
[1] "EXPRESSION:"
[1] "getcost(out.man)"
[1] "DEPENDENCIES:"
                           out.man 
"2a30b4a74e393458fe94c705419aabcb" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_21/f4590fba5b744f74a3883a5103e7687b.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:28"
[1] "EXPRESSION:"
[1] "true <- as.list(formals(epistep)$true)"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/params_22/2c5c7c936a067cd9d8176d7f02176bbb.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:28"
[1] "EXPRESSION:"
[1] "plot(out.man, type = \"params\", true = true)"
[1] "DEPENDENCIES:"
                           out.man 
"2a30b4a74e393458fe94c705419aabcb" 
                              true 
"2c5c7c936a067cd9d8176d7f02176bbb" 
[1] "FOUND r_env_cache/2.10.1/params_22/7a1a1bde90c7c12796464a2062912cfb.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:28"
[1] "EXPRESSION:"
[1] "out.man"
[1] "DEPENDENCIES:"
                           out.man 
"2a30b4a74e393458fe94c705419aabcb" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_23/296b3699dae2fc01c52ffa0feca21226.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:29"
[1] "EXPRESSION:"
[1] "out.MCmanage <- MCmanage(init, epistep, vacgrid, costs)"
[1] "DEPENDENCIES:"
                           vacgrid 
"6136d4c9ffd47d46dc71c25ad39bafc6" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_24/35ff202aa6b7c15b03cbdc4a7c4d2d84.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:29"
[1] "EXPRESSION:"
[1] "plot(out.MCmanage)"
[1] "DEPENDENCIES:"
                      out.MCmanage 
"35ff202aa6b7c15b03cbdc4a7c4d2d84" 
[1] "FOUND r_env_cache/2.10.1/MCmanepis_25/f77efdeb75f39a246eeeabbfc6cf7a72.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:29"
[1] "EXPRESSION:"
[1] "plot(out.MCmanage, type = \"costs\")"
[1] "DEPENDENCIES:"
                      out.MCmanage 
"35ff202aa6b7c15b03cbdc4a7c4d2d84" 
[1] "FOUND r_env_cache/2.10.1/MCmancosts_26/2f6d74fe60b00d0bdc73dbbd9bca22f3.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:29"
[1] "EXPRESSION:"
[1] "getvac(out.MCmanage)"
[1] "DEPENDENCIES:"
                      out.MCmanage 
"35ff202aa6b7c15b03cbdc4a7c4d2d84" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_27/937152b769d7a844081f3b8349e28d77.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:29"
[1] "EXPRESSION:"
[1] "plot(out.MCmanage, type = \"fracs\")"
[1] "DEPENDENCIES:"
                      out.MCmanage 
"35ff202aa6b7c15b03cbdc4a7c4d2d84" 
[1] "FOUND r_env_cache/2.10.1/MCmanfracs_28/01ac82f7d0ecdea0b82359a462eec947.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:29"
[1] "EXPRESSION:"
[1] "plot(out.MCmanage, type = \"stops\")"
[1] "DEPENDENCIES:"
                      out.MCmanage 
"35ff202aa6b7c15b03cbdc4a7c4d2d84" 
[1] "FOUND r_env_cache/2.10.1/MCmanstops_29/b6a250c13d0431dd7737b705bd97800d.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:29"
[1] "EXPRESSION:"
[1] "cinit <- getcost(init.MCepi)"
[1] "DEPENDENCIES:"
                        init.MCepi 
"d2c2299ce31834724f50f25965f8032e" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_30/6a5df1ae4f745e23c4e414a55c844ecd.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:30"
[1] "EXPRESSION:"
[1] "copt <- getcost(opt.MCepi)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_30/0ff5ff348651505aae21159f4869ce83.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:30"
[1] "EXPRESSION:"
[1] "cman <- getcost(out.MCmanage)"
[1] "DEPENDENCIES:"
                      out.MCmanage 
"35ff202aa6b7c15b03cbdc4a7c4d2d84" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_30/da79f1f00c18f6bdcec34c4773fd2291.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:30"
[1] "EXPRESSION:"
[1] "data.frame(rbind(cinit, copt, cman), row.names = c(\"init\", \"opt\",      \"man\"))"
[1] "DEPENDENCIES:"
                             cinit 
"6a5df1ae4f745e23c4e414a55c844ecd" 
                              cman 
"da79f1f00c18f6bdcec34c4773fd2291" 
                              copt 
"0ff5ff348651505aae21159f4869ce83" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_30/a40d0d24af1252b786b8e84b8a0726c9.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:30"
[1] "EXPRESSION:"
[1] "bad <- list(b = 0.001, k = 10, nu = 0.9, mu = 0)"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_31/9c60d43cfb84255e4258278d51b0e163.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:30"
[1] "EXPRESSION:"
[1] "costs.bad <- optvac(init, bad, vacgrid, costs)"
[1] "DEPENDENCIES:"
                               bad 
"9c60d43cfb84255e4258278d51b0e163" 
                           vacgrid 
"6136d4c9ffd47d46dc71c25ad39bafc6" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_32/f5eaac04a8459d9a65561438406302f5.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:30"
[1] "EXPRESSION:"
[1] "pol.bad <- getpolicy(costs.bad)"
[1] "DEPENDENCIES:"
                         costs.bad 
"f5eaac04a8459d9a65561438406302f5" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_32/72de5d681de4dd9ac1fcfe772b6b5982.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:30"
[1] "EXPRESSION:"
[1] "pol.bad"
[1] "DEPENDENCIES:"
                           pol.bad 
"72de5d681de4dd9ac1fcfe772b6b5982" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_32/e6608376713e772b69f3065b4480bf70.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:30"
[1] "EXPRESSION:"
[1] "bad.MCepi <- MCepi(init, true, pol.bad[3:4], costs)"
[1] "DEPENDENCIES:"
                           pol.bad 
"72de5d681de4dd9ac1fcfe772b6b5982" 
                              true 
"2c5c7c936a067cd9d8176d7f02176bbb" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_33/4730ccca406b6ff64ef3164f02e2fc72.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:31"
[1] "EXPRESSION:"
[1] "cbad <- getcost(bad.MCepi)"
[1] "DEPENDENCIES:"
                         bad.MCepi 
"4730ccca406b6ff64ef3164f02e2fc72" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_33/7249343746cd92f08b02a6a984f1d3b0.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:31"
[1] "EXPRESSION:"
[1] "cbad"
[1] "DEPENDENCIES:"
                              cbad 
"7249343746cd92f08b02a6a984f1d3b0" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_33/f9a272d4e6decd91ab709548cbba73dc.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:31"
[1] "EXPRESSION:"
[1] "alt.epistep <- function(SIR, last = list(rem = 0, rec = 0, infect = 0,      dead = 0, Z = 0), true = list(a = 0.05, mu = 0.05, nu = 0.1,      m = 0.4, rho = 200, C = 500)) {     Z <- last$Z     fz <- Z/(Z + true$C)     pi <- 1 - exp(-true$a * fz)     infect <- rbinom(1, SIR$S, pi)     pr <- 1 - exp(-true$nu)     rec <- rbinom(1, SIR$I, pr)     pd <- 1 - exp(-true$mu)     dead <- rbinom(1, SIR$I - rec, pd)     pz <- 1 - exp(-true$m)     dz <- rbinom(1, Z, pz)     bz <- round(SIR$I * true$rho)     Z <- Z - dz + bz     return(list(rem = (rec + dead), rec = rec, infect = infect,          dead = dead, Z = Z)) }"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_35/b25520b22b54e43a73301f938286625b.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:31"
[1] "EXPRESSION:"
[1] "init1 <- list(S0 = 150, I0 = 1, R0 = 0, D0 = 0)"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_36/16ddc62509622bea432730a764d1cf3c.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:31"
[1] "EXPRESSION:"
[1] "true <- list(a = 0.065, mu = 0, nu = 0.3, m = 0.99, rho = 500,      C = 500)"
[1] "DEPENDENCIES:"
                              true 
"2c5c7c936a067cd9d8176d7f02176bbb" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_36/3504ed0a1cf5b1134bfd6cbb16d4981c.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:31"
[1] "EXPRESSION:"
[1] "alt.epistep1 <- alt.epistep"
[1] "DEPENDENCIES:"
                       alt.epistep 
"b25520b22b54e43a73301f938286625b" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_36/ad6e28167b57f771336df0843c44ab59.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:31"
[1] "EXPRESSION:"
[1] "formals(alt.epistep1)$true <- true"
[1] "DEPENDENCIES:"
                              true 
"3504ed0a1cf5b1134bfd6cbb16d4981c" 
                      alt.epistep1 
"ad6e28167b57f771336df0843c44ab59" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_36/fc92fadd441d749d1baaf8f65b2226ef.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-11:52:32"
[1] "EXPRESSION:"
[1] "out.alt <- manage(init1, alt.epistep1, NULL, NULL, T = 80)"
[1] "DEPENDENCIES:"
                      alt.epistep1 
"fc92fadd441d749d1baaf8f65b2226ef" 
                             init1 
"16ddc62509622bea432730a764d1cf3c" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:52:33"
[1] "EXPRESSION:"
[1] "true <- list(a = 0.065, mu = 0, nu = 0.3, m = 0.005, rho = 500,      C = 500)"
[1] "DEPENDENCIES:"
                              true 
"3504ed0a1cf5b1134bfd6cbb16d4981c" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:52:33"
[1] "EXPRESSION:"
[1] "alt.epistep2 <- alt.epistep"
[1] "DEPENDENCIES:"
                       alt.epistep 
"b25520b22b54e43a73301f938286625b" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:52:33"
[1] "EXPRESSION:"
[1] "formals(alt.epistep2)$true <- true"
[1] "DEPENDENCIES:"
                              true 
"456dd1b0f5362f0127a6fe2f5e585f64" 
                      alt.epistep2 
"0794f811696399f32754ca925a156ce9" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:52:33"
[1] "EXPRESSION:"
[1] "out.alt2 <- manage(init1, alt.epistep2, NULL, NULL, T = 80)"
[1] "DEPENDENCIES:"
                      alt.epistep2 
"24ec72c7de87bcf54143bd602e5d1d37" 
                             init1 
"16ddc62509622bea432730a764d1cf3c" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:52:35"
[1] "EXPRESSION:"
[1] "plot(out.alt)"
[1] "DEPENDENCIES:"
                           out.alt 
"c402e67725c9de5030c610595af844f3" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:52:35"
[1] "EXPRESSION:"
[1] "plot(out.alt2)"
[1] "DEPENDENCIES:"
                          out.alt2 
"447c5e6ce70559e86ece95b22cd7381b" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:52:35"
[1] "EXPRESSION:"
[1] "plot(out.alt, type = \"params\", showd = TRUE)"
[1] "DEPENDENCIES:"
                           out.alt 
"c402e67725c9de5030c610595af844f3" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:52:35"
[1] "EXPRESSION:"
[1] "plot(out.alt2, type = \"params\", showd = TRUE)"
[1] "DEPENDENCIES:"
                          out.alt2 
"447c5e6ce70559e86ece95b22cd7381b" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:52:36"
[1] "EXPRESSION:"
[1] "init <- list(S0 = 600, I0 = 1, R0 = 0, D0 = 0)"
[1] "DEPENDENCIES:"
list()
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:52:36"
[1] "EXPRESSION:"
[1] "time <- 80"
[1] "DEPENDENCIES:"
list()
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:52:36"
[1] "EXPRESSION:"
[1] "posterior <- manage(init, alt.epistep, NULL, NULL, T = time,      bkrate = 100)"
[1] "DEPENDENCIES:"
                       alt.epistep 
"b25520b22b54e43a73301f938286625b" 
                              init 
"6fcfea7313126f97a1ef65ab17beed9c" 
                              time 
"fc0e542f87ad9ff32396c0c40d064d7d" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:53:55"
[1] "EXPRESSION:"
[1] "plot(log(posterior$samp$b), type = \"l\", main = \"\", ylab = expression(b))"
[1] "DEPENDENCIES:"
                         posterior 
"c3f78f4d4771b03d7ec8a3ab4aae511a" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:53:57"
[1] "EXPRESSION:"
[1] "plot(posterior$samp$k, type = \"l\", main = \"\", ylab = expression(k))"
[1] "DEPENDENCIES:"
                         posterior 
"c3f78f4d4771b03d7ec8a3ab4aae511a" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:53:59"
[1] "EXPRESSION:"
[1] "plot(posterior$samp$nu, type = \"l\", main = \"\", ylab = expression(nu))"
[1] "DEPENDENCIES:"
                         posterior 
"c3f78f4d4771b03d7ec8a3ab4aae511a" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:54:00"
[1] "EXPRESSION:"
[1] "plot(posterior$samp$mu, type = \"l\", main = \"\", ylab = expression(mu))"
[1] "DEPENDENCIES:"
                         posterior 
"c3f78f4d4771b03d7ec8a3ab4aae511a" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:54:00"
[1] "EXPRESSION:"
[1] "mean.params <- as.list(apply(posterior$samp, 2, mean))"
[1] "DEPENDENCIES:"
                         posterior 
"c3f78f4d4771b03d7ec8a3ab4aae511a" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:54:00"
[1] "EXPRESSION:"
[1] "costs <- list(vac = 2.5, death = 4, infect = 1)"
[1] "DEPENDENCIES:"
list()
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:54:00"
[1] "EXPRESSION:"
[1] "vacgrid <- list(fracs = seq(0, 1, 0.1), stops = seq(2, init$S0 -      50, 50))"
[1] "DEPENDENCIES:"
                              init 
"6fcfea7313126f97a1ef65ab17beed9c" 
                           vacgrid 
"6136d4c9ffd47d46dc71c25ad39bafc6" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:54:01"
[1] "EXPRESSION:"
[1] "alt.optvac <- optvac(init, mean.params, vacgrid, costs, T = time)"
[1] "DEPENDENCIES:"
                             costs 
"c5369ff5abf8f567c07e503f2beb112b" 
                              init 
"6fcfea7313126f97a1ef65ab17beed9c" 
                       mean.params 
"aef1d811d501cbd666d88a00b88761f6" 
                              time 
"fc0e542f87ad9ff32396c0c40d064d7d" 
                           vacgrid 
"b06e4fcf3ca908aec3de499579ca3344" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:54:03"
[1] "EXPRESSION:"
[1] "alt.best <- getpolicy(alt.optvac)"
[1] "DEPENDENCIES:"
                        alt.optvac 
"43e87c8daad68356a254162f09ca0229" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:54:03"
[1] "EXPRESSION:"
[1] "plot(alt.optvac)"
[1] "DEPENDENCIES:"
                        alt.optvac 
"43e87c8daad68356a254162f09ca0229" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:54:04"
[1] "EXPRESSION:"
[1] "alt.vac.opt <- alt.best[3:4]"
[1] "DEPENDENCIES:"
                          alt.best 
"884752abdb224fdc957e4975444e6afe" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-11:54:04"
[1] "EXPRESSION:"
[1] "alt.MCepi <- MCepi(init, alt.epistep, alt.vac.opt, costs, T = time)"
[1] "DEPENDENCIES:"
                       alt.epistep 
"b25520b22b54e43a73301f938286625b" 
                       alt.vac.opt 
"6284f5873e39a2919ed90c660f27ac84" 
                             costs 
"c5369ff5abf8f567c07e503f2beb112b" 
                              init 
"6fcfea7313126f97a1ef65ab17beed9c" 
                              time 
"fc0e542f87ad9ff32396c0c40d064d7d" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-12:04:29"
[1] "EXPRESSION:"
[1] "alt.MCmanage <- MCmanage(init, alt.epistep, vacgrid, costs, T = time)"
[1] "DEPENDENCIES:"
                       alt.epistep 
"b25520b22b54e43a73301f938286625b" 
                             costs 
"c5369ff5abf8f567c07e503f2beb112b" 
                              init 
"6fcfea7313126f97a1ef65ab17beed9c" 
                              time 
"fc0e542f87ad9ff32396c0c40d064d7d" 
                           vacgrid 
"b06e4fcf3ca908aec3de499579ca3344" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-12:11:35"
[1] "EXPRESSION:"
[1] "plot(alt.MCepi, showd = TRUE)"
[1] "DEPENDENCIES:"
                         alt.MCepi 
"6bcf95c107e41d7ac2e90d2d701fb332" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-12:11:35"
[1] "EXPRESSION:"
[1] "plot(alt.MCepi, type = \"costs\")"
[1] "DEPENDENCIES:"
                         alt.MCepi 
"6bcf95c107e41d7ac2e90d2d701fb332" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-12:11:35"
[1] "EXPRESSION:"
[1] "plot(alt.MCmanage, showd = TRUE)"
[1] "DEPENDENCIES:"
                      alt.MCmanage 
"61188c13fad44d9ab9112c45a1582695" 
[1] "computing..."
[1] "==========================================="
[1] "27-04-2010-12:11:35"
[1] "EXPRESSION:"
[1] "plot(alt.MCmanage, type = \"costs\")"
[1] "DEPENDENCIES:"
                      alt.MCmanage 
"61188c13fad44d9ab9112c45a1582695" 
[1] "computing..."
[1] "==========================================="
[1] "Working dir: /home/bobby/epicvs/epi/amei/inst/doc"
[1] "27-04-2010-15:41:00"
[1] "EXPRESSION:"
[1] "seed <- 12345"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_2/6ecc3cee4446acafa978aa7735cedf7f.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:00"
[1] "EXPRESSION:"
[1] "set.seed(seed)"
[1] "DEPENDENCIES:"
                              seed 
"6ecc3cee4446acafa978aa7735cedf7f" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_2/0e1b44a61a0ace2fb0163953bac48b05.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:00"
[1] "EXPRESSION:"
[1] "vac <- list(frac = 0, stop = 0)"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_4/1cbb46ecad05db131f656701e52e6d24.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:00"
[1] "EXPRESSION:"
[1] "init.MCepi <- MCepi(init, true, vac, costs)"
[1] "DEPENDENCIES:"
                               vac 
"1cbb46ecad05db131f656701e52e6d24" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_5/d2c2299ce31834724f50f25965f8032e.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:00"
[1] "EXPRESSION:"
[1] "plot(init.MCepi)"
[1] "DEPENDENCIES:"
                        init.MCepi 
"d2c2299ce31834724f50f25965f8032e" 
[1] "FOUND r_env_cache/2.10.1/epis_6/b74ab8610420b87e1dd6ddc17800bd12.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:01"
[1] "EXPRESSION:"
[1] "plot(init.MCepi, type = \"costs\")"
[1] "DEPENDENCIES:"
                        init.MCepi 
"d2c2299ce31834724f50f25965f8032e" 
[1] "FOUND r_env_cache/2.10.1/costs_7/aeef4fb5e80bd1f6c5eff1a31e6eaa8e.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:01"
[1] "EXPRESSION:"
[1] "vacgrid <- list(fracs = seq(0, 1, 0.1), stops = seq(2, init$S0 -      75, 75))"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_8/6136d4c9ffd47d46dc71c25ad39bafc6.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:01"
[1] "EXPRESSION:"
[1] "out.optvac <- optvac(init, true, vacgrid, costs)"
[1] "DEPENDENCIES:"
                           vacgrid 
"6136d4c9ffd47d46dc71c25ad39bafc6" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_9/703572c7a1912e609926dc6133372e0f.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:01"
[1] "EXPRESSION:"
[1] "best <- getpolicy(out.optvac)"
[1] "DEPENDENCIES:"
                        out.optvac 
"703572c7a1912e609926dc6133372e0f" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_10/583dddd4cc4c97cb38b0a4704165e012.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:01"
[1] "EXPRESSION:"
[1] "worst <- getpolicy(out.optvac, which = \"worst\")"
[1] "DEPENDENCIES:"
                        out.optvac 
"703572c7a1912e609926dc6133372e0f" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_10/87f5ec50cb1ea6c5f6be9b986eb60446.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:01"
[1] "EXPRESSION:"
[1] "rbind(best, worst)"
[1] "DEPENDENCIES:"
                              best 
"583dddd4cc4c97cb38b0a4704165e012" 
                             worst 
"87f5ec50cb1ea6c5f6be9b986eb60446" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_10/8fa614174ae97d23af9225efe6c77c3c.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:01"
[1] "EXPRESSION:"
[1] "plot(out.optvac)"
[1] "DEPENDENCIES:"
                        out.optvac 
"703572c7a1912e609926dc6133372e0f" 
[1] "FOUND r_env_cache/2.10.1/optvac_11/2dc3acf6a5d632b2ea1f6957c251bea5.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:02"
[1] "EXPRESSION:"
[1] "vac.opt <- best[3:4]"
[1] "DEPENDENCIES:"
                              best 
"583dddd4cc4c97cb38b0a4704165e012" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_12/a738dfbca45e6eb1c25331fdd739b72c.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:02"
[1] "EXPRESSION:"
[1] "opt.MCepi <- MCepi(init, true, vac.opt, costs)"
[1] "DEPENDENCIES:"
                           vac.opt 
"a738dfbca45e6eb1c25331fdd739b72c" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_12/5cc568d78b57af17d64152306621f5e3.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:02"
[1] "EXPRESSION:"
[1] "plot(opt.MCepi)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/episov_13/c37c3ac54c57d8dadd5665219d72124e.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:02"
[1] "EXPRESSION:"
[1] "plot(opt.MCepi, type = \"costs\")"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/costsov_14/67ad9a26d9c4ea35e49d26eb5812d70c.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:02"
[1] "EXPRESSION:"
[1] "getvac(opt.MCepi)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_15/9ecd6e44946d5ff837bb4dcffb3a8c24.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:02"
[1] "EXPRESSION:"
[1] "T <- length(opt.MCepi$Median$C)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_16/d8cce82ec58af71c935ab28e306340af.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:03"
[1] "EXPRESSION:"
[1] "optC <- getcost(opt.MCepi)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_16/69ca0a605b3699aee6daff787d11edc6.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:03"
[1] "EXPRESSION:"
[1] "initC <- getcost(init.MCepi)"
[1] "DEPENDENCIES:"
                        init.MCepi 
"d2c2299ce31834724f50f25965f8032e" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_16/fa9b162bb4f585e9f39ba5af0ad2041a.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:03"
[1] "EXPRESSION:"
[1] "data.frame(rbind(initC, optC), row.names = c(\"init\", \"opt\"))"
[1] "DEPENDENCIES:"
                             initC 
"fa9b162bb4f585e9f39ba5af0ad2041a" 
                              optC 
"69ca0a605b3699aee6daff787d11edc6" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_16/979f9bfd8f85d50efa97caf6b7e624ad.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:03"
[1] "EXPRESSION:"
[1] "opt.MCepi"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_17/b9a1029e977fa93cdc9e292d527f4532.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:03"
[1] "EXPRESSION:"
[1] "out.man <- manage(init, epistep, vacgrid, costs)"
[1] "DEPENDENCIES:"
                           vacgrid 
"6136d4c9ffd47d46dc71c25ad39bafc6" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_18/2a30b4a74e393458fe94c705419aabcb.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:03"
[1] "EXPRESSION:"
[1] "plot(out.man)"
[1] "DEPENDENCIES:"
                           out.man 
"2a30b4a74e393458fe94c705419aabcb" 
[1] "FOUND r_env_cache/2.10.1/epi_19/d3c12da9026a5783944c9cc53b947019.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:03"
[1] "EXPRESSION:"
[1] "plot(out.man, type = \"cost\")"
[1] "DEPENDENCIES:"
                           out.man 
"2a30b4a74e393458fe94c705419aabcb" 
[1] "FOUND r_env_cache/2.10.1/cost_20/6dab79cd4ff3adb9569925a20c9fd6a0.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:03"
[1] "EXPRESSION:"
[1] "getcost(out.man)"
[1] "DEPENDENCIES:"
                           out.man 
"2a30b4a74e393458fe94c705419aabcb" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_21/f4590fba5b744f74a3883a5103e7687b.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:04"
[1] "EXPRESSION:"
[1] "true <- as.list(formals(epistep)$true)"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/params_22/2c5c7c936a067cd9d8176d7f02176bbb.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:04"
[1] "EXPRESSION:"
[1] "plot(out.man, type = \"params\", true = true)"
[1] "DEPENDENCIES:"
                           out.man 
"2a30b4a74e393458fe94c705419aabcb" 
                              true 
"2c5c7c936a067cd9d8176d7f02176bbb" 
[1] "FOUND r_env_cache/2.10.1/params_22/7a1a1bde90c7c12796464a2062912cfb.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:04"
[1] "EXPRESSION:"
[1] "out.man"
[1] "DEPENDENCIES:"
                           out.man 
"2a30b4a74e393458fe94c705419aabcb" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_23/296b3699dae2fc01c52ffa0feca21226.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:04"
[1] "EXPRESSION:"
[1] "out.MCmanage <- MCmanage(init, epistep, vacgrid, costs)"
[1] "DEPENDENCIES:"
                           vacgrid 
"6136d4c9ffd47d46dc71c25ad39bafc6" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_24/35ff202aa6b7c15b03cbdc4a7c4d2d84.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:04"
[1] "EXPRESSION:"
[1] "plot(out.MCmanage)"
[1] "DEPENDENCIES:"
                      out.MCmanage 
"35ff202aa6b7c15b03cbdc4a7c4d2d84" 
[1] "FOUND r_env_cache/2.10.1/MCmanepis_25/f77efdeb75f39a246eeeabbfc6cf7a72.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:04"
[1] "EXPRESSION:"
[1] "plot(out.MCmanage, type = \"costs\")"
[1] "DEPENDENCIES:"
                      out.MCmanage 
"35ff202aa6b7c15b03cbdc4a7c4d2d84" 
[1] "FOUND r_env_cache/2.10.1/MCmancosts_26/2f6d74fe60b00d0bdc73dbbd9bca22f3.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:05"
[1] "EXPRESSION:"
[1] "getvac(out.MCmanage)"
[1] "DEPENDENCIES:"
                      out.MCmanage 
"35ff202aa6b7c15b03cbdc4a7c4d2d84" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_27/937152b769d7a844081f3b8349e28d77.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:05"
[1] "EXPRESSION:"
[1] "plot(out.MCmanage, type = \"fracs\")"
[1] "DEPENDENCIES:"
                      out.MCmanage 
"35ff202aa6b7c15b03cbdc4a7c4d2d84" 
[1] "FOUND r_env_cache/2.10.1/MCmanfracs_28/01ac82f7d0ecdea0b82359a462eec947.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:05"
[1] "EXPRESSION:"
[1] "plot(out.MCmanage, type = \"stops\")"
[1] "DEPENDENCIES:"
                      out.MCmanage 
"35ff202aa6b7c15b03cbdc4a7c4d2d84" 
[1] "FOUND r_env_cache/2.10.1/MCmanstops_29/b6a250c13d0431dd7737b705bd97800d.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:05"
[1] "EXPRESSION:"
[1] "cinit <- getcost(init.MCepi)"
[1] "DEPENDENCIES:"
                        init.MCepi 
"d2c2299ce31834724f50f25965f8032e" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_30/6a5df1ae4f745e23c4e414a55c844ecd.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:05"
[1] "EXPRESSION:"
[1] "copt <- getcost(opt.MCepi)"
[1] "DEPENDENCIES:"
                         opt.MCepi 
"5cc568d78b57af17d64152306621f5e3" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_30/0ff5ff348651505aae21159f4869ce83.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:05"
[1] "EXPRESSION:"
[1] "cman <- getcost(out.MCmanage)"
[1] "DEPENDENCIES:"
                      out.MCmanage 
"35ff202aa6b7c15b03cbdc4a7c4d2d84" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_30/da79f1f00c18f6bdcec34c4773fd2291.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:05"
[1] "EXPRESSION:"
[1] "data.frame(rbind(cinit, copt, cman), row.names = c(\"init\", \"opt\",      \"man\"))"
[1] "DEPENDENCIES:"
                             cinit 
"6a5df1ae4f745e23c4e414a55c844ecd" 
                              cman 
"da79f1f00c18f6bdcec34c4773fd2291" 
                              copt 
"0ff5ff348651505aae21159f4869ce83" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_30/a40d0d24af1252b786b8e84b8a0726c9.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:06"
[1] "EXPRESSION:"
[1] "bad <- list(b = 0.001, k = 10, nu = 0.9, mu = 0)"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_31/9c60d43cfb84255e4258278d51b0e163.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:06"
[1] "EXPRESSION:"
[1] "costs.bad <- optvac(init, bad, vacgrid, costs)"
[1] "DEPENDENCIES:"
                               bad 
"9c60d43cfb84255e4258278d51b0e163" 
                           vacgrid 
"6136d4c9ffd47d46dc71c25ad39bafc6" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_32/f5eaac04a8459d9a65561438406302f5.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:06"
[1] "EXPRESSION:"
[1] "pol.bad <- getpolicy(costs.bad)"
[1] "DEPENDENCIES:"
                         costs.bad 
"f5eaac04a8459d9a65561438406302f5" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_32/72de5d681de4dd9ac1fcfe772b6b5982.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:06"
[1] "EXPRESSION:"
[1] "pol.bad"
[1] "DEPENDENCIES:"
                           pol.bad 
"72de5d681de4dd9ac1fcfe772b6b5982" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_32/e6608376713e772b69f3065b4480bf70.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:06"
[1] "EXPRESSION:"
[1] "bad.MCepi <- MCepi(init, true, pol.bad[3:4], costs)"
[1] "DEPENDENCIES:"
                           pol.bad 
"72de5d681de4dd9ac1fcfe772b6b5982" 
                              true 
"2c5c7c936a067cd9d8176d7f02176bbb" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_33/4730ccca406b6ff64ef3164f02e2fc72.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:06"
[1] "EXPRESSION:"
[1] "cbad <- getcost(bad.MCepi)"
[1] "DEPENDENCIES:"
                         bad.MCepi 
"4730ccca406b6ff64ef3164f02e2fc72" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_33/7249343746cd92f08b02a6a984f1d3b0.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:06"
[1] "EXPRESSION:"
[1] "cbad"
[1] "DEPENDENCIES:"
                              cbad 
"7249343746cd92f08b02a6a984f1d3b0" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_33/f9a272d4e6decd91ab709548cbba73dc.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:07"
[1] "EXPRESSION:"
[1] "alt.epistep <- function(SIR, last = list(rem = 0, rec = 0, infect = 0,      dead = 0, Z = 0), true = list(a = 0.05, mu = 0.05, nu = 0.1,      m = 0.4, rho = 200, C = 500)) {     Z <- last$Z     fz <- Z/(Z + true$C)     pi <- 1 - exp(-true$a * fz)     infect <- rbinom(1, SIR$S, pi)     pr <- 1 - exp(-true$nu)     rec <- rbinom(1, SIR$I, pr)     pd <- 1 - exp(-true$mu)     dead <- rbinom(1, SIR$I - rec, pd)     pz <- 1 - exp(-true$m)     dz <- rbinom(1, Z, pz)     bz <- round(SIR$I * true$rho)     Z <- Z - dz + bz     return(list(rem = (rec + dead), rec = rec, infect = infect,          dead = dead, Z = Z)) }"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_35/b25520b22b54e43a73301f938286625b.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:07"
[1] "EXPRESSION:"
[1] "init1 <- list(S0 = 150, I0 = 1, R0 = 0, D0 = 0)"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_36/16ddc62509622bea432730a764d1cf3c.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:07"
[1] "EXPRESSION:"
[1] "true <- list(a = 0.065, mu = 0, nu = 0.3, m = 0.99, rho = 500,      C = 500)"
[1] "DEPENDENCIES:"
                              true 
"2c5c7c936a067cd9d8176d7f02176bbb" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_36/3504ed0a1cf5b1134bfd6cbb16d4981c.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:07"
[1] "EXPRESSION:"
[1] "alt.epistep1 <- alt.epistep"
[1] "DEPENDENCIES:"
                       alt.epistep 
"b25520b22b54e43a73301f938286625b" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_36/ad6e28167b57f771336df0843c44ab59.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:07"
[1] "EXPRESSION:"
[1] "formals(alt.epistep1)$true <- true"
[1] "DEPENDENCIES:"
                              true 
"3504ed0a1cf5b1134bfd6cbb16d4981c" 
                      alt.epistep1 
"ad6e28167b57f771336df0843c44ab59" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_36/fc92fadd441d749d1baaf8f65b2226ef.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:07"
[1] "EXPRESSION:"
[1] "out.alt <- manage(init1, alt.epistep1, NULL, NULL, T = 80)"
[1] "DEPENDENCIES:"
                      alt.epistep1 
"fc92fadd441d749d1baaf8f65b2226ef" 
                             init1 
"16ddc62509622bea432730a764d1cf3c" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_36/c402e67725c9de5030c610595af844f3.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:07"
[1] "EXPRESSION:"
[1] "true <- list(a = 0.065, mu = 0, nu = 0.3, m = 0.005, rho = 500,      C = 500)"
[1] "DEPENDENCIES:"
                              true 
"3504ed0a1cf5b1134bfd6cbb16d4981c" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_37/456dd1b0f5362f0127a6fe2f5e585f64.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:07"
[1] "EXPRESSION:"
[1] "alt.epistep2 <- alt.epistep"
[1] "DEPENDENCIES:"
                       alt.epistep 
"b25520b22b54e43a73301f938286625b" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_37/0794f811696399f32754ca925a156ce9.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:08"
[1] "EXPRESSION:"
[1] "formals(alt.epistep2)$true <- true"
[1] "DEPENDENCIES:"
                              true 
"456dd1b0f5362f0127a6fe2f5e585f64" 
                      alt.epistep2 
"0794f811696399f32754ca925a156ce9" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_37/24ec72c7de87bcf54143bd602e5d1d37.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:08"
[1] "EXPRESSION:"
[1] "out.alt2 <- manage(init1, alt.epistep2, NULL, NULL, T = 80)"
[1] "DEPENDENCIES:"
                      alt.epistep2 
"24ec72c7de87bcf54143bd602e5d1d37" 
                             init1 
"16ddc62509622bea432730a764d1cf3c" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_37/447c5e6ce70559e86ece95b22cd7381b.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:08"
[1] "EXPRESSION:"
[1] "plot(out.alt)"
[1] "DEPENDENCIES:"
                           out.alt 
"c402e67725c9de5030c610595af844f3" 
[1] "FOUND r_env_cache/2.10.1/alt_38/a3463b31449fa1ecdfd7eaae8749becb.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:08"
[1] "EXPRESSION:"
[1] "plot(out.alt2)"
[1] "DEPENDENCIES:"
                          out.alt2 
"447c5e6ce70559e86ece95b22cd7381b" 
[1] "FOUND r_env_cache/2.10.1/alt2_39/04bc605107f295f80d11a5a6b85e0ca5.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:08"
[1] "EXPRESSION:"
[1] "plot(out.alt, type = \"params\", showd = TRUE)"
[1] "DEPENDENCIES:"
                           out.alt 
"c402e67725c9de5030c610595af844f3" 
[1] "FOUND r_env_cache/2.10.1/alt-params_40/95f5eb8b637a10e7289a2126b8c5d958.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:08"
[1] "EXPRESSION:"
[1] "plot(out.alt2, type = \"params\", showd = TRUE)"
[1] "DEPENDENCIES:"
                          out.alt2 
"447c5e6ce70559e86ece95b22cd7381b" 
[1] "FOUND r_env_cache/2.10.1/alt2-params_41/8b917b820dc56419beb7c65c1504639a.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:09"
[1] "EXPRESSION:"
[1] "init <- list(S0 = 600, I0 = 1, R0 = 0, D0 = 0)"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_42/6fcfea7313126f97a1ef65ab17beed9c.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:09"
[1] "EXPRESSION:"
[1] "time <- 80"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_42/fc0e542f87ad9ff32396c0c40d064d7d.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:09"
[1] "EXPRESSION:"
[1] "posterior <- manage(init, alt.epistep, NULL, NULL, T = time,      bkrate = 100)"
[1] "DEPENDENCIES:"
                       alt.epistep 
"b25520b22b54e43a73301f938286625b" 
                              init 
"6fcfea7313126f97a1ef65ab17beed9c" 
                              time 
"fc0e542f87ad9ff32396c0c40d064d7d" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_42/c3f78f4d4771b03d7ec8a3ab4aae511a.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:09"
[1] "EXPRESSION:"
[1] "plot(log(posterior$samp$b), type = \"l\", main = \"\", ylab = expression(b))"
[1] "DEPENDENCIES:"
                         posterior 
"c3f78f4d4771b03d7ec8a3ab4aae511a" 
[1] "FOUND r_env_cache/2.10.1/alt-mixing-b_43/f821df6c10a84b0744a3b9bdbe107d0a.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:09"
[1] "EXPRESSION:"
[1] "plot(posterior$samp$k, type = \"l\", main = \"\", ylab = expression(k))"
[1] "DEPENDENCIES:"
                         posterior 
"c3f78f4d4771b03d7ec8a3ab4aae511a" 
[1] "FOUND r_env_cache/2.10.1/alt-mixing-k_44/ea2ce842d9a856ddad85d3ec1fbf522f.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:09"
[1] "EXPRESSION:"
[1] "plot(posterior$samp$nu, type = \"l\", main = \"\", ylab = expression(nu))"
[1] "DEPENDENCIES:"
                         posterior 
"c3f78f4d4771b03d7ec8a3ab4aae511a" 
[1] "FOUND r_env_cache/2.10.1/alt-mixing-nu_45/f1b7dd61c80f5cb9c3036a30c798a0e2.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:10"
[1] "EXPRESSION:"
[1] "plot(posterior$samp$mu, type = \"l\", main = \"\", ylab = expression(mu))"
[1] "DEPENDENCIES:"
                         posterior 
"c3f78f4d4771b03d7ec8a3ab4aae511a" 
[1] "FOUND r_env_cache/2.10.1/alt-mixing-mu_46/ee3650dd584ce6c2cdb61eb0b4cd1ba9.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:10"
[1] "EXPRESSION:"
[1] "mean.params <- as.list(apply(posterior$samp, 2, mean))"
[1] "DEPENDENCIES:"
                         posterior 
"c3f78f4d4771b03d7ec8a3ab4aae511a" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_47/aef1d811d501cbd666d88a00b88761f6.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:10"
[1] "EXPRESSION:"
[1] "costs <- list(vac = 2.5, death = 4, infect = 1)"
[1] "DEPENDENCIES:"
list()
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_48/c5369ff5abf8f567c07e503f2beb112b.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:10"
[1] "EXPRESSION:"
[1] "vacgrid <- list(fracs = seq(0, 1, 0.1), stops = seq(2, init$S0 -      50, 50))"
[1] "DEPENDENCIES:"
                              init 
"6fcfea7313126f97a1ef65ab17beed9c" 
                           vacgrid 
"6136d4c9ffd47d46dc71c25ad39bafc6" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_48/b06e4fcf3ca908aec3de499579ca3344.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:10"
[1] "EXPRESSION:"
[1] "alt.optvac <- optvac(init, mean.params, vacgrid, costs, T = time)"
[1] "DEPENDENCIES:"
                             costs 
"c5369ff5abf8f567c07e503f2beb112b" 
                              init 
"6fcfea7313126f97a1ef65ab17beed9c" 
                       mean.params 
"aef1d811d501cbd666d88a00b88761f6" 
                              time 
"fc0e542f87ad9ff32396c0c40d064d7d" 
                           vacgrid 
"b06e4fcf3ca908aec3de499579ca3344" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_48/43e87c8daad68356a254162f09ca0229.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:10"
[1] "EXPRESSION:"
[1] "alt.best <- getpolicy(alt.optvac)"
[1] "DEPENDENCIES:"
                        alt.optvac 
"43e87c8daad68356a254162f09ca0229" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_48/884752abdb224fdc957e4975444e6afe.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:10"
[1] "EXPRESSION:"
[1] "plot(alt.optvac)"
[1] "DEPENDENCIES:"
                        alt.optvac 
"43e87c8daad68356a254162f09ca0229" 
[1] "FOUND r_env_cache/2.10.1/alt-optvac_49/054dade464fc34924285deb264f26990.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:11"
[1] "EXPRESSION:"
[1] "alt.vac.opt <- alt.best[3:4]"
[1] "DEPENDENCIES:"
                          alt.best 
"884752abdb224fdc957e4975444e6afe" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_50/6284f5873e39a2919ed90c660f27ac84.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:11"
[1] "EXPRESSION:"
[1] "alt.MCepi <- MCepi(init, alt.epistep, alt.vac.opt, costs, T = time)"
[1] "DEPENDENCIES:"
                       alt.epistep 
"b25520b22b54e43a73301f938286625b" 
                       alt.vac.opt 
"6284f5873e39a2919ed90c660f27ac84" 
                             costs 
"c5369ff5abf8f567c07e503f2beb112b" 
                              init 
"6fcfea7313126f97a1ef65ab17beed9c" 
                              time 
"fc0e542f87ad9ff32396c0c40d064d7d" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_50/6bcf95c107e41d7ac2e90d2d701fb332.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:11"
[1] "EXPRESSION:"
[1] "alt.MCmanage <- MCmanage(init, alt.epistep, vacgrid, costs, T = time)"
[1] "DEPENDENCIES:"
                       alt.epistep 
"b25520b22b54e43a73301f938286625b" 
                             costs 
"c5369ff5abf8f567c07e503f2beb112b" 
                              init 
"6fcfea7313126f97a1ef65ab17beed9c" 
                              time 
"fc0e542f87ad9ff32396c0c40d064d7d" 
                           vacgrid 
"b06e4fcf3ca908aec3de499579ca3344" 
[1] "FOUND r_env_cache/2.10.1/UNNAMED_CHUNK_52/61188c13fad44d9ab9112c45a1582695.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:11"
[1] "EXPRESSION:"
[1] "plot(alt.MCepi, showd = TRUE)"
[1] "DEPENDENCIES:"
                         alt.MCepi 
"6bcf95c107e41d7ac2e90d2d701fb332" 
[1] "FOUND r_env_cache/2.10.1/alt-MCepi-t_54/9a55ccc7399996060b9c1c1c8120519e.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:11"
[1] "EXPRESSION:"
[1] "plot(alt.MCepi, type = \"costs\")"
[1] "DEPENDENCIES:"
                         alt.MCepi 
"6bcf95c107e41d7ac2e90d2d701fb332" 
[1] "FOUND r_env_cache/2.10.1/alt-MCepi-c_55/0758c145ef2ae5ba07c511732f348a73.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:11"
[1] "EXPRESSION:"
[1] "plot(alt.MCmanage, showd = TRUE)"
[1] "DEPENDENCIES:"
                      alt.MCmanage 
"61188c13fad44d9ab9112c45a1582695" 
[1] "FOUND r_env_cache/2.10.1/alt-MCmanage-t_56/56a920ce245a80456e2ab3c523db51ec.RData"
[1] "CACHE USED"
[1] "==========================================="
[1] "27-04-2010-15:41:12"
[1] "EXPRESSION:"
[1] "plot(alt.MCmanage, type = \"costs\")"
[1] "DEPENDENCIES:"
                      alt.MCmanage 
"61188c13fad44d9ab9112c45a1582695" 
[1] "FOUND r_env_cache/2.10.1/alt-MCmanage-c_57/d5ec763793c9bad20b4ed46b82aa2d91.RData"
[1] "CACHE USED"
[1] "==========================================="
