Running 'abf.R' [0s]
  Running 'abfir.R' [0s]
  Running 'bm.R' [13s]
  Comparing 'bm.Rout' to 'bm.Rout.save' ...289c289
< # A tibble: 8 x 5
---
> # A tibble: 8 Ã 5
302c302
< # A tibble: 10 x 5
---
> # A tibble: 10 Ã 5
  Running 'bm2.R' [8s]
  Running 'bpfilter.R' [0s]
  Running 'enkf.R' [0s]
  Running 'gbm.R' [7s]
  Comparing 'gbm.Rout' to 'gbm.Rout.save' ... OK
  Running 'girf.R' [0s]
  Running 'he10.R' [9s]
  Comparing 'he10.Rout' to 'he10.Rout.save' ... OK
  Running 'ibpf.R' [0s]
  Running 'ienkf.R' [0s]
  Running 'igirf.R' [0s]
  Running 'iter_filter.R' [3s]
  Comparing 'iter_filter.Rout' to 'iter_filter.Rout.save' ... OK
  Running 'iubf.R' [0s]
  Running 'lorenz.R' [6s]
  Comparing 'lorenz.Rout' to 'lorenz.Rout.save' ... OK
  Running 'measles.R' [16s]
  Comparing 'measles.Rout' to 'measles.Rout.save' ... OK
  Running 'pfilter.R' [0s]
  Running 'plot.R' [0s]
  Running 'simulate.R' [0s]
  Running 'spatPomp.R' [0s]
  Running 'xtests.R' [3s]
Running the tests in 'tests/bm2.R' failed.
Complete output:
  > library(spatPomp)
  Loading required package: pomp
  
  Welcome to pomp!
  
  As of version 4.6, no user-visible pomp function has a name that
  includes a dot ('.'). Function names have been changed to replace the
  dot with an underscore ('_'). For more information, see the pomp blog:
  https://kingaa.github.io/pomp/blog.html.
  
  > set.seed(0)
  > 
  > b2_U <- 4
  > b2 <- bm2(U=b2_U,N=2,unit_specific_names="rho")
  > 
  > b2_bpfilter <- bpfilter(b2,Np=5,block_size=1)
  > paste("bpfilter logLik for bm2 model:",logLik(b2_bpfilter))
  [1] "bpfilter logLik for bm2 model: -12.9121635525516"
  > 
  > # here there are no transformations so use small rw.sd. to avoid negatives
  > b2_rw_list <- rep(list(0.001),times=b2_U) 
  > names(b2_rw_list) <-paste0("rho",1:b2_U)
  > b2_rw.sd <- do.call(rw_sd,b2_rw_list)
  > 
  > b2_units = seq_len(b2_U)
  > b2_nblocks = b2_U/2
  > b2_block_list = split(b2_units, sort(b2_units %% b2_nblocks))
  > b2_block_list <- lapply(b2_block_list, as.integer)
  > 
  > b2_ibpf <- ibpf(b2,
  +   params=coef(b2),
  +   sharedParNames=NULL,
  +   unitParNames="rho",
  +   Nbpf=2,
  +   spat_regression=0.1,
  +   Np=5,
  +   rw.sd=b2_rw.sd,
  +   cooling.fraction.50=0.5,
  +   block_list=b2_block_list
  + )
  > 
  > paste("ibpf logLik for b2 model:",logLik(b2_ibpf))
  [1] "ibpf logLik for b2 model: -14.1817035202796"
  > 
  > paste("kf logLik for b2:",bm2_kalman_logLik(b2))
  [1] "kf logLik for b2: -13.2725611269272"
  > 
  > #######################################################################
  > # test ibpf with argument re-use and replacement
  > # check that results match after re-use and replacement
  > #######################################################################
  > 
  > set.seed(5)
  > b2_ibpf <- ibpf(b2,Np=5,block_size=1,Nbpf=2,
  +   rw.sd=b2_rw.sd,
  +   cooling.frac=0.5, spat_regression=0.1,
  +   unitParNames="rho",sharedParNames=NULL)
  > 
  > paste("bm2 ibpf loglik: ",round(logLik(b2_ibpf),10))
  [1] "bm2 ibpf loglik:  -13.2406696135"
  > 
  > set.seed(5)
  > b2_ibpf_repeat <- ibpf(b2_ibpf,params=coef(b2), unitParNames="rho",
  +   sharedParNames=NULL,spat_regression=0.1)
  > paste("check ibpf on ibpfd_spatPomp: ",
  +   logLik(b2_ibpf_repeat)==logLik(b2_ibpf))
  [1] "check ibpf on ibpfd_spatPomp:  TRUE"
  > 
  > set.seed(5)
  > b2_ibpf_bpfilterd <- ibpf(b2_bpfilter,Np=5,block_size=1,Nbpf=2,
  +   rw.sd=b2_rw.sd,
  +   cooling.frac=0.5, spat_regression=0.1,
  +   unitParNames="rho",sharedParNames=NULL)
  > paste("check ibpf on bpfilterd_spatPomp: ",
  +   logLik(b2_ibpf_bpfilterd)==logLik(b2_ibpf))
  [1] "check ibpf on bpfilterd_spatPomp:  TRUE"
  > 
  > 
  > 
  > 
  > proc.time()
     user  system elapsed 
     3.82    0.34    8.14