Help updating pomp code for new version

[catherinebyrne]

Hello!

I haven't used pomp in a while and my code is no longer working with the new version. I wrote this code when using pomp 2.7

library(pomp)

init <- Csnippet(
  r"{
    V_r = V_0;
    V = V_0+3000;
    I = 0;
    F = F_0;
  }"
)

dmeas <- Csnippet(
  r"{
    lik = 0;
    if (!ISNA(N_F)) {
      lik += dpois(N_F,F*rho2+1e-6,1);
    }
    if (!ISNA(N_V)) {
      lik += dnorm(log(N_V),log(V),rho1,1);
    }
    lik = (give_log) ? lik: exp(lik);
    }"
)

model <- vectorfield(
  Csnippet(
    r"{
       DF = beta*I-z*F;
       DV_r = p*(exp(-(yV)*F))*I-c*V_r;
       DV = DV_r;
       DI =eta*(exp(-(yI)*F))*V_r-delta*I;
     }"
  )
)

param_names <- c("V_0","F_0","rho1","rho2","p","yV","yI","c","eta","delta","beta","z")

state_names <- c("V_r","V","I","F")

par_trans <- parameter_trans(
  log = c("rho1","p","yV","yI","c","eta","delta","Beta","z"),
  logit = c("rho2")
)

data_NA <- data.frame(
  time = seq(0,10,0.1),
  N_V = NA,
  N_F = NA
)

mcmv_NA <- pomp(
  data=data_NA,
  times="time",t0=0,
  skeleton = model,
  dmeasure=dmeas, 
  rinit = init,
  paramnames=param_names,
  statenames=state_names
)

There is no issues with this when using pomp 2.7, but I get big problems when building the pomp object with the new pomp version. For the life of me, I can't figure out what syntax needs to be updated for it to work. Any help would be greatly appreciated!!

Thanks!

[kingaa]

The above compiles for me. What version of R and pomp are you using?

Can you include more information (e.g. FAQ 1.1)?

Also, one minor thing: FAQ 4.7.

Here is a somewhat more up-to-date version (but no changes to the above are strictly necessary):

mcmv_NA <- pomp(
  data=data.frame(
    time=seq(0,10,0.1),
    monkey=NA,
    N_F=NA,
    N_V=NA
  ),
  times="time",
  t0=0,
  skeleton = model,
  dmeasure=dmeas, 
  rinit = init,
  paramnames=param_names,
  statenames=state_names
)

or even

mcmv_NA <- pomp(
  data=NULL,
  times = seq(0,10,0.1),
  t0=0,
  skeleton = model,
  dmeasure=dmeas, 
  rinit = init,
  obsnames=c("N_F","N_V"),
  paramnames=param_names,
  statenames=state_names
)

[catherinebyrne]

Thanks for trying the code! Your two alternate versions don't work for me either, unfortunately. I tried replacing "beta" with "Beta" as per FAQ 4.7 and still no.

I'm using R 4.3.1 and pomp 5.2.

The error message I get is

Error: error in building shared-object library from C snippets: in ‘Cbuilder’: compilation error: cannot compile shared-object library ‘C:/Users/C-BYR~1.LAP/AppData/Local/Temp/Rtmps5R5aY/17540/pomp_abbf2bb297d054f8ea10c1efef53f365.dll’: status = 1
compiler messages:
gcc  -I"C:/PROGRA~1/R/R-43~1.1/include" -DNDEBUG     -I"c:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c C:/Users/C-BYR~1.LAP/AppData/Local/Temp/Rtmps5R5aY/17540/pomp_abbf2bb297d054f8ea10c1efef53f365.c -o C:/Users/C-BYR~1.LAP/AppData/Local/Temp/Rtmps5R5aY/17540/pomp_abbf2bb297d054f8ea10c1efef53f365.o
sh: gcc: command not found
make: *** [C:/PROGRA~1/R/R-43~1.1/etc/x64/Makeconf:265: C:/Users/C-BYR~1.LAP/AppData/Local/Temp/Rtmps5R5aY/17540/pomp_abbf2bb297d054f8ea10c1efef53f365.o] Error 127
In addition: Warning message:
In system2(command = R.home("bin/R"), args = c("CMD", "SHLIB", "-c",  :
  running command '"C:/PROGRA~1/R/R-43~1.1/bin/R" PKG_CPPFLAGS="-I"C:/Users/c-byr.LAPTOP-UG0F9R6R/AppData/Local/R/win-library/4.3/pomp/include" -I"C:/Users/c-byr.LAPTOP-UG0F9R6R/OneDrive - math.ubc.ca/Hutch - SARS-CoV-2/mild SARS-CoV-2 infection/data"" CMD SHLIB -c -o C:/Users/C-BYR~1.LAP/AppData/Local/Temp/Rtmps5R5aY/17540/pomp_abbf2bb297d054f8ea10c1efef53f365.dll C:/Users/C-BYR~1.LAP/AppData/Local/Temp/Rtmps5R5aY/17540/pomp_abbf2bb297d054f8ea10c1efef53f365.c' had status 1

This is the output of source("https://kingaa.github.io/scripts/diagnostics.R")

-----------------------------------
 contents of site Rprofile file 
-----------------------------------
# Things you might want to change

# options(papersize="a4")
# options(editor="notepad")
# options(pager="internal")

# set the default help type
# options(help_type="text")
  options(help_type="html")

# set a site library
# .Library.site <- file.path(chartr("\\", "/", R.home()), "site-library")

# set a CRAN mirror
# local({r <- getOption("repos")
#       r["CRAN"] <- "http://my.local.cran"
#       options(repos=r)})

# Give a fortune cookie, but only to interactive sessions
# (This would need the fortunes package to be installed.)
#  if (interactive()) 
#    fortunes::fortune()

-----------------------------------
 sessionInfo 
-----------------------------------
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22621)

Matrix products: default


locale:
[1] LC_COLLATE=English_Canada.utf8  LC_CTYPE=English_Canada.utf8    LC_MONETARY=English_Canada.utf8 LC_NUMERIC=C                   
[5] LC_TIME=English_Canada.utf8    

time zone: America/Vancouver
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] plyr_1.8.8          tidyr_1.3.0         fitdistrplus_1.1-11 survival_3.5-5      MASS_7.3-60         dplyr_1.1.2         reshape2_1.4.4     
[8] ggplot2_3.4.2       pomp_5.2           

loaded via a namespace (and not attached):
 [1] Matrix_1.5-4.1    gtable_0.3.3      compiler_4.3.1    tidyselect_1.2.0  Rcpp_1.0.10       stringr_1.5.0     splines_4.3.1     scales_1.2.1     
 [9] lattice_0.21-8    coda_0.19-4       R6_2.5.1          generics_0.1.3    tibble_3.2.1      munsell_0.5.0     pillar_1.9.0      rlang_1.1.1      
[17] utf8_1.2.3        deSolve_1.35      stringi_1.7.12    cli_3.6.1         withr_2.5.0       magrittr_2.0.3    digest_0.6.31     grid_4.3.1       
[25] rstudioapi_0.14   mvtnorm_1.2-2     lifecycle_1.0.3   vctrs_0.6.3       glue_1.6.2        data.table_1.14.8 rsconnect_0.8.29  fansi_1.0.4      
[33] colorspace_2.1-0  purrr_1.0.1       tools_4.3.1       pkgconfig_2.0.3  

Any ideas?

Thanks again

[catherinebyrne]

Hi again! I figured out the problem. I hadn't updated my RTools to match my new version of R. It's working now! Thanks again for the help!

[kingaa]

Very good. I was just about to ask....