full test coverage

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: spatPomp
 Type: Package
 Title: Inference for Spatiotemporal Partially Observed Markov Processes
-Version: 0.34.6
-Date: 2024-05-12
+Version: 0.34.7
+Date: 2024-05-13
 Authors@R: c(
   person("Kidus", "Asfaw", email = "[email protected]", role = c("aut")),
   person("Edward", "Ionides", email = "[email protected]",role = c("cre","aut")),

R/as_data_frame.R

@@ -58,10 +58,11 @@ setAs(
     # convert to long format with column for stateobscovars
     no_time_colnames <- colnames(dat)[-1]
     shared_covnames_ix <- which(no_time_colnames %in% from@shared_covarnames)
-    if(length(shared_covnames_ix) > 0)
+    if(length(shared_covnames_ix) > 0) {
       to_gather <- no_time_colnames[-shared_covnames_ix]
-    else
-      to_gather <- no_time_colnames
+      stop(paste('in', sQuote('as.data.frame'),
+        ": shared covariates are not yet fully implemented in spatPomp"))
+    } else to_gather <- no_time_colnames
     to_arrange <- rlang::syms(c(timename, unitname, "stateobscovars"))
     to_final_select <- c(timename, unitname, unit_stateobscovars)
     gathered <- dat %>%

tests/bm.R

@@ -717,7 +717,7 @@ try(spatPomp(data=b_data,times="time",units="unit",t0=0,
 b_shared_covar <- data.frame(time=0:2,Z=3:5)
 model_shared_covar <- spatPomp(data=b_data,times="time",units="unit",
   t0=0,covar=b_shared_covar, shared_covarnames="Z")
-as.data.frame(b_shared_covar)
+try(as.data.frame(model_shared_covar))
 
 b_unit_covar <- data.frame(time=c(0:2,0:2),unit=rep(c("U1","U2"),each=3),
   Z=rep(3:5,times=2))

tests/bm.Rout.save

@@ -1,7 +1,7 @@
 
 R version 4.4.0 (2024-04-24) -- "Puppy Cup"
 Copyright (C) 2024 The R Foundation for Statistical Computing
-Platform: aarch64-apple-darwin20
+Platform: x86_64-apple-darwin20
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.
@@ -1132,11 +1132,9 @@ Error : in ‘spatPomp’: for unit-specific covariates, there should be a colum
 > b_shared_covar <- data.frame(time=0:2,Z=3:5)
 > model_shared_covar <- spatPomp(data=b_data,times="time",units="unit",
 +   t0=0,covar=b_shared_covar, shared_covarnames="Z")
-> as.data.frame(b_shared_covar)
-  time Z
-1    0 3
-2    1 4
-3    2 5
+> try(as.data.frame(model_shared_covar))
+Error in asMethod(object) : 
+  in ‘as.data.frame’ : shared covariates are not yet fully implemented in spatPomp
 > 
 > b_unit_covar <- data.frame(time=c(0:2,0:2),unit=rep(c("U1","U2"),each=3),
 +   Z=rep(3:5,times=2))

tests/measles.R

@@ -40,7 +40,10 @@ logLik(m2_pf)
 ## i.e., cohort=0.
 ##
 
-## A call to igirf using the moment-based guide function can test compiled code for eunit_measure, munit_measure, vunit_measure, dunit_measure, runit_measure, rprocess, skeleton, rinit and partrans. 
+## A call to igirf using the moment-based guide function can test
+## compiled code for eunit_measure, munit_measure, vunit_measure,
+## dunit_measure, runit_measure, rprocess, skeleton, rinit and partrans. 
+## It also tests igirf (method=moment) with covariates
 
 m3_params <- m_params
 m3_params["cohort"] <- 0
@@ -64,6 +67,10 @@ m3_igirf_out <- igirf(m_model, Ngirf = m3_igirf_ngirf,
 )
 logLik(m3_igirf_out)
 
+## another call to igirf tests igirf (method=bootstrap) with covariates
+m3_igirf_bootstrap_out <- igirf(m3_igirf_out,kind='bootstrap')
+logLik(m3_igirf_bootstrap_out)
+
 ## test error message
 try(measles(U=1000))
 

tests/measles.Rout.save

@@ -1,7 +1,7 @@
 
 R version 4.4.0 (2024-04-24) -- "Puppy Cup"
 Copyright (C) 2024 The R Foundation for Statistical Computing
-Platform: aarch64-apple-darwin20
+Platform: x86_64-apple-darwin20
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.
@@ -63,7 +63,10 @@ Loading required package: pomp
 > ## i.e., cohort=0.
 > ##
 > 
-> ## A call to igirf using the moment-based guide function can test compiled code for eunit_measure, munit_measure, vunit_measure, dunit_measure, runit_measure, rprocess, skeleton, rinit and partrans. 
+> ## A call to igirf using the moment-based guide function can test
+> ## compiled code for eunit_measure, munit_measure, vunit_measure,
+> ## dunit_measure, runit_measure, rprocess, skeleton, rinit and partrans. 
+> ## It also tests igirf (method=moment) with covariates
 > 
 > m3_params <- m_params
 > m3_params["cohort"] <- 0
@@ -91,6 +94,16 @@ Warning messages:
 > logLik(m3_igirf_out)
 [1] -86380.55
 > 
+> ## another call to igirf tests igirf (method=bootstrap) with covariates
+> m3_igirf_bootstrap_out <- igirf(m3_igirf_out,kind='bootstrap')
+Warning messages:
+1: in 'table_lookup': extrapolating at 1.965003e+03. 
+2: in 'table_lookup': extrapolating at 1.965002e+03. 
+3: in 'table_lookup': extrapolating at 1.965002e+03. 
+4: in 'table_lookup': extrapolating at 1.965002e+03. 
+> logLik(m3_igirf_bootstrap_out)
+[1] -86123.26
+> 
 > ## test error message
 > try(measles(U=1000))
 Error in measles(U = 1000) :