From bd81c81607e7396a9f6f9706e8b72aece49ec9e1 Mon Sep 17 00:00:00 2001 From: Ed Ionides Date: Mon, 13 May 2024 17:04:25 -0400 Subject: [PATCH] creeping toward full coverage --- R/abf.R | 15 ++++++------- R/abfir.R | 15 +++---------- R/girf.R | 2 +- R/igirf.R | 26 +++++++++++------------ man/abf.Rd | 2 +- man/abfir.Rd | 2 +- man/igirf.Rd | 2 +- src/fcstsampvar.c | 5 ----- tests/bm.R | 21 +++++++++++++++++- tests/bm.Rout.save | 40 +++++++++++++++++++++++++++++------ tests/bm2.Rout.save | 2 +- tests/concat.Rout.save | 2 +- tests/gbm.Rout.save | 2 +- tests/he10.R | 8 ++++++- tests/he10.Rout.save | 10 +++++++-- tests/iter_filter.Rout.save | 2 +- tests/lorenz.Rout.save | 2 +- tests/measles.Rout.save | 2 +- tests/measles2.Rout.save | 2 +- tests/param_formats.Rout.save | 2 +- 20 files changed, 104 insertions(+), 60 deletions(-) diff --git a/R/abf.R b/R/abf.R index a62e0b7..983257d 100644 --- a/R/abf.R +++ b/R/abf.R @@ -108,7 +108,7 @@ setMethod( "abf", signature=signature(object="spatPomp"), function (object, Nrep, Np, nbhd, params, - tol = 1e-300, + tol = 1.0e-100, ..., verbose=getOption("verbose",FALSE)) { ep <- paste0("in ",sQuote("abf"),": ") @@ -222,9 +222,6 @@ abf_internal <- function (object, Np, nbhd, tol, ..., verbose, .gnsi = TRUE) { params <- coef(object) pompLoad(object,verbose=FALSE) gnsi <- as.logical(.gnsi) - if (length(params)==0) pStop_(ep,sQuote("params")," must be specified") - if (missing(tol)) pStop(ep,sQuote("tol")," must be specified") - times <- time(object,t0=TRUE) ntimes <- length(times)-1 nunits <- length(unit_names(object)) @@ -246,10 +243,12 @@ abf_internal <- function (object, Np, nbhd, tol, ..., verbose, .gnsi = TRUE) { if (!is.numeric(Np)) pStop(ep,sQuote("Np")," must be a number, a vector of numbers, or a function") Np <- as.integer(Np) - if (is.matrix(params)) { - if (!all(Np==ncol(params))) - pStop_(ep,"when ",sQuote("params")," is provided as a matrix, do not specify ",sQuote("Np")) - } + ## matrix parameters not currently supported + ## if (is.matrix(params)) { + ## if (!all(Np==ncol(params))) + ## pStop_(ep,"when ",sQuote("params"), + ## " is provided as a matrix, do not specify ",sQuote("Np")) + ## } params <- as.matrix(params) diff --git a/R/abfir.R b/R/abfir.R index 5bed18d..1cffb69 100644 --- a/R/abfir.R +++ b/R/abfir.R @@ -91,9 +91,8 @@ setMethod( "abfir", signature=signature(object="spatPomp"), function (object, Np, Nrep, nbhd, - Ninter, tol = (1e-300), params, ..., + Ninter, tol = (1e-100), params, ..., verbose=getOption("verbose",FALSE) ) { - ep <- paste0("in ",sQuote("abfir"),": ") ## declare global variable since foreach's u uses non-standard evaluation i <- 1 @@ -205,15 +204,11 @@ abfir_internal <- function (object, Np, nbhd, unit_obsnames = object@unit_obsnames, unit_accumvars = object@unit_accumvars) params <- coef(object) - verbose = FALSE pompLoad(object,verbose=verbose) on.exit(pompUnload(object,verbose=verbose)) gnsi <- as.logical(.gnsi) - if (length(params)==0) pStop_(ep,sQuote("params")," must be specified") - if (missing(tol)) pStop_(ep,sQuote("tol")," must be specified") - - times <- time(object,t0=TRUE) + times <- time(object,t0=TRUE) N <- length(times)-1 U <- length(unit_names(object)) @@ -278,10 +273,7 @@ abfir_internal <- function (object, Np, nbhd, log=TRUE, .gnsi=gnsi ), - error = function (e) { - pStop_("abfir error in calculation of weights: ", - conditionMessage(e)) - } + error = function (e) pStop_("abfir error in calculation of weights: ", conditionMessage(e)) ) log_cond_densities[,,n] <- log_weights[,,1] @@ -375,7 +367,6 @@ abfir_internal <- function (object, Np, nbhd, } ## resample down to one particle, making Np copies of, say, particle #1. xas <- xf[,1] - if (verbose) cat("abfir timestep",n,"of",N,"finished\n") } diff --git a/R/girf.R b/R/girf.R index 9d96ce8..e39e914 100644 --- a/R/girf.R +++ b/R/girf.R @@ -129,7 +129,7 @@ setMethod( ..., verbose = getOption("verbose", FALSE)) { - if (missing(tol)) tol <- 1e-300 + if (missing(tol)) tol <- 1e-100 if (missing(Ninter)) Ninter <- length(unit_names(object)) kind = match.arg(kind) diff --git a/R/igirf.R b/R/igirf.R index d21a3cf..0e990b7 100644 --- a/R/igirf.R +++ b/R/igirf.R @@ -97,7 +97,7 @@ setMethod( signature=signature(data="spatPomp"), definition=function (data,Ngirf,Np,rw.sd,cooling.type,cooling.fraction.50, Ninter,lookahead=1,Nguide,kind=c('bootstrap', 'moment'), - tol = 1e-300, + tol = 1e-100, ..., verbose = getOption("verbose", FALSE)) { ep <- paste0("in ", sQuote("igirf") , " : ") @@ -276,7 +276,7 @@ igirf.momgirf <- function (object, params, Ninter, lookahead, Nguide, gnsi <- as.logical(.gnsi) verbose <- as.logical(verbose) girfiter <- as.integer(girfiter) - ep <- paste0("in ",sQuote("igirf")," : ") + ep <- paste0("in ",sQuote("igirf"), " (method=moment) : ") if (length(tol) != 1 || !is.finite(tol) || tol < 0) pStop_(ep, sQuote("tol")," should be a small positive number.") @@ -333,7 +333,7 @@ igirf.momgirf <- function (object, params, Ninter, lookahead, Nguide, times=times[(nt+2):(nt+1+lookahead_steps)], params=tp_with_guides, gnsi=TRUE), - error = function (e) pStop_("in ", sQuote("igirf"), " : ", conditionMessage(e)) + error = function (e) pStop_("in ", sQuote("igirf_moment"), " : ", conditionMessage(e)) ) fcst_samp_var <- xx dim(fcst_samp_var) <- c(length(unit_names(object)), lookahead_steps, Np) @@ -371,7 +371,7 @@ igirf.momgirf <- function (object, params, Ninter, lookahead, Nguide, times=times[(nt+2):(nt+1+lookahead_steps)], params=tparams, gnsi=TRUE), - error = function (e) pStop_("in ", sQuote("igirf"), " : ",conditionMessage(e)) + error = function (e) pStop_("in ", sQuote("igirf_moment"), " : ",conditionMessage(e)) ) dim(meas_var_skel) <- c(length(unit_names(object)), lookahead_steps, Np) fcst_var_upd <- array(0, dim = c(length(unit_names(object)), lookahead_steps, Np)) @@ -388,7 +388,7 @@ igirf.momgirf <- function (object, params, Ninter, lookahead, Nguide, times=times[(nt+2):(nt+1+lookahead_steps)], params=array.tparams, gnsi=TRUE), - error = function (e) pStop_("in ", sQuote("igirf"), " : ", conditionMessage(e)) + error = function (e) pStop_("in ", sQuote("igirf_moment"), " : ", conditionMessage(e)) ) mom_match_param <- mmp dim(mom_match_param) <- c(dim(tparams)[1], length(unit_names(object)), lookahead_steps, Np) @@ -409,7 +409,7 @@ igirf.momgirf <- function (object, params, Ninter, lookahead, Nguide, log=TRUE, .gnsi=gnsi )), - error = function (e) pStop_("in igirf : error in calculation of log_dmeas_weights: ", conditionMessage(e)) + error = function (e) pStop_("in igirf_moment : error in calculation of log_dmeas_weights: ", conditionMessage(e)) ) ## uncomment for debugging: tracking down particles with NA weight @@ -446,7 +446,7 @@ igirf.momgirf <- function (object, params, Ninter, lookahead, Nguide, log=TRUE, .gnsi=gnsi ), - error = function (e) pStop_("in igirf : error in calculation of log_meas_weights: ", conditionMessage(e)) + error = function (e) pStop_("in igirf_moment : error in calculation of log_meas_weights: ", conditionMessage(e)) ) gnsi <- FALSE log_weights <- as.numeric(log_meas_weights) + log_s_not_1_weights @@ -455,7 +455,7 @@ igirf.momgirf <- function (object, params, Ninter, lookahead, Nguide, if (any(log_weights>-Inf)) { coef(object,transform=TRUE) <- apply(params,1L,weighted.mean,w=exp(log_weights)) } else { - warning("igirf: ","filtering failure at last filter iteration; using ", + warning("igirf_moment: ","filtering failure at last filter iteration; using ", "unweighted mean for point estimate.") coef(object,transform=TRUE) <- apply(params,1L,mean) } @@ -476,7 +476,7 @@ igirf.momgirf <- function (object, params, Ninter, lookahead, Nguide, fsv=fcst_samp_var, tol=tol ), - error = function (e) pStop_("in igirf : ", conditionMessage(e)) + error = function (e) pStop_("in igirf_moment : ", conditionMessage(e)) ) cond.loglik[nt+1, s] <- xx$loglik + max_log_weights x <- xx$states @@ -514,7 +514,7 @@ igirf.bootgirf <- function (object, params, Ninter, lookahead, Nguide, verbose <- as.logical(verbose) girfiter <- as.integer(girfiter) Np <- as.integer(Np) - ep <- paste0("in ",sQuote("ibootgirf"),": ") + ep <- paste0("in ",sQuote("igirf")," (method=bootstrap) : ") if (length(tol) != 1 || !is.finite(tol) || tol < 0) stop(ep,sQuote("tol")," should be a small positive number.",call.=FALSE) @@ -623,7 +623,7 @@ igirf.bootgirf <- function (object, params, Ninter, lookahead, Nguide, log=TRUE, .gnsi=gnsi )), - error = function (e) pStop_("error in calculation of log_dmeas_weights: ", conditionMessage(e)) + error = function (e) pStop_("error in igirf_bootstrap calculation of log_dmeas_weights: ", conditionMessage(e)) ) ## uncomment for debugging: tracking down particles with NA weight @@ -668,7 +668,7 @@ igirf.bootgirf <- function (object, params, Ninter, lookahead, Nguide, log=TRUE, .gnsi=gnsi ), - error = function (e) pStop_("error in calculation of log_meas_weights: ", conditionMessage(e)) + error = function (e) pStop_("error in igirf_bootstrap calculation of log_meas_weights: ", conditionMessage(e)) ) gnsi <- FALSE log_weights <- as.numeric(log_meas_weights) + log_s_not_1_weights @@ -699,7 +699,7 @@ igirf.bootgirf <- function (object, params, Ninter, lookahead, Nguide, fsv=array(0,dim=c(length(unit_names(object)), lookahead_steps, Np)), tol=tol ), - error = function (e) pStop_("error in igirf computations : ", conditionMessage(e)) + error = function (e) pStop_("error in igirf_bootsrap computations : ", conditionMessage(e)) ) guidesim_index = guidesim_index[xx$ancestry] cond.loglik[nt+1, s] <- xx$loglik + max_log_weights diff --git a/man/abf.Rd b/man/abf.Rd index 8c8946b..f43a161 100644 --- a/man/abf.Rd +++ b/man/abf.Rd @@ -14,7 +14,7 @@ Np, nbhd, params, - tol = 1e-300, + tol = 1e-100, ..., verbose = getOption("verbose", FALSE) ) diff --git a/man/abfir.Rd b/man/abfir.Rd index 36d26e6..5a0fd92 100644 --- a/man/abfir.Rd +++ b/man/abfir.Rd @@ -14,7 +14,7 @@ Nrep, nbhd, Ninter, - tol = (1e-300), + tol = (1e-100), params, ..., verbose = getOption("verbose", FALSE) diff --git a/man/igirf.Rd b/man/igirf.Rd index 1c44591..9155852 100644 --- a/man/igirf.Rd +++ b/man/igirf.Rd @@ -27,7 +27,7 @@ lookahead = 1, Nguide, kind = c("bootstrap", "moment"), - tol = 1e-300, + tol = 1e-100, ..., verbose = getOption("verbose", FALSE) ) diff --git a/src/fcstsampvar.c b/src/fcstsampvar.c index d7b3aa9..9043a2d 100644 --- a/src/fcstsampvar.c +++ b/src/fcstsampvar.c @@ -80,11 +80,6 @@ SEXP do_fcst_samp_var (SEXP object, SEXP X, SEXP Np, SEXP times, SEXP params, SE PROTECT(F = ret_array(nunits, nreps, ntimes)); nprotect++; switch (mode) { - case Rfun: { - } - - break; - case native: case regNative: { int *oidx, *sidx, *pidx, *cidx; spatPomp_unit_measure_mean *ff = NULL; diff --git a/tests/bm.R b/tests/bm.R index 2eceb2d..91a288d 100644 --- a/tests/bm.R +++ b/tests/bm.R @@ -137,7 +137,9 @@ abf(b_model_zero_dmeasure,Nrep=2,Np=Np,verbose=TRUE) b_abfir <- abfir(b_model, Nrep = 2, Np = Np, nbhd = b_bag_nbhd) paste("bm abfir loglik: ",round(logLik(b_abfir),10)) -abfir(b_abfir,verbose=TRUE,accumvars="X1") +capture.output( + abfir(b_abfir,verbose=TRUE,accumvars="X1") +) -> b_abfir_out abfir(b_model, Nrep = 2, Np = Np) try(abfir(b_model)) try(abfir(b_model,Nrep=2)) @@ -146,6 +148,10 @@ try(abfir(b_model,Nrep=2,Np=1:10)) try(abfir(b_model,Nrep=2,Np=Np,params=unname(coef(b_model)))) try(abfir(b_model_zero_dmeasure,Nrep = 3, Np = Np)) +# test abfir when all particles fail... +# make this happen by setting a high tol +abfir(b_abfir,tol=1000) + ## -------------------------------------------------------------- ## bpfilter tested on bm ## ______________________________________________________________ @@ -274,6 +280,11 @@ girf(b_model_with_accumvars,Np = 3,lookahead = 2, Nguide = 3, girf(b_model_with_accumvars,Np = 3,lookahead = 2, Nguide = 3, kind = 'boot',Ninter=2) +# test girf when all particles fail... +# make this happen by setting a high tol +girf(b_girf_mom,tol=1000) + + ## ------------------------------------------------------------ ## Now, we test the inference methods @@ -397,6 +408,7 @@ igirf(b_igirf_boot_geom,Np=3, try(igirf(b_igirf_boot_geom,Np=function(x) 4)) try(igirf(b_igirf_boot_geom,Np=function(x) "JUNK")) try(igirf(b_igirf_boot_geom,Np=5:15)) +try(igirf(b_igirf_boot_geom,tol=-1)) igirf(b_model_with_accumvars,kind='moment', Ngirf = 2, Nguide=2, @@ -529,6 +541,7 @@ b_sim3v2@data <- exp(b_sim3v2@data) plot(b_sim3v2,type="l",log=TRUE) plot(b_sim3[[2]],type="h",plot_unit_names=FALSE) dev.off() +plot(b_sim3[[2]],type="h",plot_unit_names=TRUE) -> b_sim3_plot print(b_model) @@ -645,6 +658,11 @@ b_array.params2 <- array(c(b_p,b_p), dimnames = list(params = rownames(b_p))) try(munit_measure(b_model, x=b_s2, vc=b_vc, Np=3, unit = 2, time=1,params=b_array.params2)) +## trigger error messages in fcstsampvar.c +try(.Call("do_fcst_samp_var",b_model,b_s,3,1:10,b_array.params,FALSE)) +try(.Call("do_fcst_samp_var",b_model,b_s2,3,1,b_array.params2,FALSE)) + + ## test spatPomp_Csnippet variable construction spatPomp_Csnippet("lik=u;",unit_statenames="A",unit_obsnames=c("B","C"), unit_covarnames="D", @@ -699,6 +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) b_unit_covar <- data.frame(time=c(0:2,0:2),unit=rep(c("U1","U2"),each=3), Z=rep(3:5,times=2)) diff --git a/tests/bm.Rout.save b/tests/bm.Rout.save index 380a3b7..08da44e 100644 --- a/tests/bm.Rout.save +++ b/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: x86_64-apple-darwin20 +Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. @@ -182,8 +182,9 @@ abf timestep 2 of 2 finished > paste("bm abfir loglik: ",round(logLik(b_abfir),10)) [1] "bm abfir loglik: -11.4654403221" > -> abfir(b_abfir,verbose=TRUE,accumvars="X1") - +> capture.output( ++ abfir(b_abfir,verbose=TRUE,accumvars="X1") ++ ) -> b_abfir_out > abfir(b_model, Nrep = 2, Np = Np) > try(abfir(b_model)) @@ -202,6 +203,11 @@ Error : in ‘abfir’: ‘params’ must be a named vector Error in spatPomp:::abfir_internal(object = object, Np = Np, nbhd = nbhd, : task 1 failed - "incorrect number of dimensions" > +> # test abfir when all particles fail... +> # make this happen by setting a high tol +> abfir(b_abfir,tol=1000) + +> > ## -------------------------------------------------------------- > ## bpfilter tested on bm > ## ______________________________________________________________ @@ -388,6 +394,12 @@ Error : in ‘girf’: ‘Np’ must be a single positive integer + kind = 'boot',Ninter=2) > +> # test girf when all particles fail... +> # make this happen by setting a high tol +> girf(b_girf_mom,tol=1000) + +> +> > > ## ------------------------------------------------------------ > ## Now, we test the inference methods @@ -558,7 +570,7 @@ Error : in ‘igirf’ : Error: ‘cooling.fraction.50’ must be in (0,1]. > > try(igirf(b_model,kind="moment",Ngirf=2,rw.sd=b_rw.sd,cooling.fraction.50=0.5,cooling.type="geometric",Np=3,Nguide=4,tol=-1)) -Error : in ‘igirf’ : Error: in ‘igirf’ : ‘tol’ should be a small positive number. +Error : in ‘igirf’ : Error: in ‘igirf’ (method=moment) : ‘tol’ should be a small positive number. > > @@ -574,6 +586,9 @@ Error : in ‘igirf’ : Error: ‘Np’ must be a single positive integer > try(igirf(b_igirf_boot_geom,Np=5:15)) Error : in ‘igirf’ : Error: ‘Np’ must be a single positive integer +> try(igirf(b_igirf_boot_geom,tol=-1)) +Error : in ‘igirf’ : Error: in ‘igirf’ (method=bootstrap) : ‘tol’ should be a small positive number. + > > > igirf(b_model_with_accumvars,kind='moment', Ngirf = 2, Nguide=2, @@ -591,9 +606,9 @@ Error : in ‘igirf’ : Error: ‘Np’ must be a single positive integer Warning messages: 1: In igirf.momgirf(object = object, Ninter = Ninter, Nguide = Nguide, : - igirf: filtering failure at last filter iteration; using unweighted mean for point estimate. + igirf_moment: filtering failure at last filter iteration; using unweighted mean for point estimate. 2: In igirf.momgirf(object = object, Ninter = Ninter, Nguide = Nguide, : - igirf: filtering failure at last filter iteration; using unweighted mean for point estimate. + igirf_moment: filtering failure at last filter iteration; using unweighted mean for point estimate. > igirf(b_model_zero_dmeasure,kind='boot', Ngirf = 2, Nguide=2, + rw.sd = b_rw.sd, cooling.type = "hyperbolic", cooling.fraction.50 = 0.5, + Np=3, Ninter = 1) @@ -785,6 +800,7 @@ Error : in ‘iubf’: ‘Nparam’ must be at least 3 > dev.off() null device 1 +> plot(b_sim3[[2]],type="h",plot_unit_names=TRUE) -> b_sim3_plot > > print(b_model) @@ -1039,6 +1055,13 @@ Error : length of 'times' and 3rd dimension of 'x' do not agree. > try(munit_measure(b_model, x=b_s2, vc=b_vc, Np=3, unit = 2, time=1,params=b_array.params2)) Error : larger number of replicates is not a multiple of smaller. > +> ## trigger error messages in fcstsampvar.c +> try(.Call("do_fcst_samp_var",b_model,b_s,3,1:10,b_array.params,FALSE)) +Error : length of 'times' and 3rd dimension of 'x' do not agree. +> try(.Call("do_fcst_samp_var",b_model,b_s2,3,1,b_array.params2,FALSE)) +Error : larger number of replicates is not a multiple of smaller. +> +> > ## test spatPomp_Csnippet variable construction > spatPomp_Csnippet("lik=u;",unit_statenames="A",unit_obsnames=c("B","C"), + unit_covarnames="D", @@ -1109,6 +1132,11 @@ 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 > > b_unit_covar <- data.frame(time=c(0:2,0:2),unit=rep(c("U1","U2"),each=3), + Z=rep(3:5,times=2)) diff --git a/tests/bm2.Rout.save b/tests/bm2.Rout.save index b605127..46ea275 100644 --- a/tests/bm2.Rout.save +++ b/tests/bm2.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: x86_64-apple-darwin20 +Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. diff --git a/tests/concat.Rout.save b/tests/concat.Rout.save index 1f3b410..f935dbb 100644 --- a/tests/concat.Rout.save +++ b/tests/concat.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: x86_64-apple-darwin20 +Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. diff --git a/tests/gbm.Rout.save b/tests/gbm.Rout.save index b11bff5..1484736 100644 --- a/tests/gbm.Rout.save +++ b/tests/gbm.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: x86_64-apple-darwin20 +Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. diff --git a/tests/he10.R b/tests/he10.R index e74b893..563ec95 100644 --- a/tests/he10.R +++ b/tests/he10.R @@ -210,10 +210,16 @@ try(h_ibpf2 <- ibpf(h_model2, )) ## test error message when munit_measure is undefined +## this also tests setup of covariates for girf_moment try(girf(h_model,kind="moment", Np=10,Ninter=2,Nguide=10,lookahead=1,tol=1e-5)) -# Create second ibpfd_spatPomp object with different chain length, to test error +## test girf_bootstrap with covariates +h_girf <- girf(h_model,kind="bootstrap", + Np=5,Ninter=2,Nguide=5,lookahead=2,tol=1e-5) + +# Create second ibpfd_spatPomp object with different chain length, +# to test error h_ibpf3 <- ibpf(h_model, params=coef(h_model), sharedParNames=sharedParNames, diff --git a/tests/he10.Rout.save b/tests/he10.Rout.save index bb7a372..1cd5409 100644 --- a/tests/he10.Rout.save +++ b/tests/he10.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: x86_64-apple-darwin20 +Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. @@ -290,11 +290,17 @@ Error : in ‘argument "Nbpf" is missing, with no default’: ibpf Error : in ‘ibpf’: ‘rprocess’, ‘dunit_measure’ are needed basic components. > > ## test error message when munit_measure is undefined +> ## this also tests setup of covariates for girf_moment > try(girf(h_model,kind="moment", + Np=10,Ninter=2,Nguide=10,lookahead=1,tol=1e-5)) Error : girf with kind = 'moment' requires munit_measure > -> # Create second ibpfd_spatPomp object with different chain length, to test error +> ## test girf_bootstrap with covariates +> h_girf <- girf(h_model,kind="bootstrap", ++ Np=5,Ninter=2,Nguide=5,lookahead=2,tol=1e-5) +> +> # Create second ibpfd_spatPomp object with different chain length, +> # to test error > h_ibpf3 <- ibpf(h_model, + params=coef(h_model), + sharedParNames=sharedParNames, diff --git a/tests/iter_filter.Rout.save b/tests/iter_filter.Rout.save index 0541c1a..bbc3fea 100644 --- a/tests/iter_filter.Rout.save +++ b/tests/iter_filter.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: x86_64-apple-darwin20 +Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. diff --git a/tests/lorenz.Rout.save b/tests/lorenz.Rout.save index 0448a68..68ab53b 100644 --- a/tests/lorenz.Rout.save +++ b/tests/lorenz.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: x86_64-apple-darwin20 +Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. diff --git a/tests/measles.Rout.save b/tests/measles.Rout.save index c2c7764..cf9aeb8 100644 --- a/tests/measles.Rout.save +++ b/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: x86_64-apple-darwin20 +Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. diff --git a/tests/measles2.Rout.save b/tests/measles2.Rout.save index 3686bf2..8180356 100644 --- a/tests/measles2.Rout.save +++ b/tests/measles2.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: x86_64-apple-darwin20 +Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. diff --git a/tests/param_formats.Rout.save b/tests/param_formats.Rout.save index dd7b321..34eaced 100644 --- a/tests/param_formats.Rout.save +++ b/tests/param_formats.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: x86_64-apple-darwin20 +Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions.