diff --git a/DESCRIPTION b/DESCRIPTION index 063dc5746..ba8b378b4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: pomp2 Type: Package Title: Statistical Inference for Partially Observed Markov Processes -Version: 2.0.6.1 -Date: 2018-10-02 +Version: 2.0.6.2 +Date: 2018-12-13 Authors@R: c(person(given=c("Aaron","A."),family="King", role=c("aut","cre"),email="kingaa@umich.edu"), person(given=c("Edward","L."),family="Ionides",role=c("aut")), diff --git a/R/mif2.R b/R/mif2.R index 2de5d3788..054e00bee 100644 --- a/R/mif2.R +++ b/R/mif2.R @@ -583,7 +583,7 @@ perturbn.kernel.sd <- function (rw.sd, time, paramnames) { unrec <- names(rw.sd)[!names(rw.sd) %in% paramnames] pStop_("the following parameter(s), ", "given random walks in ",sQuote("rw.sd"),", are not present in ", - sQuote("start"),": ",paste(sapply(unrec,sQuote),collapse=","),".") + sQuote("params"),": ",paste(sapply(unrec,sQuote),collapse=","),".") } ivp <- function (sd, lag = 1L) { sd*(seq_along(time)==lag) diff --git a/TODO.md b/TODO.md index 02d2ab791..7c19bc55c 100644 --- a/TODO.md +++ b/TODO.md @@ -50,6 +50,7 @@ - what does a generic `pomp.fun` interface look like? - should parameter transformations allow renaming of variables? - would require attention to `rw.sd`, e.g. +- weighted particle filter ## For pomp: diff --git a/inst/NEWS b/inst/NEWS index 9beddae28..787a76957 100644 --- a/inst/NEWS +++ b/inst/NEWS @@ -1,5 +1,25 @@ _N_e_w_s _f_o_r _p_a_c_k_a_g_e '_p_o_m_p' +_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _2._0._6: + + • More examples have been included. + + • Minor changes to error messages. + +_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _2._0._5: + + • The names of the ‘objfun’ methods have been changed to + ‘probe_objfun’, ‘spect_objfun’, ‘traj_objfun’, and + ‘nlf_objfun’. + +_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _2._0._4: + + • The package directory structure has been modified to include + a new ‘examples’ directory, which holds the examples used in + the documentation. + + • The names of the ‘objfun’ methods have been shortened. + _C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _2._0._3: • It is now permissible that the sequence of observation times diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd index bdf765f13..554c2e141 100644 --- a/inst/NEWS.Rd +++ b/inst/NEWS.Rd @@ -1,5 +1,22 @@ \name{NEWS} \title{News for package `pomp'} +\section{Changes in \pkg{pomp} version 2.0.6}{ + \itemize{ + \item More examples have been included. + \item Minor changes to error messages. + } +} +\section{Changes in \pkg{pomp} version 2.0.5}{ + \itemize{ + \item The names of the \sQuote{objfun} methods have been changed to \code{probe_objfun}, \code{spect_objfun}, \code{traj_objfun}, and \code{nlf_objfun}. + } +} +\section{Changes in \pkg{pomp} version 2.0.4}{ + \itemize{ + \item The package directory structure has been modified to include a new \file{examples} directory, which holds the examples used in the documentation. + \item The names of the \sQuote{objfun} methods have been shortened. + } +} \section{Changes in \pkg{pomp} version 2.0.3}{ \itemize{ \item It is now permissible that the sequence of observation times (and sequences of covariate times) be merely non-decreasing sequences. diff --git a/tests/mif2.Rout.save b/tests/mif2.Rout.save index 90372e341..96f0f27c4 100644 --- a/tests/mif2.Rout.save +++ b/tests/mif2.Rout.save @@ -135,7 +135,7 @@ Error : in 'mif2': 'rw.sd' should be specified using the 'rw.sd' function. See ' > try(mif2(po,Nmif=1,Np=100,rw.sd=rw.sd())) Error : in 'mif2': in 'rw.sd': parameters must be referenced by name. > try(mif2(po,Nmif=1,Np=100,rw.sd=rw.sd(a=9))) -Error : in 'mif2': the following parameter(s), given random walks in 'rw.sd', are not present in 'start': 'a'. +Error : in 'mif2': the following parameter(s), given random walks in 'rw.sd', are not present in 'params': 'a'. > try(mif2(po,Nmif=1,Np=100,rw.sd=rw.sd(sigma=1:1000))) Error : in 'mif2': 'rw.sd' spec for parameter 'sigma' does not evaluate to a vector of the correct length ('length(time(object))'=10). > try(mif2(po,Nmif=1,Np=100,rw.sd=rw.sd(sigma=0.1))) @@ -154,9 +154,9 @@ Error : in 'mif2': 'cooling.fraction.50' must be in (0,1]. + cooling.type="geometric",tol=-3)) Error : in 'mif2': 'tol' should be a small positive number. > try(mif2(po,params=NULL,Nmif=1,Np=100,rw.sd=rw.sd(sigma=0.1))) -Error : in 'mif2': the following parameter(s), given random walks in 'rw.sd', are not present in 'start': 'sigma'. +Error : in 'mif2': the following parameter(s), given random walks in 'rw.sd', are not present in 'params': 'sigma'. > try(mif2(po,params=list(),Nmif=1,Np=100,rw.sd=rw.sd(sigma=0.1))) -Error : in 'mif2': the following parameter(s), given random walks in 'rw.sd', are not present in 'start': 'sigma'. +Error : in 'mif2': the following parameter(s), given random walks in 'rw.sd', are not present in 'params': 'sigma'. > try(mif2(po,params=list(NULL),Nmif=1,Np=100,rw.sd=rw.sd(sigma=0.1))) Error : in 'mif2': (list) object cannot be coerced to type 'double' > try(mif2(po,params=c(3,2,1),Nmif=1,Np=100,rw.sd=rw.sd(sigma=0.1))) @@ -205,7 +205,7 @@ Error : in 'mif2': 'rprocess', 'dmeasure' are needed basic components. > try(mif2(po,Nmif=2,Np=50,rw.sd=rw.sd(sigma=0.01),cooling.fraction.50=0.1,rprocess=NULL)) Error : in 'mif2': 'rprocess', 'dmeasure' are needed basic components. > try(mif2(po,Nmif=2,Np=50,rw.sd=rw.sd(sigma=0.01),cooling.fraction.50=0.1,params=NULL)) -Error : in 'mif2': the following parameter(s), given random walks in 'rw.sd', are not present in 'start': 'sigma'. +Error : in 'mif2': the following parameter(s), given random walks in 'rw.sd', are not present in 'params': 'sigma'. > > theta <- coef(po) > theta["sigma"] <- 0.2