re-export magrittr::%>%

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: pomp2
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 2.0.6.2
+Version: 2.0.7.1
 Date: 2018-12-13
 Authors@R: c(person(given=c("Aaron","A."),family="King",
 		role=c("aut","cre"),email="[email protected]"),
@@ -22,8 +22,8 @@ Authors@R: c(person(given=c("Aaron","A."),family="King",
 URL: https://kingaa.github.io/pomp/
 Description: Tools for data analysis with partially observed Markov process (POMP) models (also known as stochastic dynamical systems, hidden Markov models, and nonlinear, non-Gaussian, state-space models).  The package provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods.  It is also a versatile platform for implementation of inference methods for general POMP models.
 Depends: R(>= 3.5.0), methods
-Imports: stats, graphics, digest, mvtnorm, deSolve, coda, reshape2
-Suggests: magrittr, plyr, ggplot2, knitr, tidyr, dplyr, subplex
+Imports: stats, graphics, digest, mvtnorm, deSolve, coda, reshape2, magrittr
+Suggests: plyr, ggplot2, knitr, tidyr, dplyr, subplex
 SystemRequirements: For Windows users, Rtools (see https://cran.r-project.org/bin/windows/Rtools/).
 License: GPL-3
 LazyData: true
@@ -106,6 +106,7 @@ Collate:
     'ou2.R'
     'parmat.R'
     'parus.R'
+    'pipe.R'
     'pred_mean.R'
     'pred_var.R'
     'show.R'

NAMESPACE

@@ -11,6 +11,7 @@ S3method(c,Mif2)
 S3method(c,Pfilter)
 S3method(c,Pmcmc)
 S3method(c,Pomp)
+export("%>%")
 export(Csnippet)
 export(as.pomp)
 export(bake)
@@ -159,6 +160,7 @@ importFrom(graphics,polygon)
 importFrom(graphics,rect)
 importFrom(graphics,text)
 importFrom(graphics,title)
+importFrom(magrittr,"%>%")
 importFrom(mvtnorm,dmvnorm)
 importFrom(mvtnorm,rmvnorm)
 importFrom(reshape2,melt)

R/pipe.R

@@ -0,0 +1,4 @@
+##' @importFrom magrittr %>%
+##' @docType import
+##' @export
+magrittr::`%>%`

inst/NEWS

@@ -1,5 +1,9 @@
 _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._7:
+
+        • The ‘magrittr’ pipe operator, ‘%>%’, is now re-exported.
+
 _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.

inst/NEWS.Rd

@@ -1,5 +1,10 @@
 \name{NEWS}
 \title{News for package `pomp'}
+\section{Changes in \pkg{pomp} version 2.0.7}{
+  \itemize{
+    \item The \pkg{magrittr} pipe operator, \code{\%>\%}, is now re-exported.
+  }
+}
 \section{Changes in \pkg{pomp} version 2.0.6}{
   \itemize{
     \item More examples have been included.

tests/R_v_C.R

@@ -4,7 +4,6 @@ png(filename="R_v_C-%02d.png",res=100)
 ## ----packages------------------------------------------------------------
 library(pomp2)
 library(ggplot2)
-library(magrittr)
 
 ## ----seed,echo=FALSE-----------------------------------------------------
 set.seed(56300069)

tests/R_v_C.Rout

@@ -26,7 +26,6 @@ Welcome to pomp version 2!
 For information on upgrading your pomp version < 2 code, see the
 'pomp version 2 upgrade guide' at https://kingaa.github.io/pomp/.
 > library(ggplot2)
-> library(magrittr)
 > 
 > ## ----seed,echo=FALSE-----------------------------------------------------
 > set.seed(56300069)
@@ -112,16 +111,16 @@ For information on upgrading your pomp version < 2 code, see the
 > ## ----comparison----------------------------------------------------------
 > system.time(simulate(gompertz,nsim=10000,format="arrays"))
    user  system elapsed 
-  7.624   0.064   7.688 
+  8.072   0.064   8.137 
 > system.time(simulate(Gompertz,nsim=10000,format="arrays"))
    user  system elapsed 
-  0.356   0.000   0.355 
+  0.396   0.004   0.400 
 > system.time(pfilter(gompertz,Np=1000))
    user  system elapsed 
-  0.636   0.000   0.637 
+  0.696   0.000   0.695 
 > system.time(pfilter(Gompertz,Np=1000))
    user  system elapsed 
-  0.052   0.000   0.050 
+  0.060   0.000   0.059 
 > 
 > dev.off()
 null device 

tests/abc.R

@@ -3,7 +3,6 @@
 png(filename="abc-%02d.png",res=100)
 
 library(pomp2)
-library(magrittr)
 
 ou2() -> ou2
 

tests/abc.Rout.save

@@ -25,7 +25,6 @@ Type 'q()' to quit R.
 Welcome to pomp version 2!
 For information on upgrading your pomp version < 2 code, see the
 'pomp version 2 upgrade guide' at https://kingaa.github.io/pomp/.
-> library(magrittr)
 > 
 > ou2() -> ou2
 > 

tests/basic_probes.R

@@ -1,7 +1,6 @@
 options(digits=3)
 
 library(pomp2)
-library(magrittr)
 library(dplyr)
 library(tidyr)
 library(ggplot2)

tests/basic_probes.Rout.save

@@ -23,7 +23,6 @@ Type 'q()' to quit R.
 Welcome to pomp version 2!
 For information on upgrading your pomp version < 2 code, see the
 'pomp version 2 upgrade guide' at https://kingaa.github.io/pomp/.
-> library(magrittr)
 > library(dplyr)
 
 Attaching package: 'dplyr'
@@ -37,13 +36,6 @@ The following objects are masked from 'package:base':
     intersect, setdiff, setequal, union
 
 > library(tidyr)
-
-Attaching package: 'tidyr'
-
-The following object is masked from 'package:magrittr':
-
-    extract
-
 > library(ggplot2)
 > 
 > set.seed(255066335)

tests/concat.R

@@ -1,7 +1,6 @@
 options(digits=3)
 
 library(pomp2)
-library(magrittr)
 
 try(pomp2:::concat())
 try(pomp2:::concat("a","b"))

tests/concat.Rout.save

@@ -23,7 +23,6 @@ Type 'q()' to quit R.
 Welcome to pomp version 2!
 For information on upgrading your pomp version < 2 code, see the
 'pomp version 2 upgrade guide' at https://kingaa.github.io/pomp/.
-> library(magrittr)
 > 
 > try(pomp2:::concat())
 Error : 'c' is not defined for objects of mixed class.

tests/covmat.R

@@ -1,7 +1,6 @@
 options(digits=3)
 
 library(pomp2)
-library(magrittr)
 library(tidyr)
 library(dplyr)
 

tests/covmat.Rout.save

@@ -23,15 +23,7 @@ Type 'q()' to quit R.
 Welcome to pomp version 2!
 For information on upgrading your pomp version < 2 code, see the
 'pomp version 2 upgrade guide' at https://kingaa.github.io/pomp/.
-> library(magrittr)
 > library(tidyr)
-
-Attaching package: 'tidyr'
-
-The following object is masked from 'package:magrittr':
-
-    extract
-
 > library(dplyr)
 
 Attaching package: 'dplyr'

tests/dp.R

@@ -3,7 +3,6 @@ png(filename="dp-%02d.png",res=100)
 
 library(pomp2)
 library(ggplot2)
-library(magrittr)
 library(dplyr)
 library(tidyr)
 
@@ -53,12 +52,11 @@ sims %>%
   facet_grid(variable~.id,scales="free_y")+
   labs(title="death process, Gillespie",subtitle=expression(mu==0.01))
 stopifnot(
-  sims %>%
-    group_by(.id) %>%
-    mutate(s=cumsum(ct),Nn=(N+s)==100) %>%
-    filter(!Nn) %>%
-    nrow() %>%
-    equals(0)
+(sims %>%
+   group_by(.id) %>%
+   mutate(s=cumsum(ct),Nn=(N+s)==100) %>%
+   filter(!Nn) %>%
+   nrow()) == 0
 )
 
 create_example(simulator="onestep",times=c(0,1,10,100,1000)) %>%
@@ -79,14 +77,13 @@ sims %>%
   ggplot(aes(x=time,y=value,group=interaction(.id,variable)))+
   geom_step()+
   facet_grid(variable~.id,scales="free_y")+
-   labs(title="death process, onestep",subtitle=expression(mu==0.01))
+  labs(title="death process, onestep",subtitle=expression(mu==0.01))
 stopifnot(
-  sims %>%
-    group_by(.id) %>%
-    mutate(s=cumsum(ct),Nn=(N+s)==100) %>%
-    filter(!Nn) %>%
-    nrow() %>%
-    equals(0)
+(sims %>%
+   group_by(.id) %>%
+   mutate(s=cumsum(ct),Nn=(N+s)==100) %>%
+   filter(!Nn) %>%
+   nrow()) == 0
 )
 
 create_example(simulator="euler",times=c(0,1,10,100,1000)) %>%
@@ -109,12 +106,11 @@ sims %>%
   facet_grid(variable~.id,scales="free_y")+
   labs(title="death process, Euler",subtitle=expression(mu==0.01))
 stopifnot(
-  sims %>%
-    group_by(.id) %>%
-    mutate(s=cumsum(ct),Nn=(N+s)==100) %>%
-    filter(!Nn) %>%
-    nrow() %>%
-    equals(0)
+(sims %>%
+   group_by(.id) %>%
+   mutate(s=cumsum(ct),Nn=(N+s)==100) %>%
+   filter(!Nn) %>%
+   nrow()) == 0
 )
 
 create_example(mu=1) %>%

tests/dp.Rout.save

@@ -25,7 +25,6 @@ Welcome to pomp version 2!
 For information on upgrading your pomp version < 2 code, see the
 'pomp version 2 upgrade guide' at https://kingaa.github.io/pomp/.
 > library(ggplot2)
-> library(magrittr)
 > library(dplyr)
 
 Attaching package: 'dplyr'
@@ -39,13 +38,6 @@ The following objects are masked from 'package:base':
     intersect, setdiff, setequal, union
 
 > library(tidyr)
-
-Attaching package: 'tidyr'
-
-The following object is masked from 'package:magrittr':
-
-    extract
-
 > 
 > set.seed(49596868L)
 > 
@@ -103,12 +95,11 @@ Warning message:
 +   facet_grid(variable~.id,scales="free_y")+
 +   labs(title="death process, Gillespie",subtitle=expression(mu==0.01))
 > stopifnot(
-+   sims %>%
-+     group_by(.id) %>%
-+     mutate(s=cumsum(ct),Nn=(N+s)==100) %>%
-+     filter(!Nn) %>%
-+     nrow() %>%
-+     equals(0)
++ (sims %>%
++    group_by(.id) %>%
++    mutate(s=cumsum(ct),Nn=(N+s)==100) %>%
++    filter(!Nn) %>%
++    nrow()) == 0
 + )
 > 
 > create_example(simulator="onestep",times=c(0,1,10,100,1000)) %>%
@@ -139,14 +130,13 @@ Warning message:
 +   ggplot(aes(x=time,y=value,group=interaction(.id,variable)))+
 +   geom_step()+
 +   facet_grid(variable~.id,scales="free_y")+
-+    labs(title="death process, onestep",subtitle=expression(mu==0.01))
++   labs(title="death process, onestep",subtitle=expression(mu==0.01))
 > stopifnot(
-+   sims %>%
-+     group_by(.id) %>%
-+     mutate(s=cumsum(ct),Nn=(N+s)==100) %>%
-+     filter(!Nn) %>%
-+     nrow() %>%
-+     equals(0)
++ (sims %>%
++    group_by(.id) %>%
++    mutate(s=cumsum(ct),Nn=(N+s)==100) %>%
++    filter(!Nn) %>%
++    nrow()) == 0
 + )
 > 
 > create_example(simulator="euler",times=c(0,1,10,100,1000)) %>%
@@ -179,12 +169,11 @@ Warning message:
 +   facet_grid(variable~.id,scales="free_y")+
 +   labs(title="death process, Euler",subtitle=expression(mu==0.01))
 > stopifnot(
-+   sims %>%
-+     group_by(.id) %>%
-+     mutate(s=cumsum(ct),Nn=(N+s)==100) %>%
-+     filter(!Nn) %>%
-+     nrow() %>%
-+     equals(0)
++ (sims %>%
++    group_by(.id) %>%
++    mutate(s=cumsum(ct),Nn=(N+s)==100) %>%
++    filter(!Nn) %>%
++    nrow()) == 0
 + )
 > 
 > create_example(mu=1) %>%

tests/getting_started.R

@@ -65,7 +65,6 @@ parus <- pomp(data=parus.dat,time="year",t0=1959,
 simStates <- simulate(parus,nsim=10,params=c(r=0.2,K=200,sigma=0.5,N.0=200),format="arrays")$states
 
 ## ----logistic-plot1,echo=FALSE-------------------------------------------
-library(magrittr)
 library(tidyr)
 
 simStates %>%
@@ -193,10 +192,10 @@ simulate(tm,nsim=10,format="data.frame",include.data=TRUE) %>%
     theme_bw()
 
 ## ----parus-dprior--------------------------------------------------------
-parus %<>%
+parus %>%
   pomp(dprior=Csnippet("
     lik = dunif(r,0,5,1)+dunif(K,100,600,1)+dunif(sigma,0,2,1);
     lik = (give_log) ? lik : exp(lik);
-  "),paramnames=c("r","K","sigma"))
+  "),paramnames=c("r","K","sigma")) -> parus
 
 dev.off()