improve 'melt' method; update tests for R version 3.6.0

kingaa · May 19, 2019 · 1da69b2 · 1da69b2
1 parent 1e6e3ec
commit 1da69b2
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Showing 239 changed files with 349 additions and 278 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: pomp2
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 2.0.13.2
-Date: 2019-04-18
+Version: 2.0.14.1
+Date: 2019-05-19
 Authors@R: c(person(given=c("Aaron","A."),family="King",
 		role=c("aut","cre"),email="[email protected]"),
 	  person(given=c("Edward","L."),family="Ionides",role=c("aut")),

diff --git a/NAMESPACE b/NAMESPACE
@@ -110,6 +110,7 @@ exportMethods(filter.traj)
 exportMethods(flow)
 exportMethods(forecast)
 exportMethods(logLik)
+exportMethods(melt)
 exportMethods(mif2)
 exportMethods(nlf_objfun)
 exportMethods(obs)

diff --git a/R/as_data_frame.R b/R/as_data_frame.R
@@ -44,8 +44,7 @@ setAs(
 ##' @method as.data.frame pomp
 ##' @rdname as_data_frame
 ##'
-##' @param x the object to be coerced
-##' @param \dots ignored
+##' @inheritParams base::as.data.frame
 ##' @export
 ##'
 as.data.frame.pomp <- function (x, ...) as(x,"data.frame")
@@ -70,12 +69,21 @@ setAs(
       ess=eff.sample.size(from),
       cond.loglik=cond.logLik(from)
     )
-    if (length(pm)>0)
-      out <- cbind(out,pred.mean=t(pm))
-    if (length(pv)>0)
-      out <- cbind(out,pred.var=t(pv))
-    if (length(fm)>0)
-      out <- cbind(out,filter.mean=t(fm))
+    if (length(pm)>0) {
+      pm <- as.data.frame(t(pm))
+      names(pm) <- paste0("pred.mean.",names(pm))
+      out <- cbind(out,pm)
+    }
+    if (length(pv)>0) {
+      pv <- as.data.frame(t(pv))
+      names(pv) <- paste0("pred.var.",names(pv))
+      out <- cbind(out,pv)
+    }
+    if (length(fm)>0) {
+      fm <- as.data.frame(t(fm))
+      names(fm) <- paste0("filter.mean.",names(fm))
+      out <- cbind(out,fm)
+    }
     out
   }
 )
@@ -127,12 +135,21 @@ setAs(
       as(as(from,"pomp"),"data.frame"),
       cond.loglik=cond.logLik(from)
     )
-    if (length(pm)>0)
-      out <- cbind(out,pred.mean=t(pm))
-    if (length(fm)>0)
-      out <- cbind(out,filter.mean=t(fm))
-    if (length(fc)>0)
-      out <- cbind(out,forecast=t(fc))
+    if (length(pm)>0) {
+      pm <- as.data.frame(t(pm))
+      names(pm) <- paste0("pred.mean.",names(pm))
+      out <- cbind(out,pm)
+    }
+    if (length(fm)>0) {
+      fm <- as.data.frame(t(fm))
+      names(fm) <- paste0("filter.mean.",names(fm))
+      out <- cbind(out,fm)
+    }
+    if (length(fc)>0) {
+      fc <- as.data.frame(t(fc))
+      names(fc) <- paste0("forecast.",names(fc))
+      out <- cbind(out,fc)
+    }
     out
   }
 )

diff --git a/R/melt.R b/R/melt.R
@@ -2,3 +2,17 @@
 ##' @docType import
 ##' @export
 reshape2::melt
+
+##' @name melt,pomp-method
+##' @include melt.R
+##' @rdname as_data_frame
+##' @details A \sQuote{pomp} object can be melted into a data frame.
+##' @inheritParams reshape2::melt
+##' @export
+setMethod(
+  "melt",
+  signature=signature(data="pomp"),
+  definition=function (data, ...) {
+    melt(as(data,"data.frame"),...)
+  }
+)
diff --git a/man/as_data_frame.Rd b/man/as_data_frame.Rd
diff --git a/src/euler.c b/src/euler.c
@@ -169,7 +169,7 @@ SEXP euler_model_simulator (SEXP func, SEXP xstart, SEXP tstart, SEXP times, SEX
 
     break;
 
-  default:
+  default: // # nocov
 
     errorcall(R_NilValue,"unrecognized 'mode' %d",mode); // # nocov
 
@@ -263,7 +263,7 @@ SEXP euler_model_simulator (SEXP func, SEXP xstart, SEXP tstart, SEXP times, SEX
 
           break;
 
-        default:
+        default: // # nocov
 
           errorcall(R_NilValue,"unrecognized 'mode' %d",mode); // # nocov
 

diff --git a/src/partrans.c b/src/partrans.c
@@ -138,7 +138,7 @@ SEXP do_partrans (SEXP object, SEXP params, SEXP dir, SEXP gnsi)
 
     break;
 
-  default:
+  default:  // #nocov
 
     break;  // #nocov
 

diff --git a/src/pomp_fun.c b/src/pomp_fun.c
@@ -85,7 +85,7 @@ SEXP pomp_fun_handler (SEXP pfun, SEXP gnsi, pompfunmode *mode,
       }
         break;
 
-      default:
+      default: // #nocov
         break; // #nocov
       }
 

diff --git a/src/ssa.c b/src/ssa.c
@@ -265,9 +265,9 @@ SEXP SSA_simulator (SEXP func, SEXP xstart, SEXP tstart, SEXP times, SEXP params
 
   switch (mode) {
 
-  case undef: default:
+  case undef: default:  // #nocov
 
-    errorcall(R_NilValue,"unrecognized 'mode' %d",mode); // # nocov
+    errorcall(R_NilValue,"unrecognized 'mode' %d",mode); // #nocov
 
   case native: case regNative:
 

diff --git a/src/trajectory.c b/src/trajectory.c
@@ -108,7 +108,7 @@ SEXP iterate_map (SEXP object, SEXP times, SEXP t0, SEXP x0, SEXP params, SEXP g
 
     break;
 
-  default:
+  default: // #nocov
 
     break; // #nocov
 
@@ -238,7 +238,7 @@ SEXP pomp_desolve_setup (SEXP object, SEXP x0, SEXP params, SEXP gnsi) {
 
     break;
 
-  default:
+  default: // #nocov
 
     errorcall(R_NilValue,"in 'pomp_desolve_setup': unrecognized 'mode'"); // # nocov
 
@@ -272,7 +272,7 @@ void pomp_vf_eval (int *neq, double *t, double *y, double *ydot, double *yout, i
 
     break;
 
-  default:
+  default: // #nocov
 
     errorcall(R_NilValue,"in 'pomp_vf_eval': unrecognized 'mode'"); // # nocov
 
@@ -324,7 +324,7 @@ void pomp_desolve_takedown (void) {
 
     break;
 
-  default:
+  default: // #nocov
 
     errorcall(R_NilValue,"in 'pomp_desolve_takedown': unrecognized 'mode'"); // # nocov
 

diff --git a/tests/R_v_C-01.png b/tests/R_v_C-01.png
diff --git a/tests/R_v_C-02.png b/tests/R_v_C-02.png
diff --git a/tests/R_v_C.Rout b/tests/R_v_C.Rout
@@ -1,6 +1,6 @@
 
-R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
-Copyright (C) 2018 The R Foundation for Statistical Computing
+R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
+Copyright (C) 2019 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -26,6 +26,11 @@ 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)
+Registered S3 methods overwritten by 'ggplot2':
+  method         from 
+  [.quosures     rlang
+  c.quosures     rlang
+  print.quosures rlang
 > 
 > ## ----seed,echo=FALSE-----------------------------------------------------
 > set.seed(56300069)
@@ -111,16 +116,16 @@ For information on upgrading your pomp version < 2 code, see the
 > ## ----comparison----------------------------------------------------------
 > system.time(simulate(gompertz,nsim=10000,format="arrays"))
    user  system elapsed 
-  8.032   0.088   8.120 
+  6.936   0.008   6.944 
 > system.time(simulate(Gompertz,nsim=10000,format="arrays"))
    user  system elapsed 
-  0.380   0.008   0.387 
+  0.279   0.008   0.287 
 > system.time(pfilter(gompertz,Np=1000))
    user  system elapsed 
-  0.696   0.004   0.703 
+  0.615   0.000   0.616 
 > system.time(pfilter(Gompertz,Np=1000))
    user  system elapsed 
-  0.056   0.000   0.058 
+  0.045   0.000   0.045 
 > 
 > dev.off()
 null device 

diff --git a/tests/abc-01.png b/tests/abc-01.png
diff --git a/tests/abc-02.png b/tests/abc-02.png
diff --git a/tests/abc-03.png b/tests/abc-03.png
diff --git a/tests/abc-04.png b/tests/abc-04.png
diff --git a/tests/abc-05.png b/tests/abc-05.png
diff --git a/tests/abc-06.png b/tests/abc-06.png
diff --git a/tests/abc-07.png b/tests/abc-07.png
diff --git a/tests/abc.Rout.save b/tests/abc.Rout.save
@@ -1,6 +1,6 @@
 
-R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
-Copyright (C) 2018 The R Foundation for Statistical Computing
+R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
+Copyright (C) 2019 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/bake.Rout.save b/tests/bake.Rout.save
@@ -1,6 +1,6 @@
 
-R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
-Copyright (C) 2018 The R Foundation for Statistical Computing
+R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
+Copyright (C) 2019 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/basic_probes.R b/tests/basic_probes.R
@@ -1,9 +1,11 @@
 options(digits=3)
 
 library(pomp2)
-library(dplyr)
-library(tidyr)
-library(ggplot2)
+suppressPackageStartupMessages({
+  library(dplyr)
+  library(tidyr)
+  library(ggplot2)
+})
 
 set.seed(255066335)
 

diff --git a/tests/basic_probes.Rout.save b/tests/basic_probes.Rout.save
@@ -1,6 +1,6 @@
 
-R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
-Copyright (C) 2018 The R Foundation for Statistical Computing
+R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
+Copyright (C) 2019 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -23,20 +23,11 @@ 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(dplyr)
-
-Attaching package: 'dplyr'
-
-The following objects are masked from 'package:stats':
-
-    filter, lag
-
-The following objects are masked from 'package:base':
-
-    intersect, setdiff, setequal, union
-
-> library(tidyr)
-> library(ggplot2)
+> suppressPackageStartupMessages({
++   library(dplyr)
++   library(tidyr)
++   library(ggplot2)
++ })
 > 
 > set.seed(255066335)
 > 

diff --git a/tests/blowflies-01.png b/tests/blowflies-01.png
diff --git a/tests/blowflies-02.png b/tests/blowflies-02.png
diff --git a/tests/blowflies-03.png b/tests/blowflies-03.png
diff --git a/tests/blowflies-04.png b/tests/blowflies-04.png
diff --git a/tests/blowflies-05.png b/tests/blowflies-05.png
diff --git a/tests/blowflies-06.png b/tests/blowflies-06.png
diff --git a/tests/blowflies.Rout.save b/tests/blowflies.Rout.save
@@ -1,6 +1,6 @@
 
-R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
-Copyright (C) 2018 The R Foundation for Statistical Computing
+R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
+Copyright (C) 2019 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.

diff --git a/tests/bsmc2-01.png b/tests/bsmc2-01.png
diff --git a/tests/bsmc2-02.png b/tests/bsmc2-02.png
diff --git a/tests/bsmc2-03.png b/tests/bsmc2-03.png
diff --git a/tests/bsmc2-04.png b/tests/bsmc2-04.png
diff --git a/tests/bsmc2.R b/tests/bsmc2.R
@@ -2,9 +2,11 @@ png(filename="bsmc2-%02d.png",res=100)
 options(digits=2)
 
 library(pomp2)
-library(tidyr)
-library(dplyr)
-library(ggplot2)
+suppressPackageStartupMessages({
+  library(dplyr)
+  library(tidyr)
+  library(ggplot2)
+})
 
 gompertz() -> gompertz
 set.seed(398585L)
-Original file line number
+Diff line change
@@ Expand Up @@
         break;
-      default:
+      default:  // #nocov
         break;  // #nocov
@@ Expand Down @@