diff --git a/DESCRIPTION b/DESCRIPTION index 62a675a..a83e543 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: phylopomp Type: Package Title: Phylodynamic Inference for POMP Models -Version: 0.10.2.0 -Date: 2024-02-12 +Version: 0.10.3.0 +Date: 2024-02-14 Authors@R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="kingaa@umich.edu",comment=c(ORCID="0000-0001-6159-3207")), person(given=c("Qianying"),family="Lin",role=c("aut"),comment=c(ORCID="0000-0001-8620-9910")) ) diff --git a/R/treeplot.R b/R/treeplot.R index 3aeeb6e..f9f19d2 100644 --- a/R/treeplot.R +++ b/R/treeplot.R @@ -83,7 +83,8 @@ treeplot <- function ( separate(label,into=c("nodecol","deme","label")) |> mutate( deme=if_else(deme=="NA",NA_character_,deme), - label=if_else(label=="NA",NA_character_,label) + label=if_else(label=="NA",NA_character_,label), + y=y-3 ) -> dat ndeme <- max(1L,length(unique(dat$deme))-1L) @@ -131,6 +132,7 @@ treeplot <- function ( scale_alpha_manual(values=c(`TRUE`=1,`FALSE`=0))+ guides(alpha="none",color="none")+ expand_limits(x=c(dat$x,t0,time))+ + coord_cartesian(ylim=c(0,NA),expand=TRUE,default=FALSE)+ theme_tree2()+ theme(...) -> pl diff --git a/inst/NEWS b/inst/NEWS index e070268..2b47531 100644 --- a/inst/NEWS +++ b/inst/NEWS @@ -14,6 +14,8 @@ _C_h_a_n_g_e_s _i_n '_p_h_y_l_o_p_o_m_p' _v_e_r_s_i_o_n • Parameter name changes in some of the examples. + • In plotting, trees are shifted down on the y axis. + _C_h_a_n_g_e_s _i_n '_p_h_y_l_o_p_o_m_p' _v_e_r_s_i_o_n _0._9: • Inclusion of ‘pomp’ methods for SEIRS model. diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd index 4da1aea..9392515 100644 --- a/inst/NEWS.Rd +++ b/inst/NEWS.Rd @@ -7,6 +7,7 @@ \item The genealogy description (\code{getInfo(description=TRUE)}) now reports both deme and lineage. \item \code{curtail()} more carefully rewinds the history. \item Parameter name changes in some of the examples. + \item In plotting, trees are shifted down on the y axis. } 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