From a016e635f915c6fbf2afbf82601beb9e6925794e Mon Sep 17 00:00:00 2001 From: wcornwell Date: Mon, 26 Oct 2015 10:41:44 +1100 Subject: [PATCH] attempt with zenodo --- DESCRIPTION | 2 +- R/plant_lookup.R | 1 + R/sysdata.rda | Bin 1441 -> 1425 bytes createlookup.R | 1 + man/lookup_table.Rd | 3 ++- 5 files changed, 5 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 6230fec..281664b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: taxonlookup Title: A dynamically-updating versioned taxonomic resource for vascular plants -Version: 0.3.1 +Version: 0.3.2 Date: 2015-08-03 Description: This is a taxon lookup table for land plants. It is built from a set of scripts that dynamically build a versioned genus-family-order-higher taxa lookup table from canonical sources on the web. It uses semantic versioning to keep track of changes. Depends: R (>= 3.1.0) diff --git a/R/plant_lookup.R b/R/plant_lookup.R index afb040e..e2322e0 100644 --- a/R/plant_lookup.R +++ b/R/plant_lookup.R @@ -1,3 +1,4 @@ + ##' Lookup table relating plant genera, families and orders along with ##' number of species in each genus. Data persists across package ##' installations. diff --git a/R/sysdata.rda b/R/sysdata.rda index a66c349d437d2a5ba69bd2e8afd73d029e988126..1bdca27dd4d0c9bdc28fc515cdb3200604a98e10 100644 GIT binary patch literal 1425 zcmV;C1#bEuiwFP!000001MOVhZre5#R+Db2{}OM*fL`_qda*aKmCP+rcSbyHMQ;XL zW^7^-sZmlJy?im+i5nhSvPFrMWXAy5I?1$H~2^kGY3J<}c$A zorEXhNq7>TgvTR<{k}V(3&Mi+4BSAO)j*#PQD$l6vxza$iSL+Y$Hq^6cwisB8sh+M zA7WB$Rd`et%8pE&>`2dxa3kmsrpON6^fN~bTYEB zKGji|ovQq83LaHEruiwZKVRN|zvTLec(}w4A@kfe(vB&jM|IR;qY6Lk#-XC$Bp=0e ztL1Oru{XgXX94;mJCiEZ9c?W}D)F>_BuW;Ha#B#andI%-%=55IXa&Kq($=AlCOImm z8|GdACYqD9i%>;*mOayYirOjamudWY^_TV2G+$NYt~)NK_nY$nP~%!&4*Otx6j6$~ z)JgM5vZAB+SQV}N?dU~O#-47Zx+G?!siIBqo_(Wk{`4@bDuH!C%1t z=+L!$cA33uvx?0&hoTI&VigbE}Wok6;fWh3_ zB`9}$vuh*IM>KNfb)yuS%JDkpYHvn4Y}e_ZP8`h{VQ#+qfV?`_N}4_<`8ig;isIVG zPxkii9@$-AYI7D;v6N%LR+`Qx*-`PO>|9kJP5EZRR~0|heBE6i7q^v^hGsJfb+u~G zX}s99e6HwqK@Zt_SX=${E&VI}xlc=DKWqC2r>z+3HJDMHf z)tqLx6Y30;l2g4QFDi?8y$vvH?2OTZGWVFi!t8)l0oq0psyFBQ1BbIk?9n~1yHq`9 z`K9WwZhX4@s+zav*=c6))YdZW*gh-MG|uj?&%-$$B1o`x(mg=e^RNWZ7EwPh0&>u6m{2`A^(QP2LGh z+^0zSnwfQ(opO1(b>>QK)^du#kheJd`c@7*SUyIskUy%JBD!MhNz$>gD|qFS=+(es z@^)w7l0f8+Bl8ROWMHC+sR0;c>Ikvl;NkZ}|_h!bFqV+U9Ze8ka05JLE{4&)OqGo&1bAs99Zhb4^?q1EAe& zQQacMSVntI`~b=Pv~T<+o`bx&;ef&3O&~U123Zt!0XIP;M~HJdVx5sFVS;1=+9N?I z(Agdl`tO3tuB=J{%vg5}S@JHzJd`1dT8IFg4+JFVri5jtMA7?Xu>|?LY6M_A<{&5^ zW6xhAK<*zRu|PhyCy34g>dT2pdWXk8F!t0+Wv?d0;mCuuPe4+&Cd3DH{5WA?H)nvG z?ycyM)QLbniv|c=hfk;sqB}+R6iDAicKWb)F1 zC|JUj1Xz$v%%ATBk}VrckrF`yBqi%XhP4ED&pFs#QX;9Ft4}|-Kea8(dSRWs5Pwg^ zzc0l<)_2xRt0l&t7G%D_{2#_=;%|uV7-e2;StqZ>#y8^C7q8zQCif;j<{k=}zlcM0 zG#-sdA|5WVL&z*Q$FzNl_)#5o#Ha#i-8@wMo76); z4z=9QJNCvn@r)`W)+)ljzt-6#W?65t3gpNN)i3kwkB@08DknEABV_&+%wI#^HWnv zKilRO-KH|9$Xs1qigM6_wd`00hB7f!b<4jE)=_Ivu;4d#%ntBNlT?0jyC%Xn(pD* zpk~+!cZNmD>D~~E+E%>Y2AMT>Mrcl%dq^LNwos~oZKDO%n}hvxHtV!K<@9vpNSE5o<&=R--s0@*J9*i`j*3c|>I(rp;A98B|f!1$+xua)>yWSFAG>B}|YkKzk?z z1wPwDLjRpJ8OpL0z>HPLkS)JPn1?b&Q40~E^MQcmT$iw{lqh|>BrtugU|96yX1*vuKw zrh6kgBy}QC&!Pds*5MN>lju&+9l1@E>V&y~*To;4ISV$!6y(zBUm%mu|HkfD5(W-n z-~CL)k!T8t^ghS)jbiIuic*^c1$rYKh9d7HnZxTpsqZ2O&)z;Ajn?$uJIH~BIT0OR vdjDgz-udAW^Y(r6$m@t!x^BU1V|ym*_??i+Ti)~W|MK+>Z_TERJXZh!=i1aT diff --git a/createlookup.R b/createlookup.R index ecc5c06..44c5979 100644 --- a/createlookup.R +++ b/createlookup.R @@ -83,6 +83,7 @@ matchPlantListFamiliesToApweb<-function(tplGenera){ tplGenera$apweb.family<-tplGenera$family badFamilies<-unique(tplGenera$apweb.family[!tplGenera$apweb.family%in%apFamilies$acceptedFamilies&tplGenera$group!="Bryophytes"&tplGenera$apweb.family%in%apFamilies$family]) tplGenera$apweb.family[tplGenera$apweb.family%in%badFamilies]<-apFamilies$synonym[match(tplGenera$apweb.family,apFamilies$family)][tplGenera$apweb.family%in%badFamilies] + tplGenera$apweb.family[tplGenera$apweb.family=="Compositae"]<-"Asteraceae" return(tplGenera) } diff --git a/man/lookup_table.Rd b/man/lookup_table.Rd index 801d967..ae2e29f 100644 --- a/man/lookup_table.Rd +++ b/man/lookup_table.Rd @@ -30,7 +30,7 @@ with one row per species and with species as row names.} Build a lookup table for a set of species, connecting the species names to plant genera, families and orders } \details{ -##' The data within this lookup table comes from two sources: +The data within this lookup table comes from two sources: 1. The Plant List v1.1. (http://www.theplantlist.org/) for accepted genera to families and species richness within each @@ -52,6 +52,7 @@ lookup_table("Pinus ponderosa") # # # control how you want the function to handle non-matches +# lookup_table(c("Pinus ponderosa","Neitheragenus noraspecies")) # lookup_table(c("Pinus ponderosa","Neitheragenus noraspecies"),missing_action="NA")