Package: vegtable 0.1.9

vegtable: Handling Vegetation Data Sets

Import and handling data from vegetation-plot databases, especially data stored in 'Turboveg 2' (<https://www.synbiosys.alterra.nl/turboveg/>). Also import/export routines for exchange of data with 'Juice' (<https://www.sci.muni.cz/botany/juice/>) are implemented.

Authors:Miguel Alvarez [aut, cre]

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vegtable.pdf |vegtable.html✨
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NEWS

# Install 'vegtable' in R:
install.packages('vegtable', repos = c('https://kamapu.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/kamapu/vegtable/issues

Datasets:

On CRAN:

46 exports 7 stars 1.71 score 87 dependencies 1 mentions 49 scripts 362 downloads

Last updated 2 months agofrom:9a97a87940. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 08 2024
R-4.5-winWARNINGSep 08 2024
R-4.5-linuxWARNINGSep 08 2024
R-4.4-winWARNINGSep 08 2024
R-4.4-macWARNINGSep 08 2024
R-4.3-winWARNINGSep 08 2024
R-4.3-macWARNINGSep 08 2024

Exports:add_relevesadd_releves<-as.listcleancount_taxacount_taxa<-cover_transcross2dbcrosstabledf2coverconvertdf2vegtabledominanceevennessheaderheader<-layers2samplesmake_cocktailnew_layernew_layer<-new_relationnew_relation<-read_juicerelation2headerrichnessset_formulaset_groupset_pseudoshannonshowsimpsonsubsetsummarytaxa2samplestrait_proportiontrait_statstv2coverconverttv2vegtableupdate_detused_conceptsused_synonymsveg_aggregateveg_diversityveg_relationveg_relation<-vegtable_statwrite_juice

Dependencies:askpassbase64encbibliobitbit64blobbslibcachemclicommonmarkcpp11crayoncrosstalkcrulcurlDBIdbplyrdigestdplyrDTevaluatefansifastmapfontawesomeforeignfsgenericsgluehighrhoardrhtmltoolshtmlwidgetshttpcodehttpuvhttrindicspeciesjquerylibjsonliteknitrlaterlatticelazyevallifecyclemagrittrmemoisemimeminiUIopensslpermutepillarpkgconfigplogrplyrpromisespurrrqdapRegexR6rappdirsRcpprcrossrefrlangrmarkdownRSQLitesassshinysourcetoolsspstringdiststringistringrsystaxlisttibbletidyrtidyselecttinytextriebeardurltoolsutf8vctrsvegdatawithrxfunxml2xtableyamlyamlme

Readme and manuals

Help Manual

Help pageTopics
Merge relevés from data frames into vegtable objectsadd_releves add_releves,vegtable,data.frame-method add_releves<- add_releves<-,vegtable,data.frame-method
Coerce objects to listsas as.list,coverconvert-method as.list,vegtable-method coerce,coverconvert,list-method coerce,vegtable,list-method
Conversion of aspect classes to azimuthaspect_conv aspect_conv-data
Conversion of Braun-Blanquet codes to cover percentagebraun_blanquet braun_blanquet-data
Clean orphaned records in vegtable objectclean clean,vegtable-method clean_once
Count taxa included in vegtable objectscount_taxa count_taxa,formula,vegtable-method count_taxa,vegtable,missing-method count_taxa<- count_taxa<-,vegtable,formula-method
Convert cover scales to percent covercover_trans cover_trans,character,coverconvert-method cover_trans,factor,coverconvert-method cover_trans,numeric,coverconvert-method cover_trans,vegtable,missing-method
Cover conversion tablescoverconvert coverconvert-class
Generating cross tables from database listscross2db cross2db,data.frame-method cross2db,matrix-method cross2db.data.frame cross2db.matrix crosstable crosstable,formula,data.frame-method crosstable,formula,vegtable-method
Create coverconvert objectsdf2coverconvert df2coverconvert,data.frame-method df2coverconvert,list-method df2coverconvert.data.frame df2coverconvert.list
Convert a data frame into a vegtable object.df2vegtable df2vegtable,data.frame,numeric,missing-method df2vegtable,data.frame,numeric,numeric-method
Dutch dune meadows as vegtabledune_veg dune_veg-data
Select or replace elements in objects$ $,coverconvert-method $,vegtable-method $<- $<-,coverconvert,coverconvert-method $<-,vegtable,ANY-method $<-,vegtable-method Extract [ [,coverconvert,ANY,ANY,ANY-method [,coverconvert-method [,vegtable,ANY,ANY,ANY-method [,vegtable-method [<- [<-,vegtable-method
Retrieve or replace slot header in vegtable objectsheader header,vegtable-method header<- header<-,vegtable,data.frame-method
Vegetation-plots from KenyaKenya_veg Kenya_veg-data
Add information from slot 'layers' into slot 'samples'layers2samples layers2samples,vegtable,character,character-method layers2samples,vegtable,character,missing-method
Produce a Cocktail classificationmake_cocktail make_cocktail,shaker,vegtable-method set_formula set_formula,shaker,taxlist,character-method set_formula,shaker,vegtable,character-method set_group set_group,shaker,taxlist,character-method set_group,shaker,vegtable,character-method set_pseudo set_pseudo,shaker,taxlist,character-method set_pseudo,shaker,vegtable,character-method
Retrieve names of vegtable and coverconvert objectsdimnames dimnames,vegtable-method names names,coverconvert-method names,vegtable-method names<-,coverconvert-method
Insert new classification of vegetation layersnew_layer new_layer,vegtable,data.frame-method new_layer<- new_layer<-,vegtable,character-method new_layer<-,vegtable,data.frame-method
Insert a new variable as relation in vegtable objectnew_relation new_relation,vegtable-method new_relation.vegtable new_relation<- new_relation<-,vegtable,character,character-method new_relation<-,vegtable,missing,character-method
Insert variables from relations into headerrelation2header relation2header,vegtable-method relation2header.vegtable
Class containing Cocktail algorithms.shaker shaker-class
Subset functions for vegtable objectssubset subset,vegtable-method
Summary method for vegtable objectsprint,coverconvert-method print,shaker-method print,vegtable-method show,coverconvert-method show,shaker-method show,vegtable-method summary summary,coverconvert-method summary,shaker-method summary,vegtable-method
Insert taxon information into samplestaxa2samples taxa2samples,vegtable-method taxa2samples.vegtable
Statistics and proportion for taxon traitstrait_proportion trait_proportion,character,vegtable-method trait_proportion,formula,vegtable-method trait_stats trait_stats,character,vegtable-method trait_stats,formula,vegtable-method
Import of vegetation data from Turboveg databasestv2coverconvert tv2vegtable
Update by determined specimensupdate_det update_det,vegtable,character-method update_det,vegtable-method
Retrieve synonyms or taxon concepts used in a data setused_concepts used_concepts,vegtable-method used_concepts.vegtable used_synonyms used_synonyms,vegtable-method used_synonyms.vegtable
Aggregating information into a data frameveg_aggregate veg_aggregate,formula,vegtable,function-method
Calculation of statistics at plot leveldominance evenness richness shannon simpson veg_diversity veg_diversity,vegtable-method veg_diversity.vegtable veg_diverstiy
Information on vegetation layersveg_layers veg_layers-data
Retrieve or replace relations in vegtable objectsveg_relation veg_relation,vegtable,character-method veg_relation<- veg_relation<-,vegtable,data.frame-method
General statistics from vegtable objectsvegtable_stat vegtable_stat,vegtable-method vegtable_stat.vegtable
Class vegtable.vegtable vegtable-class
Vegetation-plots from TanzaniaWetlands Wetlands-data Wetlands_veg
Exporting tables for Juiceread_juice write_juice write_juice,vegtable,character,formula-method