picolaDataFlowering

The goal of picolaDataFlowering is to provide a lodgepole pine flowering phenology dataset in an accessible format. This package contains 16 years of interior lodgepole pine (Pinus contorta ssp. latifolia) phenology data for pollen shed and cone receptivity.

The data were collected in seed orchards in British Columbia between 1997 and 2012. Orchard trees are clones and offspring of parents sourced from across the province. Seed orchards measured pollen shed, cone receptivity, date cones were picked, and the weight of the cones. Not all orchards measured all variables in all years. Only pollen shed and cone receptivity are surfaced in the package, but date of cone harvest and weight are available in the raw data.

Installation

You can install the development version of picolaDataFlowering from GitHub with:

# install.packages("devtools")
devtools::install_github("scisus/picolaDataFlowering")

Example

Read in phenology data sets from the package.

## basic example code

state <- picolaDataFlowering::picola_state
head(state)
#>   Index DoY       Date Phenophase_Recorded State    Sex Year  Site Orchard
#> 1   343 148 1997-05-28                   4     2 FEMALE 1997 PGTIS     220
#> 2   343 150 1997-05-30                   4     2 FEMALE 1997 PGTIS     220
#> 3   343 153 1997-06-02                   4     2 FEMALE 1997 PGTIS     220
#> 4   343 155 1997-06-04                   -     3 FEMALE 1997 PGTIS     220
#> 5   343 157 1997-06-06                   -     3 FEMALE 1997 PGTIS     220
#> 6   343 159 1997-06-08                   -     3 FEMALE 1997 PGTIS     220
#>   Genotype Tree X  Y      Source
#> 1      980   28 D 47 Rita Wagner
#> 2      980   28 D 47 Rita Wagner
#> 3      980   28 D 47 Rita Wagner
#> 4      980   28 D 47 Rita Wagner
#> 5      980   28 D 47 Rita Wagner
#> 6      980   28 D 47 Rita Wagner

event <- picolaDataFlowering::picola_event
head(event)
#>   Index State Year DoY      Event_Label Event_Obs       Date    Sex      Site
#> 1     1     1 2006 125 before_flowering         1 2006-05-05 FEMALE Kalamalka
#> 2     1     2 2006 126  first_flowering         2 2006-05-06 FEMALE Kalamalka
#> 3     1     2 2006 127   last_flowering         3 2006-05-07 FEMALE Kalamalka
#> 4     1     3 2006 128   past_flowering         4 2006-05-08 FEMALE Kalamalka
#> 5     2     1 2006 124 before_flowering         1 2006-05-04 FEMALE Kalamalka
#> 6     2     2 2006 125  first_flowering         2 2006-05-05 FEMALE Kalamalka
#>   Orchard Genotype Tree X  Y      Source
#> 1     230     1460   NA N 18 Chris Walsh
#> 2     230     1460   NA N 18 Chris Walsh
#> 3     230     1460   NA N 18 Chris Walsh
#> 4     230     1460   NA N 18 Chris Walsh
#> 5     230     1467   NA J  5 Chris Walsh
#> 6     230     1467   NA J  5 Chris Walsh

Lodgepole pine in BC generally flowers in May and June.

Data is from 259 genotypes grown at 7 BC seed orchard sites and observed between 1997 and 2012.

Data sets provided with this package include:

• picola_event and picola_state: two versions of the flowering phenology data. picola_event is formatted for the model in picolaModel and contains only the observations necessary for the model. picola_state contains all observations and original phenology coding.
• picola_parent_locs: provenance information for genotypes grown in the orchards
• picola_site_coord_elev: locations and elevations of seed orchard sites and two northern sites used for comparison in picolaModel analysis
• picola_SPUs: lodgepole pine SPUs and their representation in this phenology dataset