processPlantSurveys: Process GTMNERR Plant Survey Data

In ksauby/GTMNERRproc: Data processing functions for GTMNERR data.

Description

Steps:

• Fix column names

• format dates

• format PlantIDs

• format convert "999" values to NA

• format change "yes"/"no" values of the insect survey, missing, and dead columns to 0/1

• format numeric columns

• add total segment column

• add fruit count column

• add fruit/flower count column

• check for observations of 0 pads, 0 height, or 0 width; if there are observations, stop

• add column, "DemographicSurvey"

  • survey 1 - spring/summer 2013

  • survey 2 - fall/winter 2013/2014

  • survey 3 - spring/summer 2014

  • survey 4 - winter 2015

  • survey 5 - spring/summer 2015

• addFecundityYear

  • 2012 - Date >= "2012-12-02" & Date < "2013-05-01"

  • 2013 - Date >= "2013-05-01" & Date < "2014-05-01"

  • 2014 - Date >= "2014-05-01" & Date < "2015-05-01"

  • 2015 - Date >= "2015-05-01"

Column Names:

• PlantMeasureID Record number if Microsoft Access database

• First_Observer_Initials Initials of primary observer (should always be KS, for Kristen Sauby)

• Second_Observer_Initials Initials of secondary observer; CJP - Cory Penca; YP - Yani Paulay; KS - Kristen Sauby; JW: Juliana Welch; CW: Cedric Worman; AP: Adam Payton

• Date Date

• PlantID Unique number for the individual plant

• Plant_collected Were plant samples collected?

• Time

• PlantPictures identifying numbers of photos taken

• PlantPictures_Direction direction that the photo(s) was(were) taken

• CA_t Presence/absence (1/0) of Cactoblastis cactorum

• CACA_collected Were samples of Cactoblastis cactorum collected?

• CACA_quantity Number of Cactoblastis cactorum samples collected

• ME_t Presence/absence (1/0) of Melitara prodenialis

• MEPR_collected Were samples of Melitara prodenialis collected?

• MEPR_quantity Number of Melitara prodenialis samples collected

• CH_t Presence/absence (1/0) of Chelinidea vittiger

• CHVI_collected Were samples of Chelinidea vittiger collected?

• CHVI_quantity Number of Chelinidea vittiger samples collected

• DA_t Presence/absence (1/0) of Dactylopius species

• DACT_collected Were samples of Dactylopius species collected?

• DACT_quantity Number of Dactylopius species samples collected

• Unknown_Moth_t Presence/absence (1/0) of unknown moth

• UnknownMoth_collected Were samples of unknown moth collected?

• UnknownMoth_quantity Number of unknown moth samples collected

• Old_Moth_Evidence_t Evidence of past moth infestation

• Old_Moth_Evidence_recent Whether evidence of past moth infestation appears recent or old

• Fungus Presence/absence (1/0) of plant fungal infection

• Gerstaeckeria Presence/absence (1/0) of Gerstaeckeria

• Plant_Segments_total Number of segments

• Plant_Segments_w_leaves New, green segments with leaves

• Plant_Segments_wo_leaves Green segments without leaves

• Plant_Segments_woody number of woody segments/trunks; these segments are entirely brown on the outside

• Height_t maximum height in cm

• Width_t maximum width in cm

• Perpen_Width width, perpendicular to max width, in cm

• Num_FlowerBuds Number of flower buds

• Num_Fruit_red Number of red fruit

• Num_Fruit_green Number of green fruit

• Num_Flowers Number of flowers

• Num_Fruit use this when number is recorded but distinction by color is not made

• Pollinators

• Spiders

• Ants

• Other_collected_quantity

• Plant_Notes

• Insect_Notes

• Other_Notes

• Dead Whether the plant is observed to be dead; 0 or 1

• Missing

• OutsideOfPlot "Yes" if plant is no longer in plot

• PlotPlantID Unique number for the individual plant; if a plant is counted in multiple plots, a letter is appended to the plant ID here (e.g., 9606a) and then removed for analysis

• Size_t The sum of Plant_Segments_total, Plant_Segments_w_leaves, Plant_Segments_wo_leaves, and Plant_Segments_woody

• Fruit_t The sum of Num_Fruit_red, Num_Fruit_green, and Num_Fruit

• Fruit_Flowers_t The sum of Num_FlowerBuds, Num_Flowers, Num_Fruit_red, Num_Fruit_green, and Num_Fruit

Usage

processPlantSurveys(Plant.Surveys, Plant.Info)

ksauby/GTMNERRproc documentation built on May 20, 2019, 6:42 p.m.