exPt1 INB2

The INB2 (Inbreeding2) experiment compares fitness of Echinacea from three cross types. This experiment was planted in the main common garden experimental plot (exPt1) in 2006. The INB2 dataset contains two files: 1. pedigree data & 2. annual fitness measurements. See explanations of the pedigree and annual fitness files below.

1. Pedigree and pre-planting data. (1,318 records)

cgPlaId: common garden plant identifier — A unique identification number for each plant. Records without cgPlaId did not make it to the common garden planting stage. (integer)
row: & pos: Row (E/W) and Position (N/S) coordinates locating each plant in the plot, in meters (numeric)
matCgPlaId: maternal plant identifier — cgPlaId for Dam used in cross (integer)
matFam: maternal family — Id for grandDam in remnant EA pop (integer)
matPop: maternal population — remnant of origin for grandDam (text)
sireCgPlaId: sire plant identifier — cgPlaId for Sire used in cross (integer)
sireFam: sire family — Id for grandDam in remnant EA pop (integer)
sirePop: sire population — remnant of origin for grandDam (text)
crossLevel: cross level — 3 cross types: I = inbred, W = within remnant, B = between remnants (text)
pinBox: post-it-note box — identifier for box in which post-it-note was stored (integer)
pin: post-it-note identifier — number of the post-it-note on which achene was stuck (integer)
seedNo: seed number — location of achene stuck to the post-it-note (in ascending order from left to right) (integer)
pod: identifier for group of achenes that were crossed at the same time and share parents (integer)
podSize: number of achenes in pod (integer)
dishTray: petri dish tray identifier (integer)
acheneMass: achene mass in mg (numeric)
plugTray: plug tray identifier — germinants planted in plug trays (integer)
plug: plug identifier — location of germinant in plug tray (integer)
ht1_14, ht2_14, ht1_21, ht2_21, ht3_21, ht1_28, ht2_28, ht3_28, ht4_28, ht1_35, ht2_35, ht3_35, ht4_35: height of each leaf on certain day, ht2_21 = height of second leaf measured in mm 21 days after radicle emergence (integer)
cohort: date that germinant was transferred from petri dish to plug tray

2. Annual fitness measurements
We annually assess fitness for each plant. The fields in this file include the following:

cgPlaId: common garden plant identifier — A unique identification number for each plant.
measureYr: measure year — year that measurements were taken
ld: living during a given year (1 = yes, 0 = no);
fl: flowering during a given year (1 = yes, 0 = no), any plant with a stem we categorize as flowering (some stems don’t produce a head or lose their head before flowering resulting in a year where a plant is flowering and has head count zero);
hdCt: count of heads for a given year (zero if a plant doesn’t flower during a given year);
achCt: sum of achenes produced by all heads on a plant during a given year (zero if a plant doesn’t flower during a given year). Achene counts that are not yet included have missing values.

The key field ‘cgPlaId’ links the two files. INB2ExpAnnualFitness.csv includes only plants that survived to be planted in the common garden.

Here are links to the INB2 dataset, saved as an ascii comma-separated-values files:

INB2Pedigree.csv this file is not likely to be updated.

INB2ExpAnnualFitness.csv

R users: Here are a few lines of code to get you started!

# import the annual measurements
aa <- read.csv("http://echinaceaproject.org/data/INB2ExpAnnualFitness.csv")
str(aa)
tail(aa)

# Quick look at head counts
table(aa$hdCt, aa$measureYr, useNA = "always")

# Find missing values in achCt
table(aa$achCt, aa$measureYr, useNA = "always")

# Reshape the dataframe to a ‘wide’ format
ww <- reshape(aa, 
              v.names = c("ld", "fl", "hdCt", "achCt"), 
              idvar = "cgPlaId",
              timevar = "measureYr", 
              direction = "wide")
str(ww) # 1443 records
head(ww)

# Import the pedigree table 
pp <- read.csv("http://www.echinaceaproject.org/data/INB2Pedigree.csv")
str(pp) # 1318 rcords
tail(pp)

# Merge the pedigree and annual measurement tables 
inb2 <- merge(pp, ww, all.x = TRUE)
str(inb2) # 1318 sprouts have pedigree info
length(unique(inb2$cgPlaId)) # 1136 of these were planted outside
1443 - 1136 # 307 of the planting locations have no pedigree info

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10:30 AM 02/11/2015 GK
Update on achene count progress: We plan to post a INB2 dataset that includes 2013 & 2014 achene counts at the end of March!
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12:46 PM 12/18/2014 GK

This posting of the INB2 dataset includes survival, flowering, and head count data through 2014 and achene counts through 2012. We hope to include achene counts for 2013 by the end of January 2015. Check back for updates!

INB2ExpAnnualFitness.csv will remain the most up to date link to the INB2 Annual Fitness dataset.
INB2Exp20141218.csv is a permanent link to this version of the dataset.

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