exPt1 1997 Cohort

The 1997 cohort dataset contains annual fitness measurements for Echinacea plants planted in the 1997 cohort of the main common garden experimental plot (exPt1). Each plant in the plot is assigned an identification number that we call ‘cgPlaId‘ (common garden plant identifier). The location of each plant in the plot is given using the coordinates ‘row‘ and ‘pos‘ (position), both are measured in meters. ‘measureYr‘ is the year the plant was observed. ‘pop‘ is the population of origin — the remnant from which the maternal plant originated. Plants with population of origin unknown have been removed from the dataset.

We annually assess the following for each plant:
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, also known as capitula, 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). 2001 and 2017 to present achene counts have yet to be included.
*NOTE* here is an explanation for negative numbers in acheneCt: We use “-9999” as code for “missing data” in the achCt field for each head. If the plant had multiple heads & a count was missing for one of the heads, -9999 was summed together with the good achene count(s). So far, we don’t have any instances where more than one head has a missing achene count per plant; but if we do, I’ll make a note of it. So if hdCt > 1 & acheneCt < 0 adding 9999 to acheneCt will give you the acheneCt for the heads that are not missing data.

Here is a link to the 1997 cohort dataset, saved as an ascii comma-separated-values file:

exPt1Cohort1997.csv

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10:30 AM 10/13/2020 GK

This update to the 1997 Cohort dataset includes 2014-2016 achene counts and annual assessments through 2019.

exPt1Cohort1997.csv will remain the most up to date link to the 1997 cohort dataset.
exPt1Cohort1997.20201013.csv is a permanent link to this version of the dataset.

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12:00 PM 12/17/2014 GK

This update to the 1997 Cohort dataset includes 2013 achene counts.

exPt1Cohort1997.20141217.csv is a permanent link to this version of the dataset.

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10:20 AM 10/16/2014 GK

This update to the 1997 Cohort dataset includes 2014 annual status data. We are several weeks away from including 2013 achene counts. Check back soon for updates!

exPt1Cohort1997.20141016.csv is a permanent link to this version of the dataset.

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18 November 2013 GK

This update to the 1997 Cohort dataset includes 2011 & 2012 achene count data and 2013 annual status data.

cg1 1997 Cohort Aster Data November 2013

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7 June 2013 GK

This update to the 1997 Cohort dataset includes 2010 achene count data. Also, here is an explanation for negative numbers in achene count:

harvest year 2003, cgPlaId 674, 2 hds, one had 159 achenes, the other is missing data (reason unknown)
harvest year 2006, cgPlaId 722, 5 hds, 136, 143, 175, 153, and last is missing data (hd dropped in cg during harvest and found in 2007–not able to count achenes)
harvest year 2002, cgPlaId 1082, 1 hd, missing data (hd cleaned, but envelope missing)

cg1 1997 Cohort Aster Data June 2013

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25 April 2013

Here is a link to the 1997 Cohort dataset. This dataset includes updates based on quality control queries run in April 2013.

cg1 1997 Cohort Aster Data April 2013

This dataset contains the following data for common garden cohort 1997:

cgPlaId — common garden plant Id (numeric)
measureYr — measure year / year plant was observed (numeric)
pop — population of origin / remnant from which maternal plant originated (text)
row — common garden location coordinate / easting or row coordinate in meters (numeric)
pos — common garden location coordinate / northing or position coordinate in meters (numeric)
ld — living during observation year / 1 = yes, 0 = no (binary)
fl — flowering during observation year / 1 = yes, 0 = no (binary)
hdCt — head count / if flowering, count of capitula per plant; not including “dud” heads (numeric)
achCt*** — achene count / count of achenes per plant (numeric) ***includes achene counts through 2009, except 2001!

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

ee <- read.csv("http://www.echinaceaproject.org/data/exPt1Cohort1997.csv")
str(ee)
head(ee)

# Quick look at head counts

table(ee$hdCt, ee$measureYr, useNA = "always")

# Find missing values in achCt

table(ee$achCt, ee$measureYr, useNA = "always")

# Here’s how to reshape the dataframe to a ‘wide’ format

ww <- reshape(ee, 
              v.names = c("ld", "fl", "hdCt", "achCt"), 
              idvar = "cgPlaId",
              timevar = "measureYr", 
              direction = "wide")
head(ww)

# What about codes in achCt-9999 -9816 -9392?

ee[ee$achCt < 0 & !is.na(ee$achCt), ]
ww[ww$cgPlaId %in% 674, ]
ww[ww$cgPlaId %in% 722, ]
ww[ww$cgPlaId %in% 1082, ]
table(ee[, 7:8])
table(ee[is.na(ee$achCt), 8:9], useNA = "always")