sectional seed set in remnants; topMidBot

Here is the dataset for seed set data collected in remnants and processed in sections — top, middle, and bottom of head. See headIDtoAKA for linking the seed set dataset to location information.

Data are stored in a csv file with the following fields:
headID: unique identifier for each head, tag-tt-year
year: year in which heads were collected
acheneCt: total number of achenes produced by head (includes rays)
topFull: number of full achenes from sample of top achenes
midFull:
number of full achenes from sample of mid achenes
botFull:
number of full achenes from sample of bottom achenes
topPartial: number of partial achenes from sample of top achenes
midPartial: number of partial achenes from sample of mid achenes
botPartial: number of partial achenes from sample of bottom achenes
topEmpty:
number of empty achenes from sample of top achenes
midEmpty
: number of empty achenes from sample of mid achenes
botEmpty: number of empty achenes from sample of bottom achenes
dataSource: name of CSV and R script used to compile data
seedSetNote: notes
seedSetType: x-ray or weigh

remSectionalSeedSet.csv will remain the most up-to-date link to the sectional seed set in remnants dataset.

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2018-05-31 sw

This is a link to data from 2014 – 2016.

This update includes 48 new records from the remnant extremes experiment from 2016. Heads were cleaned by Nicolette McManus and TEH ushered the dataset. This update also includes fixes to previously uploaded records. The problems fixed include a) column names that that were on the wrong columns, b) information about uninformative records that wasn’t included, and c) duplicated records. I also deleted five records of heads that had zero achenes or zero informative achenes (pesky division by zero). Here are the headIDs of those: “12710-wht-2016” “14055-grn-2016” “19135-red-2015” “19276-red-2016” “19430-bac-2016”

TEH will soon prepare a dataset from the rich-hood study that includes information about several heads where the achenes were removed, counted, and classified by sections.

See headIDtoAKA for linking the seed set dataset to location information.

remSectionalSeedSet.csv will remain the most up to date link to the sectional seed set in remnants dataset.
remSectionalSeedSet20180531.csv is a permanent link to this version of the dataset.

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02/01/2017 gk

This is a link to data from 2014 – 2016. We will post updates that include data from remExtremes in 2016.

Amy’s 2016 Remnant Harvest Data Summary (sppBonus, regRem, extremeRem): This data set contains reproductive information from 142 flowering Echinacea heads collected from 19 remnants during summer 2016 plus 32 heads selected from Staffanson Prairie Preserve as part of the sppBonus experiment. We excluded heads used in the compatibility crossing experiment from our lists. We randomly selected 5 heads from remnants. In large remnants, we also selected 4 extreme plants (most isolated, least isolated, earliest to flower, latest to flower) as focal plants from a list of individuals included in our phenology study. For sppBonus, we randomly selected 16 heads each unit (E and W) from a list of plants for which we had assessed seed set in a previous year. We excluded plants used in the compatibility crossing experiment from our list of potential heads to be harvested.

We determined if a head was harvestable if it met the following criteria: 1) normal (produced pollen, and not missing or damaged), 2) missing 25% or fewer achenes. If a randomly selected plant had no harvestable heads, we randomly selected another from that site. If an ‘extreme’ plant had no harvestable heads, we selected the next most extreme individual from that site.

If a focal plant had multiple harvestable heads, we selected one head at random for harvest (see headRandomizer.xlsx from mapsMakeFor2016-08-22harvest.R).

We harvested the heads in September and October. Several interns (MK, ES, JM, SH) cleaned the heads in Fall 2016. They separated the top 30 and bottom 30 achenes (excluding ray achenes from bot sample) for each head and randomly selected a sample 30 achenes from the middle using the rectangular grid randomization scheme. They recorded the number of uninformative achenes in their sample from each section.

Interns counted the total number of achenes and the number in top, bottom, and middle sections to quantify seed set. They x-rayed the samples from each section and counted the number of full, partial, or empty achenes in each sample (details regarding their classification methods can be found here). We (SN and AW) estimated seed set using the estimateSeedSet function in the echinaceaLab package.

See headIDtoAKA for linking the seed set dataset to location information.

remSectionalSeedSet.csv will remain the most up to date link to the sectional seed set in remnants dataset.
remSectionalSeedSet20170201.csv is a permanent link to this version of the dataset.

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06/03/2016 gk

This is a link to data from 2015. We will post updates that include data from previous years, as other heads from remnants have been sampled by section.

Danny’s Description (2015 data): This data set contains reproductive information from 159 flowering Echinacea heads collected from 21 remnants during summer 2015. We randomly selected 5 heads from each remnant as well as the 4 extreme plants (most isolated, least isolated, earliest to flower, latest to flower) as focal plants from a list of individuals included in our phenology study. One head from each focal plant was then selected at random for harvest. We excluded heads used in the AII crossing experiment from our list of potentially harvestable heads. Heads were harvested in September, dried, and taken to the CBG for cleaning. Several interns (JC, AL, SAW, and MC) helped clean these heads. We separated the top 30 and bottom 30 achenes (excluding ray achenes from bot sample) for each head and randomly selected 30 achenes from the middle for x-ray. The total number of achenes was counted (rays + disc) and the top, bot, and mid (referred to as mid) achenes were used to quantify seed set. Achenes were X-rayed and scored as full, partial, or empty by SAW. Whole head seed set can be estimated using the estimate SeedSet function in the echinaceaLab package.

Note: There was some overlap between random and extreme plants so there are 159 heads total which does not equal 107 randoms + 57 extremes

See headIDtoAKA for linking the seed set dataset to location information.

remSectionalSeedSet20160603.csv is a permanent link to this version of the dataset.