README.md

In vanichols/PFIweeds2020: Provides Easy Access to 2020 PFI Weed Seedbank Project Data

PFIweeds2020

The goal of PFIweeds2020 is to grant easy access to data and analysis functions for the 2020 Practical Farmers of Iowa project looking at the effect of cover-cropping on the weed seedbank.

Overview

We sampled soil from three long-term (10+ years) sites with experiments using a winter rye cover crop in a corn/soybean rotation compared to the same rotation without a winter cover crop. We took that soil back to a greenhouse, germinated the seeds, then counted/identified the weeds as we plucked them from their cozy homes and threw them on the ground. The results will be available in a publication coming soon…

Installation

The development version from GitHub can be accessed with:

# install.packages("devtools")
devtools::install_github("vanichols/PFIweeds2020")

Example

library(PFIweeds2020)

Look at the list of weeds we found

head(pfi_weedsplist)
#>       common_name         scientific_name  code possible_mislabel photo_path
#> 1      water hemp amaranthus tuberculatus AMATU              <NA>         C4
#> 2 lamb's quarters       chenopodium album CHEAL              <NA>         C3
#> 3     velvet leaf    abutilon theophrasti ABUTH              <NA>         C3
#> 4    rye (cereal)          secale cereale SECCE              <NA>         C3
#> 5      nightshade      solanum ptycanthum SOLPT             SOPT7         C3
#> 6        purslane      portulaca oleracea POROL              <NA>         C4
#>   functional_grp        family
#> 1           forb amaranthaceae
#> 2           forb amaranthaceae
#> 3           forb     malvaceae
#> 4          grass       poaceae
#> 5           forb    solanaceae
#> 6           forb portulacaceae

You really want to see the raw data?

head(pfi_ghobsraw)
#>     obs_date obs_initials electrec_initials site_name field sys_trt cc_trt
#> 1 2019-05-03           gn                eo      Boyd   B44  silage    rye
#> 2 2019-05-03           gn                eo      Boyd   B44  silage     no
#> 3 2019-05-03           gn                eo      Boyd   B44  silage     no
#> 4 2019-05-03           gn                eo      Boyd   B44  silage    rye
#> 5 2019-05-03           gn                eo      Boyd   B44  silage     no
#> 6 2019-05-03           gn                eo      Boyd   B44  silage    rye
#>   crop_2019 rep blockID       trayID AMATU CHEAL ABUTH SECCE SOLPT POROL RAPSA
#> 1      corn   2   B44_2 B44_2-rye-t2     2     7    NA    NA    NA    NA    NA
#> 2      corn   2   B44_2  B44_2-no-t1     3    NA    NA    NA    NA    NA    NA
#> 3      corn   4   B44_4  B44_4-no-t2    18    NA    NA    NA    NA    NA    NA
#> 4      corn   1   B44_1 B44_1-rye-t3    NA     3    NA    NA    NA    NA    NA
#> 5      corn   1   B44_1  B44_1-no-t1    39    10    NA    NA    NA    NA    NA
#> 6      corn   1   B44_1 B44_1-rye-t2    18    16    NA    NA    NA    NA    NA
#>   SETFA EUPMA SETVI POLAV CONCA TAROF DIGSA PLAMA OXAST POLPY UG UB
#> 1    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA NA NA
#> 2    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA NA NA
#> 3    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA NA NA
#> 4    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA NA NA
#> 5    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA NA NA
#> 6    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA NA NA

You can use a custom function to quickly summarise it: Total number of weeds in each experimental unit:

head(pfi_ghobsraw %>% pfifun_sum_byeu())
#> # A tibble: 6 x 8
#> # Groups:   site_name, field, sys_trt, cc_trt, rep [6]
#>   site_name field sys_trt cc_trt   rep blockID totseeds totseeds_m2
#>   <chr>     <chr> <chr>   <chr>  <dbl> <chr>      <dbl>       <dbl>
#> 1 Boyd      B42   grain   no         1 B42_1         34        663.
#> 2 Boyd      B42   grain   no         2 B42_2         12        234.
#> 3 Boyd      B42   grain   no         3 B42_3          9        175.
#> 4 Boyd      B42   grain   no         4 B42_4          7        136.
#> 5 Boyd      B42   grain   no         5 B42_5         17        331.
#> 6 Boyd      B42   grain   rye        1 B42_1        116       2261.

There is more! Probably more than you want…

vanichols/PFIweeds2020 documentation built on Oct. 14, 2020, 5:39 p.m.