I have a vegetation survey dataset where each row represents one species identified within a plot. I need to summarize this data by plot #, and generate fields for total # of species per plot, native species per plot, nonnative species per plot, total % cover per plot, native % cover per plot, and nonnative % cover per plot. I've grouped by plot and used summarize to generate these fields. Everything is working except the native % cover and nonnative % cover. It’s not giving me an error but it’s returning weird numbers that don’t add up. The first plot (B1) looks right, but every other plot is wrong, and I can’t figure out why or what it’s doing.
A sample of my data looks like:
| Plot# | num | Aspect (Bottom, North, South/West, Top/East) | Date | Surveyor | Seed Mix (high/low) | Annual (Yes/No) | Biochar (Yes/No) | Species | % Cover | Native_Status | Photo (yes/no) | Note | Sci_Name | Com_Name | Duration | Family | Habit | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| B1 | 1 | Bottom | 45058 | JT | High | No | No | ANTHCOT | 75 | L48 (I) | Anthemis cotula L. | stinking chamomile | Annual | Asteraceae | Forb/herb | |||
| B1 | 1 | Bottom | 45058 | JT | High | No | No | ECHIVUL | 10 | L48 (I) | Echium vulgare L. | common viper's bugloss | Annual, Biennial, Perennial | Boraginaceae | Forb/herb | |||
| B1 | 1 | Bottom | 45058 | JT | High | No | No | LACTSER | 4 | L48 (I) | Lactuca serriola L. | prickly lettuce | Annual, Biennial | Asteraceae | Forb/herb | |||
| B1 | 1 | Bottom | 45058 | JT | High | No | No | FESTIDA | 1 | L48 (N) | Festuca idahoensis Elmer | Idaho fescue | Perennial | Poaceae | Graminoid | |||
| B1 | 1 | Bottom | 45058 | JT | High | No | No | AVENFAT | 1 | L48 (I) | Avena fatua L. | wild oat | Annual | Poaceae | Graminoid | |||
| B1 | 1 | Bottom | 45058 | JT | High | No | No | CLARPUL | 0.5 | L48 (N) | Clarkia pulchella Pursh | pinkfairies | Annual | Onagraceae | Forb/herb | |||
| B1 | 1 | Bottom | 45058 | JT | High | No | No | ACHIMIL | 1 | L48 (N) | Achillea millefolium L. | common yarrow | Perennial | Asteraceae | Forb/herb | |||
| B1 | 1 | Bottom | 45058 | JT | High | No | No | MADI1S1 | 0.5 | L48 (N) | Madia sp. | tarweed | 0 | Asteraceae | 0 | |||
| B1 | 1 | Bottom | 45058 | JT | High | No | No | SISYALT | 30 | L48 (I) | Sisymbrium altissimum L. | tall tumblemustard | Annual, Biennial | Brassicaceae | Forb/herb | |||
| B2 | 2 | Bottom | 45058 | JT | High | No | Yes | ACHIMIL | 80 | L48 (N) | Achillea millefolium L. | common yarrow | Perennial | Asteraceae | Forb/herb | |||
| B2 | 2 | Bottom | 45058 | JT | High | No | Yes | SISYALT | 25 | L48 (I) | Sisymbrium altissimum L. | tall tumblemustard | Annual, Biennial | Brassicaceae | Forb/herb | |||
| B2 | 2 | Bottom | 45058 | JT | High | No | Yes | ANTHCOT | 12 | L48 (I) | Anthemis cotula L. | stinking chamomile | Annual | Asteraceae | Forb/herb | |||
| B2 | 2 | Bottom | 45058 | JT | High | No | Yes | LUPISER | 0.5 | L48 (N) | Lupinus sericeus Pursh | silky lupine | Perennial | Fabaceae | Subshrub, Forb/herb | |||
| B2 | 2 | Bottom | 45058 | JT | High | No | Yes | CLARPUL | 1 | L48 (N) | Clarkia pulchella Pursh | pinkfairies | Annual | Onagraceae | Forb/herb | |||
| B2 | 2 | Bottom | 45058 | JT | High | No | Yes | LACTSER | 3 | L48 (I) | Lactuca serriola L. | prickly lettuce | Annual, Biennial | Asteraceae | Forb/herb | |||
| B2 | 2 | Bottom | 45058 | JT | High | No | Yes | ECHIVUL | 5 | L48 (I) | Echium vulgare L. | common viper's bugloss | Annual, Biennial, Perennial | Boraginaceae | Forb/herb | |||
| B2 | 2 | Bottom | 45058 | JT | High | No | Yes | ERIOHER | 0.5 | L48 (N) | Eriogonum heracleoides Nutt. | parsnipflower buckwheat | Perennial | Polygonaceae | Subshrub, Forb/herb | |||
| B2 | 2 | Bottom | 45058 | JT | High | No | Yes | AVENFAT | 0.5 | L48 (I) | Avena fatua L. | wild oat | Annual | Poaceae | Graminoid | |||
| B2 | 2 | Bottom | 45058 | JT | High | No | Yes | FESTIDA | 0.5 | L48 (N) | Festuca idahoensis Elmer | Idaho fescue | Perennial | Poaceae | Graminoid |
My code looks like:
#Generate summary table of plots. Sp_tot=# of species ID'd, sp_N=# of native species ID'd, sp_NonN=# 0f nonnative species ID'd,
# Cov_Tot=total % cover, Cov_N=% cover of native species, Cov_NonN=% COver of nonnative species, Aspect=Aspect of plot,
#Seed Mix=high/low diversity mix applied, biochar= biochar added yes or no, annual= annual seed mix added yes or no
Plot_Summary<-df %>%
group_by(Plot.) %>%
summarize(Sp_Tot=sum(Species==Species, na.rm = TRUE),
sp_N=sum(Native_Status=='L48 (N)', na.rm = TRUE),
sp_NonN=sum(Native_Status=='L48 (I)', na.rm = TRUE),
Cov_Tot=sum(X..Cover, na.rm = TRUE),
Cov_N=sum(df[which(Native_Status=='L48 (N)'),"X..Cover"], na.rm = TRUE), ##This isn't working right!!
Cov_NonN=sum(df[which(Native_Status=='L48 (I)'), "X..Cover"], na.rm = TRUE), ##This isn't working right!!
Aspect=first(Aspect..Bottom..North..South.West..Top.East.),
Seed_Mix=first(Seed.Mix..high.low.),
biochar=first(Biochar..Yes.No.),
annual=first(Annual..Yes.No.)) %>%
arrange(Plot.)
The resulting data frame looks like:
| Plot. | Sp_Tot | sp_N | sp_NonN | Cov_Tot | Cov_N | Cov_NonN | Aspect | Seed_Mix | biochar | annual |
|---|---|---|---|---|---|---|---|---|---|---|
| B1 | 9 | 4 | 5 | 123 | 3 | 120 | Bottom | High | No | No |
| B10 | 8 | 5 | 3 | 64.5 | 78 | 15 | Bottom | High | No | Yes |
| B11 | 8 | 5 | 3 | 75 | 78 | 15 | Bottom | High | No | No |
| B12 | 9 | 4 | 5 | 66.5 | 106.5 | 16.5 | Bottom | High | Yes | No |
| B13 | 11 | 6 | 5 | 54.5 | 185.5 | 42.5 | Bottom | Low | No | No |
| B14 | 9 | 4 | 4 | 74 | 107 | 15.5 | Bottom | Low | Yes | No |
| B15 | 10 | 7 | 2 | 77 | 109 | 14 | Bottom | Low | Yes | Yes |
| B16 | 10 | 5 | 5 | 44.5 | 107 | 96 | Bottom | Low | No | Yes |
| B17 | 11 | 8 | 3 | 97 | 117.5 | 110.5 | Bottom | High | No | Yes |
| B18 | 9 | 4 | 4 | 51.5 | 110 | 12 | Bottom | High | Yes | Yes |
| B19 | 9 | 5 | 4 | 112 | 117 | 6 | Bottom | High | No | No |
| B2 | 10 | 5 | 5 | 128 | 157.5 | 45.5 | Bottom | High | Yes | No |
| B20 | 11 | 6 | 5 | 111 | 108.5 | 119.5 | Bottom | High | Yes | No |
| B21 | 9 | 5 | 3 | 47.5 | 87.5 | 5.5 | Bottom | Low | No | Yes |
| B22 | 8 | 5 | 3 | 59.5 | 90.5 | 2.5 | Bottom | Low | No | No |
| B23 | 7 | 3 | 4 | 55.5 | 5.5 | 87 | Bottom | Low | Yes | No |
| B24 | 7 | 4 | 3 | 71 | 77.5 | 15 | Bottom | Low | Yes | Yes |
| B3 | 8 | 6 | 2 | 104.5 | 79 | 14 | Bottom | High | No | Yes |
| B4 | 9 | 6 | 3 | 47 | 111 | 12 | Bottom | High | Yes | Yes |
| B5 | 6 | 2 | 4 | 78.5 | 11 | 80.5 | Bottom | Low | Yes | No |
| B6 | 9 | 4 | 5 | 127.5 | 77 | 46 | Bottom | Low | No | No |
| B7 | 6 | 3 | 3 | 60.5 | 76.5 | 15 | Bottom | Low | Yes | Yes |
| B8 | 11 | 6 | 4 | 52.5 | 91.5 | 106.5 | Bottom | Low | No | Yes |
| B9 | 8 | 4 | 4 | 92 | 81 | 12 | Bottom | High | Yes | Yes |
| N1 | 12 | 9 | 3 | 24.5 | 155.5 | 84.5 | Bottom | Low | Yes | No |
| N10 | 11 | 6 | 5 | 33.5 | 116 | 112 | North | Low | No | No |
| N11 | 16 | 9 | 6 | 34 | 50.5 | 194 | North | Low | No | No |
| N12 | 15 | 8 | 6 | 49 | 123.5 | 117 | North | Low | No | Yes |
| N13 | 11 | 7 | 4 | 23.5 | 133.5 | 94.5 | North | High | Yes | Yes |
| N14 | 12 | 9 | 3 | 24.5 | 234.5 | 5.5 | North | High | No | Yes |
| N15 | 14 | 9 | 5 | 28.5 | 204 | 37.5 | North | High | Yes | No |
| N16 | 10 | 5 | 5 | 37.5 | 119.5 | 83.5 | North | High | No | No |
Notice Cov_N and Cov_NonN don't add up to Cov_Tot, except for the very first plot. Can anyone tell me what I'm doing wrong and what I might do to fix it? Thanks!