library(readr)
## Warning: package 'readr' was built under R version 4.0.4
library(tidyr)
## Warning: package 'tidyr' was built under R version 4.0.4
library(ggplot2)
## Warning: package 'ggplot2' was built under R version 4.0.4
library(Hmisc)
## Warning: package 'Hmisc' was built under R version 4.0.5
## Loading required package: lattice
## Loading required package: survival
## Warning: package 'survival' was built under R version 4.0.4
## Loading required package: Formula
## Warning: package 'Formula' was built under R version 4.0.3
##
## Attaching package: 'Hmisc'
## The following objects are masked from 'package:base':
##
## format.pval, units
library(plyr)
## Warning: package 'plyr' was built under R version 4.0.4
##
## Attaching package: 'plyr'
## The following objects are masked from 'package:Hmisc':
##
## is.discrete, summarize
library(RColorBrewer)
## Warning: package 'RColorBrewer' was built under R version 4.0.3
library(reshape2)
## Warning: package 'reshape2' was built under R version 4.0.4
##
## Attaching package: 'reshape2'
## The following object is masked from 'package:tidyr':
##
## smiths
library(PupillometryR)
## Warning: package 'PupillometryR' was built under R version 4.0.4
## Loading required package: dplyr
## Warning: package 'dplyr' was built under R version 4.0.5
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:plyr':
##
## arrange, count, desc, failwith, id, mutate, rename, summarise,
## summarize
## The following objects are masked from 'package:Hmisc':
##
## src, summarize
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
## Loading required package: rlang
## Warning: package 'rlang' was built under R version 4.0.4
library(nlme)
## Warning: package 'nlme' was built under R version 4.0.4
##
## Attaching package: 'nlme'
## The following object is masked from 'package:dplyr':
##
## collapse
library(lme4)
## Warning: package 'lme4' was built under R version 4.0.4
## Loading required package: Matrix
##
## Attaching package: 'Matrix'
## The following objects are masked from 'package:tidyr':
##
## expand, pack, unpack
##
## Attaching package: 'lme4'
## The following object is masked from 'package:nlme':
##
## lmList
library(readr)
wd_rv <- read_csv("~/Proposed papers/Weed species/Muoni Weed Analysis/wd_rv.csv")
##
## -- Column specification --------------------------------------------------------
## cols(
## season = col_character(),
## site = col_character(),
## sampling_time = col_double(),
## crop = col_character(),
## replicate = col_double(),
## treatment_org = col_character(),
## treatment = col_character(),
## species_org = col_character(),
## species = col_character(),
## group = col_character(),
## weed_density = col_double()
## )
names(wd_rv)
## [1] "season" "site" "sampling_time" "crop"
## [5] "replicate" "treatment_org" "treatment" "species_org"
## [9] "species" "group" "weed_density"
attach(wd_rv)
species=as.factor(species)
treatment=as.factor(treatment)
crop=as.factor(crop)
group=as.factor(group)
dominant<-subset(wd_rv,group=="Group A")
attach(dominant)
## The following objects are masked _by_ .GlobalEnv:
##
## crop, group, species, treatment
## The following objects are masked from wd_rv:
##
## crop, group, replicate, sampling_time, season, site, species,
## species_org, treatment, treatment_org, weed_density
LM <- lm(weed_density ~ sampling_time+season+treatment_org+species_org,data = dominant)
summary(LM)
##
## Call:
## lm(formula = weed_density ~ sampling_time + season + treatment_org +
## species_org, data = dominant)
##
## Residuals:
## Min 1Q Median 3Q Max
## -36.986 -11.941 -4.812 3.133 311.593
##
## Coefficients:
## Estimate Std. Error t value
## (Intercept) 14.8873 2.7467 5.420
## sampling_time -2.5786 0.7845 -3.287
## season2010/11 -2.5583 1.9044 -1.343
## season2011/12 -11.1174 1.6150 -6.884
## season2012/13 -12.5722 1.9044 -6.602
## treatment_orgAtrazine+Glyphosate -1.5635 2.1731 -0.719
## treatment_orgAtrazine+Glyphosate+Metalachlor -2.7698 2.1731 -1.275
## treatment_orgGlyphosate -0.4841 2.1731 -0.223
## treatment_orgManual weeding 4.5397 2.1731 2.089
## treatment_orgParaquat 2.0595 2.1731 0.948
## species_orggalinsoga parviflora 9.7831 1.7743 5.514
## species_orgleucas martinicensis 5.1720 1.7743 2.915
## species_orgricardia scabra 20.1376 1.7743 11.349
## Pr(>|t|)
## (Intercept) 6.93e-08 ***
## sampling_time 0.00104 **
## season2010/11 0.17935
## season2011/12 8.54e-12 ***
## season2012/13 5.62e-11 ***
## treatment_orgAtrazine+Glyphosate 0.47196
## treatment_orgAtrazine+Glyphosate+Metalachlor 0.20265
## treatment_orgGlyphosate 0.82374
## treatment_orgManual weeding 0.03687 *
## treatment_orgParaquat 0.34342
## species_orggalinsoga parviflora 4.13e-08 ***
## species_orgleucas martinicensis 0.00361 **
## species_orgricardia scabra < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 24.39 on 1499 degrees of freedom
## Multiple R-squared: 0.134, Adjusted R-squared: 0.1271
## F-statistic: 19.34 on 12 and 1499 DF, p-value: < 2.2e-16
par(mfrow = c(2,2))
plot(LM)
#lmm6 <- lme(weed_density ~ season+sampling_time+treatment_org+sampling_time:treatment_org,
#random = ~1|replicate, method = "ML",data = dominant)
#summary(lmm6)
Graphical Presentation
library(readr)
group_a <- read_csv("~/Proposed papers/Weed species/Muoni Weed Analysis/group_a.csv")
##
## -- Column specification --------------------------------------------------------
## cols(
## season = col_character(),
## site = col_character(),
## sampling_time = col_double(),
## crop = col_character(),
## replicate = col_double(),
## treatment_org = col_character(),
## treatment = col_character(),
## species_org = col_character(),
## species = col_character(),
## group = col_character(),
## weed_density = col_double()
## )
attach(group_a)
## The following objects are masked _by_ .GlobalEnv:
##
## crop, group, species, treatment
## The following objects are masked from dominant:
##
## crop, group, replicate, sampling_time, season, site, species,
## species_org, treatment, treatment_org, weed_density
## The following objects are masked from wd_rv:
##
## crop, group, replicate, sampling_time, season, site, species,
## species_org, treatment, treatment_org, weed_density
group_b <- read_csv("~/Proposed papers/Weed species/Muoni Weed Analysis/group_b.csv")
##
## -- Column specification --------------------------------------------------------
## cols(
## season = col_character(),
## site = col_character(),
## sampling_time = col_double(),
## crop = col_character(),
## replicate = col_double(),
## treatment_org = col_character(),
## treatment = col_character(),
## species_org = col_character(),
## species = col_character(),
## group = col_character(),
## weed_density = col_double()
## )
attach(group_b)
## The following objects are masked _by_ .GlobalEnv:
##
## crop, group, species, treatment
## The following objects are masked from group_a:
##
## crop, group, replicate, sampling_time, season, site, species,
## species_org, treatment, treatment_org, weed_density
## The following objects are masked from dominant:
##
## crop, group, replicate, sampling_time, season, site, species,
## species_org, treatment, treatment_org, weed_density
## The following objects are masked from wd_rv:
##
## crop, group, replicate, sampling_time, season, site, species,
## species_org, treatment, treatment_org, weed_density
group_c <- read_csv("~/Proposed papers/Weed species/Muoni Weed Analysis/group_c.csv")
##
## -- Column specification --------------------------------------------------------
## cols(
## season = col_character(),
## site = col_character(),
## sampling_time = col_double(),
## crop = col_character(),
## replicate = col_double(),
## treatment_org = col_character(),
## treatment = col_character(),
## species_org = col_character(),
## species = col_character(),
## group = col_character(),
## weed_density = col_double()
## )
attach(group_c)
## The following objects are masked _by_ .GlobalEnv:
##
## crop, group, species, treatment
## The following objects are masked from group_b:
##
## crop, group, replicate, sampling_time, season, site, species,
## species_org, treatment, treatment_org, weed_density
## The following objects are masked from group_a:
##
## crop, group, replicate, sampling_time, season, site, species,
## species_org, treatment, treatment_org, weed_density
## The following objects are masked from dominant:
##
## crop, group, replicate, sampling_time, season, site, species,
## species_org, treatment, treatment_org, weed_density
## The following objects are masked from wd_rv:
##
## crop, group, replicate, sampling_time, season, site, species,
## species_org, treatment, treatment_org, weed_density
species=as.factor(species)
treatment=as.factor(treatment)
crop=as.factor(crop)
ggplot(data =wd_rv,
aes(x = treatment,
y = log(weed_density),
fill = treatment,
colour =treatment)) +
geom_violin(alpha = 1,
position = position_nudge(x = .2, y = 0)) +
stat_ydensity(geom = "bar", colour = "white", fill = "white", width = .8,
position = position_nudge(x = -.05, y = 0)) +
geom_jitter( width = .15,
size = .5,
alpha = 0.5) +
geom_boxplot(width = 0.5,
outlier.shape = NA,
alpha = 0.8,
color = "black",
notch=TRUE) +
theme_bw() +
theme(legend.position = "none") +
scale_color_brewer(palette = "Spectral") +
scale_fill_brewer(palette = "Spectral") +
theme(axis.text.x = element_text(angle=75, vjust=0.5, size=10))+
facet_wrap(~ group)
## Warning: Removed 5779 rows containing non-finite values (stat_ydensity).
## Warning: Removed 5779 rows containing non-finite values (stat_ydensity).
## Warning: Removed 5779 rows containing non-finite values (stat_boxplot).
Group A
ggplot(data =group_a,
aes(x = treatment,
y = log(weed_density),
fill = treatment,
colour =treatment)) +
geom_violin(alpha = 1,
position = position_nudge(x = .2, y = 0)) +
stat_ydensity(geom = "bar", colour = "white", fill = "white", width = .8,
position = position_nudge(x = -.05, y = 0)) +
geom_jitter( width = .15,
size = .5,
alpha = 0.5) +
geom_boxplot(width = 0.5,
outlier.shape = NA,
alpha = 0.8,
color = "black",
notch=TRUE) +
theme_bw() +
theme(legend.position = "none") +
scale_color_brewer(palette = "Spectral") +
scale_fill_brewer(palette = "Spectral")
## Warning: Removed 554 rows containing non-finite values (stat_ydensity).
## Warning: Removed 554 rows containing non-finite values (stat_ydensity).
## Warning: Removed 554 rows containing non-finite values (stat_boxplot).
facet wrap by treatment
ggplot(data =group_a,
aes(x = species,
y = log(weed_density),
fill = species,
colour =species)) +
geom_violin(alpha = 1,
position = position_nudge(x = .2, y = 0)) +
stat_ydensity(geom = "bar", colour = "white", fill = "white", width = .8,
position = position_nudge(x = -.05, y = 0)) +
geom_jitter( width = .15,
size = .5,
alpha = 0.5) +
geom_boxplot(width = 0.5,
outlier.shape = NA,
alpha = 0.8,
color = "black",
notch=TRUE) +
theme_bw() +
theme(legend.position = "none") +
scale_color_brewer(palette = "Spectral") +
scale_fill_brewer(palette = "Spectral")+
facet_wrap(~treatment,ncol=3)
## Warning: Removed 554 rows containing non-finite values (stat_ydensity).
## Warning: Removed 554 rows containing non-finite values (stat_ydensity).
## Warning: Removed 554 rows containing non-finite values (stat_boxplot).
facet wrap by crop
ggplot(data =group_a,
aes(x = species,
y = log(weed_density),
fill = species,
colour =species)) +
geom_violin(alpha = 1,
position = position_nudge(x = .2, y = 0)) +
stat_ydensity(geom = "bar", colour = "white", fill = "white", width = .8,
position = position_nudge(x = -.05, y = 0)) +
geom_jitter( width = .15,
size = .5,
alpha = 0.5) +
geom_boxplot(width = 0.5,
outlier.shape = NA,
alpha = 0.8,
color = "black",
notch=TRUE) +
theme_bw() +
theme(legend.position = "none") +
scale_color_brewer(palette = "Spectral") +
scale_fill_brewer(palette = "Spectral")+
facet_wrap(~crop)
## Warning: Removed 554 rows containing non-finite values (stat_ydensity).
## Warning: Removed 554 rows containing non-finite values (stat_ydensity).
## Warning: Removed 554 rows containing non-finite values (stat_boxplot).
facet wrap site
ggplot(data =group_a,
aes(x = species,
y = log(weed_density),
fill = species,
colour =species)) +
geom_violin(alpha = 1,
position = position_nudge(x = .2, y = 0)) +
stat_ydensity(geom = "bar", colour = "white", fill = "white", width = .8,
position = position_nudge(x = -.05, y = 0)) +
geom_jitter( width = .15,
size = .5,
alpha = 0.5) +
geom_boxplot(width = 0.5,
outlier.shape = NA,
alpha = 0.8,
color = "black",
notch=TRUE) +
theme_bw() +
theme(legend.position = "none") +
scale_color_brewer(palette = "Spectral") +
scale_fill_brewer(palette = "Spectral")+
facet_wrap(~site)
## Warning: Removed 554 rows containing non-finite values (stat_ydensity).
## Warning: Removed 554 rows containing non-finite values (stat_ydensity).
## Warning: Removed 554 rows containing non-finite values (stat_boxplot).
## notch went outside hinges. Try setting notch=FALSE.
exploring by season
ggplot(data =group_a,
aes(x = species,
y = log(weed_density),
fill = species,
colour =species)) +
geom_violin(alpha = 1,
position = position_nudge(x = .2, y = 0)) +
stat_ydensity(geom = "bar", colour = "white", fill = "white", width = .8,
position = position_nudge(x = -.05, y = 0)) +
geom_jitter( width = .15,
size = .5,
alpha = 0.5) +
geom_boxplot(width = 0.5,
outlier.shape = NA,
alpha = 0.8,
color = "black",
notch=TRUE) +
theme_bw() +
theme(legend.position = "none") +
scale_color_brewer(palette = "Spectral") +
scale_fill_brewer(palette = "Spectral")+
facet_wrap(~season)
## Warning: Removed 554 rows containing non-finite values (stat_ydensity).
## Warning: Removed 554 rows containing non-finite values (stat_ydensity).
## Warning: Removed 554 rows containing non-finite values (stat_boxplot).
## notch went outside hinges. Try setting notch=FALSE.
## notch went outside hinges. Try setting notch=FALSE.
Group B
ggplot(data =group_b,
aes(x = treatment,
y = log(weed_density),
fill = treatment,
colour =treatment)) +
geom_violin(alpha = 1,
position = position_nudge(x = .2, y = 0)) +
stat_ydensity(geom = "bar", colour = "white", fill = "white", width = .8,
position = position_nudge(x = -.05, y = 0)) +
geom_jitter( width = .15,
size = .5,
alpha = 0.5) +
geom_boxplot(width = 0.5,
outlier.shape = NA,
alpha = 0.8,
color = "black",
notch=TRUE) +
theme_bw() +
theme(legend.position = "none") +
scale_color_brewer(palette = "Spectral") +
scale_fill_brewer(palette = "Spectral")
## Warning: Removed 1680 rows containing non-finite values (stat_ydensity).
## Warning: Removed 1680 rows containing non-finite values (stat_ydensity).
## Warning: Removed 1680 rows containing non-finite values (stat_boxplot).
ggplot(data =group_b,
aes(x = species,
y = log(weed_density),
fill = species,
colour =species)) +
geom_violin(alpha = 1,
position = position_nudge(x = .2, y = 0)) +
stat_ydensity(geom = "bar", colour = "white", fill = "white", width = .8,
position = position_nudge(x = -.05, y = 0)) +
geom_jitter( width = .15,
size = .5,
alpha = 0.5) +
geom_boxplot(width = 0.5,
outlier.shape = NA,
alpha = 0.8,
color = "black",
notch=TRUE) +
theme_bw() +
theme(legend.position = "none") +
scale_color_brewer(palette = "Spectral") +
scale_fill_brewer(palette = "Spectral")+
facet_wrap(~treatment,ncol=3)
## Warning: Removed 1680 rows containing non-finite values (stat_ydensity).
## Warning: Removed 1680 rows containing non-finite values (stat_ydensity).
## Warning: Removed 1680 rows containing non-finite values (stat_boxplot).
## notch went outside hinges. Try setting notch=FALSE.
## notch went outside hinges. Try setting notch=FALSE.
## notch went outside hinges. Try setting notch=FALSE.
## notch went outside hinges. Try setting notch=FALSE.
## notch went outside hinges. Try setting notch=FALSE.
## notch went outside hinges. Try setting notch=FALSE.
## notch went outside hinges. Try setting notch=FALSE.
## notch went outside hinges. Try setting notch=FALSE.
## notch went outside hinges. Try setting notch=FALSE.
## notch went outside hinges. Try setting notch=FALSE.
## notch went outside hinges. Try setting notch=FALSE.
## notch went outside hinges. Try setting notch=FALSE.
## notch went outside hinges. Try setting notch=FALSE.
## notch went outside hinges. Try setting notch=FALSE.
## notch went outside hinges. Try setting notch=FALSE.
## notch went outside hinges. Try setting notch=FALSE.
## notch went outside hinges. Try setting notch=FALSE.
Group C
ggplot(data =group_c,
aes(x = treatment,
y = log(weed_density),
fill = treatment,
colour =treatment)) +
geom_violin(alpha = 1,
position = position_nudge(x = .2, y = 0)) +
stat_ydensity(geom = "bar", colour = "white", fill = "white", width = .8,
position = position_nudge(x = -.05, y = 0)) +
geom_jitter( width = .15,
size = .5,
alpha = 0.5) +
geom_boxplot(width = 0.5,
outlier.shape = NA,
alpha = 0.8,
color = "black",
notch=TRUE) +
theme_bw() +
theme(legend.position = "none") +
scale_color_brewer(palette = "Spectral") +
scale_fill_brewer(palette = "Spectral")
## Warning: Removed 3545 rows containing non-finite values (stat_ydensity).
## Warning: Removed 3545 rows containing non-finite values (stat_ydensity).
## Warning: Removed 3545 rows containing non-finite values (stat_boxplot).
m_group_a<- lm(weed_density ~ sampling_time+season+treatment_org+species_org,data = group_a)
summary(m_group_a)
##
## Call:
## lm(formula = weed_density ~ sampling_time + season + treatment_org +
## species_org, data = group_a)
##
## Residuals:
## Min 1Q Median 3Q Max
## -36.986 -11.941 -4.812 3.133 311.593
##
## Coefficients:
## Estimate Std. Error t value
## (Intercept) 14.8873 2.7467 5.420
## sampling_time -2.5786 0.7845 -3.287
## season2010/11 -2.5583 1.9044 -1.343
## season2011/12 -11.1174 1.6150 -6.884
## season2012/13 -12.5722 1.9044 -6.602
## treatment_orgAtrazine+Glyphosate -1.5635 2.1731 -0.719
## treatment_orgAtrazine+Glyphosate+Metalachlor -2.7698 2.1731 -1.275
## treatment_orgGlyphosate -0.4841 2.1731 -0.223
## treatment_orgManual weeding 4.5397 2.1731 2.089
## treatment_orgParaquat 2.0595 2.1731 0.948
## species_orggalinsoga parviflora 9.7831 1.7743 5.514
## species_orgleucas martinicensis 5.1720 1.7743 2.915
## species_orgricardia scabra 20.1376 1.7743 11.349
## Pr(>|t|)
## (Intercept) 6.93e-08 ***
## sampling_time 0.00104 **
## season2010/11 0.17935
## season2011/12 8.54e-12 ***
## season2012/13 5.62e-11 ***
## treatment_orgAtrazine+Glyphosate 0.47196
## treatment_orgAtrazine+Glyphosate+Metalachlor 0.20265
## treatment_orgGlyphosate 0.82374
## treatment_orgManual weeding 0.03687 *
## treatment_orgParaquat 0.34342
## species_orggalinsoga parviflora 4.13e-08 ***
## species_orgleucas martinicensis 0.00361 **
## species_orgricardia scabra < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 24.39 on 1499 degrees of freedom
## Multiple R-squared: 0.134, Adjusted R-squared: 0.1271
## F-statistic: 19.34 on 12 and 1499 DF, p-value: < 2.2e-16