Dear community
To import multiple .dat weather files I am using list.files().
I intend to use the R package “ClimInd” to calculate different agroclimatic
indicators.
Question: Is there another solution to import multiple .dat files so that I can
select elements from the list, e.g. one specifi
Dear community
I have started to use the foreSIGHT package fo calculate some climatic
indicators.
Example
library(foreSIGHT)
func_avgDSD(WAAR$Ta, attArgs)
Dataset (WAAR, Ta = average daily temperature)
Year DOY Ta
1990 1 -2.45
1990 2 1.54
.
.
2001 1 4.54
,
2001 205 15.65
2001 206 20.14
.
2001 3
.. .. ..@ projargs: chr "+proj=somerc +lat_0=46.952405556
+lon_0=7.439583 +k_0=1 +x_0=260 +y_0=120 +ellps=bessel +units=m
+no_defs"
.. .. ..$ comment: chr "PROJCRS[\"unknown\",\nBASEGEOGCRS[\"unknown\",\n
DATUM[\"Unknown based
Dear community
This example code works
library(raster)
library(sp)
library(rgdal)
library(ggplot2)
# Create some sample raster data
raster_file <- raster(ncol=36, nrow=18)
raster_file[] <- 1:ncell(raster_file)
plot(raster_file)
#Create some sample polygons
cds1 <- rbind(c(-180,-20), c(-160,5),
, when selecting the third layer it
reads in number 3 (Unterregio) and number 15 (geometry). Secondly when using
stack() it does not read in the s layer (probably because there are two layers).
>
> sf <- read_sf("C:/Users/Sibylle
> Stöckli/Desktop/NCCS_Impacts_Lot2_2022/InVEST/B
quot;DEBioBedeu" "FRBioBedeu" "ITBioBedeu"
[15] "geometry"
> s<-sf$Unterregio
> r<-allrasters_pres[[1]]
Kind regards
Sibylle
-Original Message-
From: Ivan Krylov
Sent: Friday, August 23, 2024 5:30 PM
To: sibylle.stoec...@gmx.ch
Cc: 'SIB
ITBioBedeu"
[15] "geometry"
> s<-sf$Unterregio
> r<-allrasters_pres[[1]]
>
>
> rs <- stack(r, s)
> names(rs) <- c('r', 's')
Error in `names<-`(`*tmp*`, value = c("r", "s")) :
incorrect number of layer names
Dear community
I have two raster files (here r and r2: y-axis) and an equal x-axis (here s,
4 classes).
Instead of plotting two boxplots I would like to plot paired boxplots: for
each class the boxplots from r and r2 paired).
I tried to adapt the code, but I am struggling around with the error
t; To sort this sort of thing out, It would probably be useful for you
> > to find a tutorial on R's S3 class system (which is really a form
> > of multiple dispatch) and spend some time with it. There are many
> > good ones out there. This S3 system is widely use
Message-
From: Ivan Krylov
Sent: Friday, August 16, 2024 11:45 AM
To: sibylle.stoec...@gmx.ch
Cc: 'SIBYLLE STÖCKLI via R-help'
Subject: Re: [R] allequal diff
В Fri, 16 Aug 2024 11:32:58 +0200
пишет:
> # values and mask r1
> r1 <- getValues(r1)
> mask1 <- is.na(r
1 20150 NA
2 20180 NA
3 20200 3.5
Code
setwd("C:/Users/Sibylle Stöckli/Desktop/")
#.libPaths()
getwd()
#libraries laden
library("ggplot2")
library("gridExtra")
library(scales)
library(nlme)
library(arm)
library(blme
Dear community
I tried the following code using geom_boxplot() and notch=TRUE. Does anyone
know if the command �notch=TRUE� is at the wrong place in my special code
construct?
Without notch=TRUE the code provides the planned ggplot.
Kind regards
Sibylle
Code:
MS1<- MS %>% filte
ask1 & mask2)])
[1] "'is.NA' value mismatch: 389 in current 56989152 in target"
--> so there is just a mismatch in NA not in the xy pixels, right?
Sibylle
-Original Message-
From: Ivan Krylov
Sent: Friday, August 16, 2024 10:51 AM
To: sibylle.stoec...@gm
Here my idea including the error:
> m1=r1[r1="NA",]
> m2=r2_resampled[r2_resampled="NA",]
>
>
> all.equal(getValues(r1)[!m1], getValues(r2_resampled)[!m2])
[1] "Numeric: lengths (80706867, 65806339) differ"
-Original Message-----
From
LLE STÖCKLI via R-help
Cc: sibylle.stoec...@gmx.ch
Subject: Re: [R] allequal diff
В Fri, 16 Aug 2024 07:19:38 +0200
SIBYLLE STÖCKLI via R-help пишет:
> Is it possible to consider na.rm=TRUE?
> > all.equal(getValues(r1), getValues(r2_resampled), tolerance = 0)
>
> [1] "
internally for doing the comparison for
large rasters a block at a time if everything can't fit in memory at the same
time ...
On 2024-08-15 9:14 a.m., SIBYLLE STÖCKLI via R-help wrote:
> Dear community
>
>
>
> Similar to the example of the rdocumentation
Dear community
Similar to the example of the rdocumentation, my idea is to use all.equal
and to print the difference.
https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/all.equal
> d45 <- pi*(1/4 + 1:10)
> stopifnot(
+ all.equal(tan(d45), rep(1, 10))) # TRUE, b
Dear community
I tried to run my ggplot() +geom_boxplot() code using nocht=TRUE, but probably
my term noch=TRUE is at the wrong position?
Error:
Error in `geom_boxplot()`:
! Problem while converting geom to grob.
ℹ Error occurred in the 1st layer.
Caused by error in `ans[ypos] <- rep(y
lay a part, please?
Thank you
Erin Hodgess, PhD
mailto: erinm.hodg...@gmail.com <mailto:erinm.hodg...@gmail.com>
On Sun, Aug 11, 2024 at 10:10 AM SIBYLLE STÖCKLI via R-help
mailto:r-help@r-project.org> > wrote:
Dear community
Using after_stat() I was able to v
Dear community
Using after_stat() I was able to visualise ggplot with standard deviations
instead of a confidence interval as seen in the R help.
p1<-ggplot(data = MS1, aes(x= Jahr, y= QI_A,color=Bio, linetype=Bio)) +
geom_smooth(aes(fill=Bio,
ymax=after_stat(y+se*sqrt(len
/07/2024, Rui Barradas escreveu:
> Às 16:27 de 18/07/2024, SIBYLLE STÖCKLI via R-help escreveu:
>> Hi
>>
>> I am using ggplot to visualise y for a two-factorial group (Bio: 0
>> and
>> 1) x
>> = 6 years. I was able to adapt the colour of the lines (green a
uld like the additionally differentiate the
two lines (groups) in the linetype.
Sibylle
-Original Message-
From: Jeff Newmiller
Sent: Thursday, July 18, 2024 6:13 PM
To: sibylle.stoec...@gmx.ch; SIBYLLE STÖCKLI via R-help ;
r-help@r-project.org
Subject: Re: [R] ggplot two-factor
Hi
I am using ggplot to visualise y for a two-factorial group (Bio: 0 and 1) x
= 6 years. I was able to adapt the colour of the lines (green and red) and
the linetype (solid and dashed).
Challenge: my code produces now two legends. One with the colors for the
group and one with the linetype for th
Dear community
Dear Ivan
Thanks a lot. The code works now. Solution: direct and full path to the .tif
files.
I confused back and forward slash
#first import all files in a single folder as a list
rastlist <- list.files(path = "C:/Users/Sibylle
Stöckli/Desktop/NCCS_Impacts_Lot2_202
Dear Ivan
Thanks a lot.
I tried now to provide the full path. However probably the "ö" in the path
produces the error, would that be possible?
> #first import all files in a single folder as a list
> rastlist <- list.files(path = "C:\Users\Sibylle
> Stöckli\Des
lllrasters: is list() ok or should there
be a number (the number of imported .tif files?
Kind regards
Sibylle
> library(terra)
> library(raster)
> getwd()
[1] "C:/Users/Sibylle Stöckli/Desktop"
>
> #first import all files in a single folder as a list
> rastlist <- l
"color",
>
> value = c(viridis::viridis(21))
>
> [match(E(.)$type, c(factor(V(.)$name)))]) %>%
>
> set_vertex_attr(name = "trans_v_net", value = c(transitivity(., type
> =
> "local"))) %>%
>
>
+
scale_edge_width(range = c(0.2,4))+
scale_size(range = c(0.5,15)) +
theme(plot.background = element_rect(fill = "black"),
legend.position = "right",
panel.background = element_rect(fill = "black"))
dev.off()
-Original Message---
Dear community
I am using ggraph to plot a network analysis. See part 2 in the working
example.
Besides different colors for different groups of nodes:
--> geom_node_point(aes(size = V(network)$hub_score*200, color=
as.factor(V(network)$community)))
I additionally want to consider different colors
lt layout
> dev.off()
TIFFOpen: figures/AES_network_bymembership.tiff: Cannot open.
RStudioGD
2
Warning message:
In dev.off() :
unable to open TIFF file 'figures/AES_network_bymembership.tiff'
Kind regards
Sibylle
-Original Message-
From: Ivan Krylov
Sent: Monday, Feb
Dear Kimmo
First of all many thanks for the valuable advice to publish code and csv.
Noted.
Yes, "edge.width= E(.)$weight" makes definitively sense.
In the following code, which loads the tiff file, I get the following error
tiff("figures/AES_network_bymembership.tiff", width=1000, height=700,
Dear coummunity
Thanks a lot to David and Kimmo. Yes I see now that I need to provide the two
raw tables. Find here the reproducible example.
Kind regards
Sibylle
# R-labraries
library(circlize)
library(ggplot2)
library(igraph)
library(tidyverse)
library(RColorBrewer)
library(stringi)
library(s
Dear R-community
It would be nice to get some input how to find a solution for the following
error in igraph and vertex setting.
Error in intI(i, n = x@Dim[1], dn[[1]], give.dn = FALSE) :
Index größer als maximales 6
Kind regards
Sibylle
Working example
library(circlize)
library(ggplot2)
Dear R-community
It would be nice to get some input how to find a solution for the following
error in igraph and vertex setting.
Thank you very much
Sibylle
> par(bg="black")
> network %>% plot(
+ vertex.color=clrs[V(.)$community],
+ vertex.size=V(.)$hub_score*1,
+ ve
uot;black"), ncol=2)
fig1
Kind regards
Sibylle
From: John Kane
Sent: Monday, February 5, 2024 1:59 PM
To: sibylle.stoec...@gmx.ch
Cc: r-help@r-project.org
Subject: Re: [R] ggarrange & legend
Could you supply us with a MWE (minimal working example)of what you have so far?
Dear R community
It is possible to adjust the legend in combined ggplots using ggarrange with
be positions top, bottom, left and right.
My question: Is there a function to change the position of the legend to
topright or bottomleft? Right and top etc are in the middle of the axis.
Kind regards
Si
e angel of the x-axis. However, I was able to change
the first x-axis (BB...), but not the second one (Voegel). Maybe this
would solve the problem.
- If not, is there another possibility to fix the number of subplots per
line?
Kind regards
Sibylle
-Original Message-
From: R-help On Beha
m$trapcatch, w$trapcatch))
>
> do what you want (modulo layout details)?
>
> Hth -- Gerrit
>
> -
> Dr. Gerrit Eichner Mathematical Institute, Room 212
> gerrit.eich...@math.uni-giesse
Dear R users
aim
Barplot of insect trap catches (y variable trapcatch) at one specific station
(variable FiBL_Hecke) from week 1-52 ( x variable week).
It works well using the function tapply (sum trapcatch per week, males and
females not separated), however, I intend to separate the y variable
Dear R users
Does anybody know how it may be possible to plot the labels of a ordihull
function separately (in R vegan)? We have studied the bee community in 5
different habitat types. As you see from the code, we use different point types
(pch) and line types (lty). This is only possible if we
Dear R colleagues,
The effect of habitat type on bee species number was tested using a glmer model
with habitat as fixed effect (5 habitat types) and site and time as random
terms.
The idea was now to conduct post hoc tests with glht (package "multcomp") for
pairwise comparisons. The matrix was
Dear R-users
I am working with ncdf data using the variables time (1-365), lon (longitude),
lat (latitude) and the Temperature variable daily). After setting the
parameters for the model, I am able to calculate the output for each lon-lat
grid point. The model works well including one ncdf fil
Dear R members,
I understand the main principles why R-Vegan does not provide p-values for the
biplot scores and/or canonical coefficients (see also post on stackoverflow).
(i) We can obtain linear regression statistics and refit an ordination result
as multiple response linear model (lm, see a
Dear R colleagues,
I applied a pca to 130 farms (sites) and 25 variables (species) using the R
package vegan. Besides analyzing the variation explained by the different pca
axes and the variables the pca axis are correlated with, I am also interested
to analyze the correlation between the varia
Thanks a lot
Sibylle
On 23.08.2013, at 11:06, Jari Oksanen wrote:
Sibylle Stöckli gmx.ch> writes:
I applied vegan's varpart function to partition the effects of
explanatory matrices. Adj. R square for the unique fraction [a] is
0.25. Does anyone know why the decomposition by hand
Dear R-users
I applied vegan's varpart function to partition the effects of
explanatory matrices. Adj. R square for the unique fraction [a] is
0.25. Does anyone know why the decomposition by hand using rda gives
me a different result for [a] (constrained proportion is 0.32)? I used
cbind()
Dear R members,
I tried to fit an lme model and to use the glht function of multcomp.
However, the glht function gives me some errors when using
weights=varPower().
The glht error makes sense as glht needs factor levels and the model
works fine without weights=. Does anyone know a solution s
Dear R users,
I know, the topic is more related to the r-sig-ecology. I decided to
post it to the r-help as some specific topics of my question deals
with NA-values and RDA (R vegan) and an adaptated RDA code due to a
specific study design (including a second matrix).
I am calculating a RDA
Dear R-user
I used lme to fit a linear mixed model inlcuding weights=varPower().
Additionally I wanted to use glht to calculate Tukey-Kramer multiple
comparision.
error:
> glht(modelF, linfct=mcp(Species="Tukey"))
Error in glht.matrix(model = list(modelStruct = list(reStruct =
list(SubPl
Dear R users
Topic: Linear effect model fitting using the nlme package (recomended by
Pinheiro et al. 2008 for unbalanced data set).
The R help provides much info about the controversy to use the anova(lme.model)
function to present numerator df and F values. Additionally different p-values
ca
Dear R users
I would like to group my barplot graph (see example on the R help
link). The proposed R code, adding individual bars to the plot, looks
really overwhelming. My specific dataset just consists of five groups
and three different levels within each groups (the individual bars).
T
Dear R users
I would like to group my barplot graph (see example on the R help link). The
proposed R code, adding individual bars to the plot, looks really overwhelming.
My specific dataset just consists of five groups and three different levels
within each groups (the individual bars). The .t
PA$Site=="KA" & PA$part=="NE", ] ## the last comma is
important to select all the columns for the rows you've chosen
Read ?"[" or ?subset to understand more
The barplot() might work better then.
HTH,
Ivan
Le 10/27/2010 15:09, "Sibylle Stöckli" a
Original-Nachricht
Datum: Wed, 27 Oct 2010 15:09:59 +0200
Von: "Sibylle Stöckli"
An: Rhelp
Betreff: Fwd: as.list
Original-Nachricht
Datum: Wed, 27 Oct 2010 15:03:48 +0200
Von: "Sibylle Stöckli"
An: Rhelp
Betreff: as.list
Dear R-user
Original-Nachricht
Datum: Wed, 27 Oct 2010 15:03:48 +0200
Von: "Sibylle Stöckli"
An: Rhelp
Betreff: as.list
Dear R-users
sorry, here Rcode included (attachment has been removed)
I would like to read a txt file as list, to select rows and columns, and to
create bar
Dear R-users
I would like to read a txt file as list, to select rows and columns, and to
create barplots.
(1) selection of parameter site and part: ok
(2) read txt file as list: problem with (1) as there are NA's (the lines not
selected)
(3) barplot: 5 different groups of bars (the selected co
Dear R users,
x-values (EI) = Adw, EG1, LA1, Ad1, LA2, LA3...(14 levels, insect
stages)
y-valus = antpop
within the boxplot function x-values are ordered alphabetically
Idea: x-values ranked by list order (insect stage: Egg stage 1 is
followed by Larvae 1 and not by Egg stage 2 as it would
Dear R-users
Idea:
Plot a dnorm line using specific mean/sd to complete a histogram (skewed).
xs:range of y-values, ys: dnorm function
Problem:
I expected to multiply the ys function with the sample size (n=250-300). I was
wondering about a factor between 12'000 and 30'000 to match the size of
Dear R-users
Idea:
Analysing tree height frequency with hist(), normal distribution (ks.test &
shapiro.test) and skewness (package e1071 - thanks a lot for this useful
package)as an indication of possible self-thinning in an experimental tree
stand.
Problem:
Results from the ks.test and the
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