So I have a list of stars and their respective distances. My assignment is to find which stars are in a certain distance (+- 10parsec). I want to exclude some of them from further calculations in the program. The thing is I don't want to remove them completely so remove, pop etc isn't helping me. I still want those stars on the list to be present in my output csv. I just want a line saying something like those stars which don't support the if statement, don't use them in this calculation. So i guess the output would be blank for those.
I suppose it is an if or for statement, to mark those bad stars as False and then down the line use calculation that excludes those faulty stars.
I'm a physics student and this is my first python program ever! Please be cool about my ignorance...
Edit: forgive me if i include useless stuff i don't really know what's important. I also use uncertainties library if its of any use
column_names = ['id','pi','s_pi','v_r' ,'s_v', 'dis', 'X',
'ra_h', 'ra_m', 'ra_s','dec_d', 'dec_m',
'dec_s', 'ma', 's_ma', 'md', 's_md']
data = pd.read_csv("hyades_data.dat", skiprows=2, sep='\s+',
names=column_names)
calculations with all
v_r = unumpy.uarray(data['v_r'], data['s_v'])
ma = unumpy.uarray(data['ma'], data['s_ma'])
md = unumpy.uarray(data['md'], data['s_md'])
mi = unumpy.sqrt(ma**2+md**2)
r_m = v_r*unumpy.tan(th)/(4.74*mi/1000)
diff = np.abs(r_pc - r_m)
'''
if np.abs(dist-46.43) <=10:
r_m=True
else r_m=False
at this point i want to make the distiction
'''
mean_diff = diff.mean()
print("Mean : ")
print(mean_diff)
print(a_ref,d_ref)
df_va=pd.DataFrame(v_r)
df_mi = pd.DataFrame(mi)
df_rm = pd.DataFrame(r_m)
df_rpc = pd.DataFrame(r_pc)
df_diff = pd.DataFrame(diff)
#df_mean_diff = pd.DataFrame(mean_diff)
ve = v_r*np.tan(th)
output = pd.concat([data['id'], ra, dec, th_d, df_mi, df_rm, df_rpc,
df_diff,df_va], axis=1)
output.columns = ['id','ra', 'dec', 'th_d','mi', 'r_m', 'r_pc',
'dist_diff','va']
output.to_csv('results.csv', index=False)
Related
When trying to create a table with the conditional random effects in r using the gtsummary function tbl_regression from a glmmTMB mixed effects negative-binomial zero-inflated model, I get duplicate random effects rows.
Example (using Mollie Brooks' Zero-Inflated GLMMs on Salamanders Dataset):
data(Salamanders)
head(Salamanders)
library(glmmTMB)
zinbm2 = glmmTMB(count~spp + mined +(1|site), zi=~spp + mined + (1|site), Salamanders, family=nbinom2)
zinbm2_table_cond <- tbl_regression(
zinbm2,
tidy_fun = function(...) broom.mixed::tidy(..., component = "cond"),
exponentiate = TRUE,
estimate_fun = purrr::partial(style_ratio, digits = 3),
pvalue_fun = purrr::partial(style_sigfig, digits = 3))
zinbm2_table_cond
Output:
Random Effects Output (cond)
When extracting the random effects from de zero-inflated part of the model I get the same problem.
Example:
zinbm2_table_zi <- tbl_regression(
zinbm2,
tidy_fun = function(...) broom.mixed::tidy(..., component = "zi"),
exponentiate = TRUE,
estimate_fun = purrr::partial(style_ratio, digits = 3),
pvalue_fun = purrr::partial(style_sigfig, digits = 3))
zinbm2_table_zi
Output:
Random Effects Output (zi)
The problem persists if I specify the effects argument in broom.mixed.
tidy_fun = function(...) broom.mixed::tidy(..., effects = "ran_pars", component = "cond"),
Looking at confidence intervals in both outputs it seems that somehow it is extracting random effects from both parts of the model and changing the estimate of the zero-inflated random effects (in 1st image; opposite in the 2nd image) to match the conditional part estimate while keeping the CI.
I am not knowledgeable enough to understand why this is happening. Since both rows have the same label I am having difficulty removing the wrong one.
Any tips on how to avoid this problem or a workaround to remove the undesired rows?
If you need more info, let me know.
Thank you in advance.
PS: Output images were changed to link due to insufficient reputation.
I am trying in the code below to generate a report with side by side two images and a splited table but I get an error. Why this error occur?
Code:
close all;
clear all;
clc;
import mlreportgen.report.*
import mlreportgen.dom.*
import mlreportgen.utils.*
Name = {'A';'B';'C';'D';'E';'A';'B';'C';'D';'E'};
codeA = [8;3;8;0;4;8;3;8;0;4];
Height = [1;8;4;7;8;8;3;1;0;4];
Weight = [6;2;1;4;5;8;3;1;1;4];
T = table(Name,codeA,Height,Weight,codeA,Height,Weight,codeA,Height,Weight);
Image1 = Image(which('coins.png'));
Image2 = Image(which('sevilla.jpg'));
rpt = Report("myPDF","pdf");
imgStyle = {ScaleToFit(true)};
Image2.Style = imgStyle;
Image1.Style = imgStyle;
lot = Table({Image2, ' ', Image1});
lot.entry(1,1).Style = {Width('3.2in'), Height('3in')};
lot.entry(1,2).Style = {Width('.2in'), Height('3in')};
lot.entry(1,3).Style = {Width('3.2in'), Height('3in')};
lot.Style = {ResizeToFitContents(false), Width('100%')};
add(rpt, lot);
chapter = Chapter("Title",'Table Report');
table = FormalTable(T);
table.Border = 'Solid';
table.RowSep = 'Solid';
table.ColSep = 'Solid';
para = Paragraph(['The table is sliced into two tables, '...
'with the first column repeating in each table.']);
para.Style = {OuterMargin('0in','0in','0in','12pt')};
para.FontSize = '14pt';
add(chapter,para)
slicer = TableSlicer("Table",table,"MaxCols",5,"RepeatCols",1);
totcols = slicer.MaxCols - slicer.RepeatCols;
slices = slicer.slice();
for slice=slices
str = sprintf('%d repeating column and up to %d more columns',...
slicer.RepeatCols,totcols);
para = Paragraph(str);
para.Bold = true;
add(chapter,para)
add(chapter,slice.Table)
end
add(rpt,chapter)
close(rpt)
rptview(rpt)
Error:
*Index exceeds the number of array elements. Index must not exceed 10.
Error in try1 (line 26)
lot.entry(1,1).Style = {Width('3.2in'), Height('3in')};*
You define the variable
Height = [1;8;4;7;8;8;3;1;0;4];
Then you try and use the report gen function Height
lot.entry(1,1).Style = {Width('3.2in'), Height('3in')};
Because you've shadowed the Height function with a variable, MATLAB is trying to get the element of this array at index '3in', which is either nonsensical or (via some implicit ASCII conversion) is way out of range.
Per my comment on your previous question, I think the way the documentation suggests the report gen functions are imported is bad practice. By using import mlreportgen.dom.* you are putting all of the nicely name-spaced functions from that package into the common area, and in this case it has caused an unclear clash between two things. So there are two options:
Use the namespaced version of Height (and Width), if you did this with all of the report gen functions you would not need the import. The nice side-effect is you get tab-completion when typing the various functions from this package
lot.entry(1,1).Style = {mlreportgen.dom.Width('3.2in'), mlreportgen.dom.Height('3in')};
Sure, you code is longer, but it is more explicit.
... or ...
Simply don't define a variable called Height. Rename this and everything else can stay the same.
I am looking for some help here with this 3d NMDS code. I have 3 issues.
The layout of the plot moves significantly each time I execute the code.
The sites and species are sometimes far off of the plot.
The species text is often overlapping. How can I fix this?
I am unsure how to change the plotting environment to ggplot, so that might be out of the question.
library(vegan)
library(vegan3d)
library(tidyverse)
data("dune")
SiteID <- 1:20
NMDS = metaMDS(dune,distance="bray", try=500, wascores = TRUE, k=3)
NMDS1 = NMDS$points[,1]
NMDS2 = NMDS$points[,2]
NMDS3 = NMDS$points[,3]
NMDS = data.frame(NMDS1 = NMDS1, NMDS2 = NMDS2, NMDS3 = NMDS3, SiteID=SiteID)
NMDS_input <- metaMDS(dune,distance="bray",try=500,k=3,wascores = T)
pl4 <- with(NMDS, ordiplot3d(NMDS_input, pch=16, angle=50, main="Fish ion level 3", cex.lab=1.7,cex.symbols=1.5, tick.marks=FALSE))
sp <- scores(NMDS_input, choices=1:3, display="species", scaling="symmetric")
si <- scores(NMDS_input, choices=1:3, display="sites", scaling="symmetric")
text(pl4$xyz.convert(sp), rownames(sp), cex=0.7, xpd=TRUE)
sii <- as.data.frame(cbind(NMDS$SiteID,si))
with(NMDS, orditorp(pl4, labels = sii$V1, air=1, cex = 1))
labels must be character variables in orditorp. We always assumed so, but this was not checked in vegan::orditorp. Latest vegan version in github will take care of this and will also work with numeric labels.
ordiplot3d returns projected coordinates (in 2D) and if you want to plot those, you can just use the pl4 object that you saved and you do not need to use pl4$xyz.convert. This object will also be accepted in orditorp.
If you want to plot points that were not used in the original mock-3D plot, you must use pl4$xyz.convert for their 2D projection. This function will return the projected coordinates in a form that is directly accepted by standard R functions text, points (and some others), but they will not be accepted by orditorp (and I won't change this). You must make these into two-column matrix-like object; data.frame() will work.
Your example code contains a lot of un-needed code. The following is an edit with only necessary lines and fixes that make this example work with current vegan release.
library(vegan)
library(vegan3d)
data(dune)
SiteID <- as.character(1:20) # must be character
NMDS_input <- metaMDS(dune,distance="bray",try=500,k=3,wascores = T)
pl4 <- ordiplot3d(NMDS_input, pch=16, angle=50, main="Fish ion level 3", cex.lab=1.7,cex.symbols=1.5, tick.marks=FALSE) # no with(NMDS,...)
sp <- scores(NMDS_input, choices=1:3, display="species") # no arg scaling in scores.metaMDS
text(pl4$xyz.convert(sp), rownames(sp), cex=0.7, xpd=TRUE)
orditorp(pl4, labels = SiteID, air=1, cex = 1) # character labels w/points in the same location
How do I sum different fields? I want to sum all of the information for material(1) ...so I want to add 5+4+6+300 but I am unsure how. Like is there another way besides just doing material(1).May + material(1).June etc....
material(1).May= 5;
material(1).June=4;
material(1).July=6;
material(1).price=300;
material(2).May=10;
material(2).price=550;
material(3).May=90;
You can use structfun for this:
result = sum( structfun(#(x)x, material(1)) );
The inner portion (structfun(#(x)x, material(1))) runs a function each individual field in the structure, and returns the results in an array. By using the identity function (#(x)x) we just get the values. sum of course does the obvious thing.
A slightly longer way to do this is to access each field in a loop. For example:
fNames = fieldnames(material(1));
accumulatedValue = 0;
for ix = 1:length(fNames)
accumulatedValue = accumulatedValue + material(1).(fNames{ix});
end
result = accumulatedValue
For some users this will be easier to read, although for expert users the first will be easier to read. The result and (approximate) performance are the same.
I think Pursuit's answer is very good, but here is an alternative off the top of my head:
sum( cell2mat( struct2cell( material(1) )));
The following example resembles a similar problem that I'm dealing with, although the code below is merely an example, it is structured in the same format as my actual data set.
clear all
England = struct('AirT',rand(320,1),'SolRad',rand(320,1),'Rain',rand(320,1));
Wales = struct('AirT',rand(320,1),'SolRad',rand(320,1),'Rain',rand(320,1));
Ireland = struct('AirT',rand(320,1),'SolRad',rand(320,1),'Rain',rand(320,1));
Scotland = struct('AirT',rand(320,1),'SolRad',rand(320,1),'Rain',rand(320,1));
Location = struct('England',England,'Wales', Wales, 'Ireland',Ireland,'Scotland',Scotland);
FieldName={'England','Wales','Scotland','Ireland'};
Data = {England.AirT,Wales.AirT,Scotland.AirT,Ireland.AirT};
Data = [FieldName;Data];
Data = struct(Data{:});
Data = cell2mat(struct2cell(Data)');
[R,P] = corrcoef(Data,'rows','pairwise');
R_Value= [FieldName(nchoosek(1:size(R,1),2)) num2cell(nonzeros(tril(R,-1)))];
So, this script would show the correlation between pairs of Air Temperature of 4 locations. I'm looking for a way of also looking at the correlation between 'SolRad' and 'Rain' between the locations (same process as for AirT) or any variables denoted in the structure. I could do this by replacing the inputs into 'Data' but this seems rather long winded especially when involving many different variables. Any ideas on how to do this? I've tried using a loop but it seems harder than I though to try and get the data into the same format as the example.
Let's see if this helps, or is what you are thinking:
clear all
England = struct('AirT',rand(320,1),'SolRad',rand(320,1),'Rain',rand(320,1));
Wales = struct('AirT',rand(320,1),'SolRad',rand(320,1),'Rain',rand(320,1));
Ireland = struct('AirT',rand(320,1),'SolRad',rand(320,1),'Rain',rand(320,1));
Scotland = struct('AirT',rand(320,1),'SolRad',rand(320,1),'Rain',rand(320,1));
Location = struct('England',England,'Wales', Wales, 'Ireland',Ireland,'Scotland',Scotland);
% get all the location fields
FieldName = transpose(fieldnames(Location));
% get the variables recorded at the first location
CorrData = fieldnames(Location.(FieldName{1}));
% get variables which were stored at all locations(just to be safe,
% we know that they are all the same)
for ii=2:length(FieldName)
CorrData = intersect(CorrData,fieldnames(Location.(FieldName{ii})));
end
% process each variable that was recorded
for ii=1:length(CorrData)
Data = cell(1,length(FieldName));
% get the variable data from each location and store in Data
for jj=1:length(FieldName)
Data{jj} = Location.(FieldName{jj}).(CorrData{ii});
end
% process the data
Data = [FieldName;Data];
Data = struct(Data{:});
Data = cell2mat(struct2cell(Data)');
[R,P] = corrcoef(Data,'rows','pairwise');
R_Value= [FieldName(nchoosek(1:size(R,1),2)) num2cell(nonzeros(tril(R,-1)))];
% display the data, sounds good right?
fprintf(1,'Correlation for %s\n',CorrData{ii});
for jj=1:size(R_Value,1)
fprintf(1,'%s\t%s\t%f\n',R_Value{jj,1},R_Value{jj,2},R_Value{jj,3});
end
end
Let me know if I misunderstood, or if this is more involved than what you were thinking. Thanks!
fieldnames(s) and dynamic field references are your friend.
What I would suggest is to make one structure in which 'name' is a field, and the other fields are whatever you'd like. Regardless of how you set up your structure s, you can use fn = fieldnames(s); to return a cell array of the fields. You can access the contents of your structure using these names by using parentheses around the variable containing the name.
fn = fieldnames(s);
for i=1:length(fn)
disp([fn{i} ':' s.(fn{i})]
end
Whatever you do with the values is up to you, of course!